The trajectory /home/kornel/big/projects/mdanalysis/4mbs/4mbs has been analyzed with YASARA version 19.1.1.L.64 over a period of 1000.00 nanoseconds with 4001 snapshots and the AMBER14 force field. Note that the MD simulation may have been run with a different force field, but AMBER14 was used to calculate the energies in this report. To change this, edit the ForceField setting at the start of this macro.
All plots and pictures in this report [like the simulated system below] are 1024 pixels wide, you can change the figurewidth variable in this macro as needed.
The components of the system are shown in the table below.
Type | Number |
Protein molecules | 1 |
Protein residues | 346 |
Protein atoms | 5648 |
Nucleic acid molecules | 0 |
Nucleic acid residues | 0 |
Nucleic acid atoms | 0 |
Residue Mrv with 79 atoms | 1 |
Residue Pea with 125 atoms | 184 |
Element Zn | 1 |
Element Cl | 47 |
Element Na | 45 |
Water residues | 15552 |
Total number of atoms | 75476 |
Object 1 with name 4mbs has been identified as the solute and is shown below. If this is not the intended solute, please change the soluteobj variable in this macro.
A special ligand analysis has been performed for MRV, chosen automatically by YASARA with the selection Res MRV. The number of residues matching the ligand selection is 1, with 79 atoms. To change the ligand selection, edit the ligandsel variable at the beginning of this macro.
This section shows all analyses that have been performed inside the simulation cell, when all atoms share the common coordinate system of the simulation cell.
Periodic boundaries are active and considered for distance measurements. Calculations that involve groups of atoms [center of mass, regression lines, enclosing spheres..] are ambiguous and should be placed in the next section, unless it is known that the atom group does not drift through a periodic boundary.
Conformational changes of the simulated solute molecules lead to fluctuations in density. If the simulation box has a constant size, changes in density lead to changes in pressure. This is not realistic, because molecules normally "live" in a constant pressure environment. During the simulation the cell is therefore rescaled to maintain a constant cell pressure. Depending on the chosen pressure control mode, the three cell axes are either rescaled together [Manometer1D], partly together [X- and Z-axes, Manometer2D, used for membrane simulations], independently [Manometer3D], or not at all [Off]. You can deduce the pressure control mode from the plot below.
The total potential energy of the system is plotted, according to the AMBER14 force field. If you ran the simulation with a different force field, you need to adapt the ForceField command at the top of this macro accordingly.
When the simulation is started from an energy-minimized "frozen" conformation, there is usually a sharp increase in energy during the first picoseconds, since the added kinetic energy is partly stored as potential energy. Also on a larger time-scale, the potential energy will often not decrease. A common reason are counter ions. These are initially placed at the positions with the lowest potential energy, usually close to charged solute groups, from where they detach to gain entropy, but also potential energy.
The following individual components of the total potential energy are plotted: bond energies [Bond], bond angle energies [Angle], dihedral angle energies [Dihedral], planarity or improper dihedral energies [Planarity], Van der Waals energies [VdW] and electrostatic energies [Coulomb]. Force field energies help to judge the structural quality of a protein: distortions of local covalent geometry can be found by looking at the bond, angle and planarity energies. Unrealistically close contacts [bumps] lead to a high Van der Waals energy, just like a large number of hydrogen bonds [since they pull the atoms closer than their normal Van der Waals contact distance]. The Coulomb energy is the least informative, because it strongly depends on the amino acid composition [e.g. proteins with a net charge have a higher Coulomb energy].
The Van der Waals [SurfVdW], molecular [SurfMol] and solvent accessible [SurfAcc] surface areas of the solute in A^2 are plotted. The difference between these surface types can be summarized as follows:
Van der Waals surface: if you think of atoms as spheres with a given Van der Waals radius, then the Van der Waals surface consists of all the points on these spheres that are not inside another sphere. In practice, the Van der Waals surface is of limited use, because it can be found throughout a protein and does not tell much about the interaction with the solvent.
Molecular surface: this is the Van der Waals surface from the viewpoint of a solvent molecule, which is a much more useful concept. The water is assumed to be a sphere of a given radius [also called the water probe], that rolls over the solute. Those parts of the Van der Waals surface that the water probe can touch are simply copied to the molecular surface [and called the contact surface]. Clefts in the Van der Waals surface that are too narrow for the water probe to enter are replaced by the Van der Waals surface of the water probe itself [and called the reentrant surface]. So the molecular surface is a smooth composition of two Van der Waals surfaces: the one of the solute and the one of the solvent molecule while it traces the contours of the solute. Other common names for the molecular surface are solvent excluded surface or Connolly surface.
Solvent accessible surface: this surface consists of all the points that the center of the water probe [i.e. the nucleus of the oxygen atom in the water molecule] can reach while rolling over the solute. The shortest possible distance between the water oxygen nucleus and a solute atom is simply the sum of the Van der Waals radii of the solute atom and the water probe.
The number of hydrogen bonds inside the solute is plotted below. One hydrogen bond per hydrogen atom is assigned at most, picking the better one if two acceptors are available.The following formula yields the bond energy in [kJ/mol] as a function of the Hydrogen-Acceptor distance in [A] and two scaling factors:
The first scaling factor depends on the angle formed by Donor-Hydrogen-Acceptor:
The second scaling factor is derived from the angle formed by Hydrogen-Acceptor-X, where X is the atom covalently bound to the acceptor. If X is a heavy atom:
If X is a hydrogen, slightly smaller angles are allowed:
A hydrogen bond is counted if the hydrogen bond energy obtained with this formula is better than 6.25 kJ/mol [or 1.5 kcal/mol], which is 25% of the optimum value 25 kJ/mol.
The plot shows the number of hydrogen bonds between solute and solvent. Together with the plot above, it is a good indicator for successful protein folding, indicated by a decreasing number of bonds with the solvent and a growing number of bonds within the solute.
The following table shows all hydrogen bonds made by Res MRV. With 6 acceptors and 2 donors, a total number of 14 hydrogen bonds are possible - labeled HB1 to HB14.The first atom of the bonding pair is labeled Atm1 and the second Atm2, respectively. The atom ID separates atom name, residue ID and molecule name with dots. A lower-case "h" indicates hetgroups. E and D are short for the hydrogen bonding energy in [ kJ/mol ] and the distance between the bonding partners in [A]. To list other hydrogen bonds, edit the hbosel variable at the beginning of this macro.
Time [ns] | HB1Atm1 | HB1Atm2 | HB1E | HB1D | HB2Atm1 | HB2Atm2 | HB2E | HB2D | HB3Atm1 | HB3Atm2 | HB3E | HB3D | HB4Atm1 | HB4Atm2 | HB4E | HB4D | HB5Atm1 | HB5Atm2 | HB5E | HB5D | HB6Atm1 | HB6Atm2 | HB6E | HB6D | HB7Atm1 | HB7Atm2 | HB7E | HB7D | HB8Atm1 | HB8Atm2 | HB8E | HB8D | HB9Atm1 | HB9Atm2 | HB9E | HB9D | HB10Atm1 | HB10Atm2 | HB10E | HB10D | HB11Atm1 | HB11Atm2 | HB11E | HB11D | HB12Atm1 | HB12Atm2 | HB12E | HB12D | HB13Atm1 | HB13Atm2 | HB13E | HB13D | HB14Atm1 | HB14Atm2 | HB14E | HB14D |
0.00 | N2.h347.A | OE1.E316.A | 23.45 | 1.70 | N3.h347.A | OH.Y19.A | 25.00 | 1.91 | N5.h347.A | OH.Y284.A | 18.30 | 2.11 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
0.25 | N2.h347.A | OE1.E316.A | 18.57 | 1.90 | N3.h347.A | OH.Y19.A | 23.45 | 2.02 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
0.50 | N2.h347.A | OE1.E316.A | 21.10 | 1.98 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
0.75 | N2.h347.A | OE1.E316.A | 20.73 | 1.74 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
1.00 | N2.h347.A | OE1.E316.A | 25.00 | 1.61 | N3.h347.A | OH.Y19.A | 10.85 | 2.21 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
1.25 | N2.h347.A | OE1.E316.A | 21.88 | 1.77 | N3.h347.A | OH.Y19.A | 21.10 | 2.06 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
1.50 | N2.h347.A | OE1.E316.A | 23.85 | 1.78 | N3.h347.A | OH.Y19.A | 25.00 | 2.08 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
1.75 | N2.h347.A | OE1.E316.A | 18.75 | 1.78 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
2.00 | N2.h347.A | OE1.E316.A | 21.10 | 1.79 | N3.h347.A | OH.Y19.A | 25.00 | 2.08 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
2.25 | N2.h347.A | OE1.E316.A | 24.43 | 1.99 | N3.h347.A | OH.Y19.A | 21.88 | 1.80 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
The total percentages of alpha helices, beta sheets, turns, coils, 3-10 helices and pi helices are calculated and plotted. For clarification, a turn is simply a stretch of four residues that are not part of other secondary structure elements and form a hydrogen bond between the O of the first and the NH of the last residue. A coil is anything that does not fit into the other categories. Note that pi-helices [helices with hydrogen bonds between residues N and N+5] are rather unstable and thus do not normally occur in proteins, except for short bulges in alpha helices [which are often the result of single residue insertions and prolines].
The following plots show the protein secondary structure per residue as a function of simulation time. They are helpful to monitor protein folding and all other kinds of structural changes. The default secondary structure colors are used, you can change them at View > Color > Parameters > Secondary structure colors. One plot per protein molecule is shown.
The number of contacts per residue as a function of simulation time is shown in the following plots. There is one plot for each protein or nucleic acid molecule. Even though contacts between atoms separated by up to four chemical bonds are excluded, neighboring residues in the molecule usually have enough close atoms to be counted as a contact. Consequently residues with zero contacts are very rare and often glycines. The number of contacts tells you how densely a certain residue range is packed and allows to identify structurally very important residues, e.g. a phenylalanine in the hydrophobic core can contact 15 or more other residues.
The following plots show the types of contacts made with the ligand
as a function of simulation time. There is one plot for each protein or nucleic acid molecule. Three types of contacts are shown: Hydrogen bonds [red] ,hydrophobic contacts [green] and ionic interactions [blue]. Also mixtures of these three colors can show up if a certain residue is involved in more than one type of contact with the ligand [see plot legend].The following section presents data gathered outside the simulation cell, where each object has its own local coordinate system and no periodic boundaries are present. Calculations that involve the interaction between objects [common surface areas, contacts between objects..] must be placed in the previous section.
After determining the center of mass of the solute, the radius of gyration is calculated and plotted according to this formula:
In this formula, C is the center of mass, and Ri is the position of atom i of N.
Analyses performed with respect to the starting structure are shown in this section. These are also done outside the simulation cell, where each object has its own local coordinate systems and no periodic boundaries are present. To choose another reference snapshot than 0, edit the refsnapshot variable at the beginning of this macro.
The plot shows Calpha [RMSDCa], backbone [RMSDBb] and all-heavy atom [RMSDAll] RMSDs calculated according to this formula, where Ri is the vector linking the positions of atom i [of N atoms] in the reference snapshot and the current snapshot after optimal superposition:
The selection for the Calpha RMSD calculation is CA Protein or C1* NucAcid, this matched 346 atoms. The Calpha selection thus includes the main backbone carbon C1* of nucleic acids, so the plot also shows a Calpha RMSD if you simulate just nucleic acids. In simulations of protein-DNA complexes, the Calpha RMSD therefore considers the DNA too. To change the Calpha selection, edit the casel variable at the beginning of this macro.
The following plot shows the RMSD of the ligand heavy atoms over time, measured after superposing the receptor on its reference structure. This procedure delivers information about the movement of the ligand in its binding pocket.
This plot displays the RMSD of the ligand atoms over time, measured after superposing on the reference structure of the ligand. The gained data summarize the conformational changes of the ligand.
The Root Mean Square Fluctuation [RMSF] per solute residue is calculated from the average RMSF of its constituting atoms. The RMSF of atom i with j runing from 1 to 3 for the x, y, and z coordinate of the atom position vector P and k runing over the set of N evaluated snapshots is given by following formula:
Mol | Residue | First atom | RMSF[A] |
A | Mrv | 3475649 | 6.40 |
A | Zn | 3485728 | 3.98 |
The dynamic cross-correlation matrix [DCCM] is a square matrix, whose rows and columns match the selected units Atom CA Protein or C1* NucAcid. To change this selection, edit the dccmsel variable at the beginning of this macro. The DCCM shows how the movements of all selected pairs correlate. The values in the DCCM range from -1 [perfectly anti-correlated] to +1 [perfectly correlated]. The values along the diagonal are always +1 [because the motion of an atom is perfectly correlated to itself]. The DCCM element for units i and j is obtained with the following formula:
Here d is the displacement between the current position and the average position of the selected unit, and the angle brackets indicate the average over all samples. The highest correlations off the diagonal can often be found for bridged cysteines.
The image below shows the correlation directly in the solute object:
In the image below, the DCCM is visualized with colors ranging from blue [-1, fully anti-correlated] to yellow [+1, fully correlated].
DCCM | A Pro 1 | A Cys 2 | A Gln 3 | A Lys 4 | A Ile 5 | A Asn 6 | A Val 7 | A Lys 8 | A Gln 9 | A Ile 10 | A Ala 11 | A Ala 12 | A Arg 13 | A Leu 14 | A Leu 15 | A Pro 16 | A Pro 17 | A Leu 18 | A Tyr 19 | A Ser 20 | A Leu 21 | A Val 22 | A Phe 23 | A Ile 24 | A Phe 25 | A Gly 26 | A Phe 27 | A Val 28 | A Gly 29 | A Asn 30 | A Met 31 | A Leu 32 | A Val 33 | A Ile 34 | A Leu 35 | A Ile 36 | A Leu 37 | A Ile 38 | A Asn 39 | A Tyr 40 | A Lys 41 | A Arg 42 | A Leu 43 | A Lys 44 | A Ser 45 | A Met 46 | A Thr 47 | A Asp 48 | A Ile 49 | A Tyr 50 | A Leu 51 | A Leu 52 | A Asn 53 | A Leu 54 | A Ala 55 | A Ile 56 | A Ser 57 | A Asp 58 | A Leu 59 | A Phe 60 | A Phe 61 | A Leu 62 | A Leu 63 | A Thr 64 | A Val 65 | A Pro 66 | A Phe 67 | A Trp 68 | A Ala 69 | A His 70 | A Tyr 71 | A Ala 72 | A Ala 73 | A Ala 74 | A Gln 75 | A Trp 76 | A Asp 77 | A Phe 78 | A Gly 79 | A Asn 80 | A Thr 81 | A Met 82 | A Cys 83 | A Gln 84 | A Leu 85 | A Leu 86 | A Thr 87 | A Gly 88 | A Leu 89 | A Tyr 90 | A Phe 91 | A Ile 92 | A Gly 93 | A Phe 94 | A Phe 95 | A Ser 96 | A Gly 97 | A Ile 98 | A Phe 99 | A Phe 100 | A Ile 101 | A Ile 102 | A Leu 103 | A Leu 104 | A Thr 105 | A Ile 106 | A Asp 107 | A Arg 108 | A Tyr 109 | A Leu 110 | A Ala 111 | A Val 112 | A Val 113 | A His 114 | A Ala 115 | A Val 116 | A Phe 117 | A Ala 118 | A Leu 119 | A Lys 120 | A Ala 121 | A Arg 122 | A Thr 123 | A Val 124 | A Thr 125 | A Phe 126 | A Gly 127 | A Val 128 | A Val 129 | A Thr 130 | A Ser 131 | A Val 132 | A Ile 133 | A Thr 134 | A Trp 135 | A Val 136 | A Val 137 | A Ala 138 | A Val 139 | A Phe 140 | A Ala 141 | A Ser 142 | A Leu 143 | A Pro 144 | A Asn 145 | A Ile 146 | A Ile 147 | A Phe 148 | A Thr 149 | A Arg 150 | A Ser 151 | A Gln 152 | A Lys 153 | A Glu 154 | A Gly 155 | A Leu 156 | A His 157 | A Tyr 158 | A Thr 159 | A Cys 160 | A Ser 161 | A Ser 162 | A His 163 | A Phe 164 | A Pro 165 | A Tyr 166 | A Ser 167 | A Gln 168 | A Tyr 169 | A Gln 170 | A Phe 171 | A Trp 172 | A Lys 173 | A Asn 174 | A Phe 175 | A Gln 176 | A Thr 177 | A Leu 178 | A Lys 179 | A Ile 180 | A Val 181 | A Ile 182 | A Leu 183 | A Gly 184 | A Leu 185 | A Val 186 | A Leu 187 | A Pro 188 | A Leu 189 | A Leu 190 | A Val 191 | A Met 192 | A Val 193 | A Ile 194 | A Cys 195 | A Tyr 196 | A Ser 197 | A Gly 198 | A Ile 199 | A Leu 200 | A Lys 201 | A Thr 202 | A Leu 203 | A Leu 204 | A Arg 205 | A Met 206 | A Lys 207 | A Lys 208 | A Tyr 209 | A Thr 210 | A Cys 211 | A Thr 212 | A Val 213 | A Cys 214 | A Gly 215 | A Tyr 216 | A Ile 217 | A Tyr 218 | A Asn 219 | A Pro 220 | A Glu 221 | A Asp 222 | A Gly 223 | A Asp 224 | A Pro 225 | A Asp 226 | A Asn 227 | A Gly 228 | A Val 229 | A Asn 230 | A Pro 231 | A Gly 232 | A Thr 233 | A Asp 234 | A Phe 235 | A Lys 236 | A Asp 237 | A Ile 238 | A Pro 239 | A Asp 240 | A Asp 241 | A Trp 242 | A Val 243 | A Cys 244 | A Pro 245 | A Leu 246 | A Cys 247 | A Gly 248 | A Val 249 | A Gly 250 | A Lys 251 | A Asp 252 | A Gln 253 | A Phe 254 | A Glu 255 | A Glu 256 | A Val 257 | A Glu 258 | A Glu 259 | A Glu 260 | A Lys 261 | A Lys 262 | A Arg 263 | A His 264 | A Arg 265 | A Asp 266 | A Val 267 | A Arg 268 | A Leu 269 | A Ile 270 | A Phe 271 | A Thr 272 | A Ile 273 | A Met 274 | A Ile 275 | A Val 276 | A Tyr 277 | A Phe 278 | A Leu 279 | A Phe 280 | A Trp 281 | A Ala 282 | A Pro 283 | A Tyr 284 | A Asn 285 | A Ile 286 | A Val 287 | A Leu 288 | A Leu 289 | A Leu 290 | A Asn 291 | A Thr 292 | A Phe 293 | A Gln 294 | A Glu 295 | A Phe 296 | A Phe 297 | A Gly 298 | A Leu 299 | A Asn 300 | A Asn 301 | A Cys 302 | A Ser 303 | A Ser 304 | A Ser 305 | A Asn 306 | A Arg 307 | A Leu 308 | A Asp 309 | A Gln 310 | A Ala 311 | A Met 312 | A Gln 313 | A Val 314 | A Thr 315 | A Glu 316 | A Thr 317 | A Leu 318 | A Gly 319 | A Met 320 | A Thr 321 | A His 322 | A Cys 323 | A Cys 324 | A Ile 325 | A Asn 326 | A Pro 327 | A Ile 328 | A Ile 329 | A Tyr 330 | A Ala 331 | A Phe 332 | A Val 333 | A Gly 334 | A Glu 335 | A Glu 336 | A Phe 337 | A Arg 338 | A Asn 339 | A Tyr 340 | A Leu 341 | A Leu 342 | A Val 343 | A Phe 344 | A Phe 345 | A Gln 346 |
A | Pro 11.00 | 0.92 | 0.70 | 0.21 | 0.13 | 0.10 | 0.24 | 0.10 | 0.12 | 0.21 | -0.03 | 0.05 | 0.04 | 0.06 | 0.04 | 0.08 | 0.13 | 0.13 | 0.13 | 0.15 | 0.17 | 0.14 | 0.12 | 0.11 | 0.15 | 0.09 | -0.00 | 0.02 | 0.04 | 0.04 | -0.02 | 0.04 | 0.04 | -0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 | -0.01 | -0.02 | -0.05 | -0.05 | -0.07 | -0.07 | -0.09 | -0.08 | -0.11 | -0.09 | -0.05 | -0.06 | -0.09 | -0.08 | -0.00 | -0.01 | -0.05 | 0.03 | 0.06 | 0.05 | 0.02 | 0.03 | 0.01 | 0.06 | 0.09 | 0.10 | 0.08 | 0.04 | 0.06 | 0.08 | -0.00 | -0.05 | -0.01 | 0.01 | -0.02 | -0.04 | 0.02 | -0.03 | -0.12 | -0.10 | -0.08 | -0.06 | -0.08 | -0.14 | -0.08 | -0.04 | -0.09 | -0.11 | -0.06 | -0.07 | -0.15 | -0.14 | -0.06 | -0.07 | -0.10 | -0.15 | -0.08 | -0.04 | -0.11 | -0.11 | -0.07 | -0.09 | -0.13 | -0.12 | -0.07 | -0.09 | -0.15 | -0.10 | -0.04 | -0.12 | -0.15 | -0.11 | -0.10 | -0.12 | -0.14 | -0.13 | -0.06 | -0.10 | -0.16 | -0.13 | -0.10 | -0.07 | -0.12 | -0.11 | -0.14 | -0.15 | -0.13 | -0.12 | -0.14 | -0.14 | -0.12 | -0.14 | -0.15 | -0.13 | -0.15 | -0.17 | -0.17 | -0.17 | -0.19 | -0.20 | -0.19 | -0.21 | -0.19 | -0.23 | -0.27 | -0.17 | -0.20 | -0.21 | -0.15 | -0.10 | -0.09 | -0.10 | -0.12 | -0.13 | -0.15 | -0.14 | -0.07 | -0.01 | 0.00 | -0.04 | -0.07 | -0.12 | -0.08 | -0.18 | -0.22 | -0.17 | -0.18 | -0.22 | -0.07 | -0.04 | -0.21 | -0.18 | 0.04 | -0.06 | -0.20 | -0.10 | 0.08 | -0.04 | -0.15 | -0.05 | 0.00 | -0.07 | -0.09 | -0.05 | -0.04 | -0.07 | -0.10 | -0.10 | -0.10 | -0.12 | -0.14 | -0.13 | -0.15 | -0.15 | -0.11 | -0.12 | -0.16 | -0.14 | -0.13 | -0.14 | -0.11 | -0.05 | -0.07 | -0.05 | 0.05 | 0.04 | 0.01 | -0.01 | -0.08 | -0.04 | -0.06 | -0.07 | -0.06 | -0.01 | 0.02 | 0.03 | 0.06 | 0.00 | 0.05 | 0.00 | 0.06 | 0.08 | 0.04 | 0.03 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.06 | 0.03 | -0.03 | -0.16 | -0.19 | -0.20 | -0.13 | -0.08 | -0.08 | -0.09 | -0.06 | -0.05 | -0.05 | -0.03 | 0.00 | 0.01 | -0.03 | -0.04 | -0.07 | -0.08 | -0.11 | -0.14 | -0.11 | -0.11 | -0.10 | -0.08 | 0.02 | 0.07 | 0.03 | -0.01 | -0.13 | -0.16 | -0.20 | -0.05 | 0.02 | -0.06 | -0.03 | -0.03 | -0.07 | -0.03 | -0.01 | -0.01 | -0.02 | -0.00 | 0.04 | 0.06 | 0.02 | 0.06 | 0.10 | 0.09 | 0.08 | 0.05 | 0.11 | 0.12 | 0.05 | 0.06 | 0.14 | 0.04 | -0.03 | 0.06 | 0.08 | -0.07 | -0.01 | 0.22 | 0.01 | -0.08 | 0.11 | 0.25 | 0.11 | 0.10 | 0.37 | 0.45 | 0.41 | 0.34 | 0.40 | 0.42 | 0.36 | 0.34 | 0.37 | 0.33 | 0.27 | 0.27 | 0.26 | 0.21 | 0.18 | 0.16 | 0.15 | 0.14 | 0.10 | 0.06 | 0.07 | 0.03 | 0.02 | 0.03 | -0.02 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | -0.00 | 0.01 | -0.02 | -0.15 | -0.15 | -0.07 | -0.15 | -0.28 | -0.24 | -0.15 | -0.23 | -0.23 | 0.00 | 0.05 | -0.02 | 0.01 |
A | Cys 20.92 | 1.00 | 0.79 | 0.39 | 0.36 | 0.35 | 0.43 | 0.25 | 0.26 | 0.36 | -0.03 | 0.08 | 0.10 | 0.10 | 0.10 | 0.16 | 0.20 | 0.20 | 0.20 | 0.22 | 0.22 | 0.18 | 0.15 | 0.14 | 0.14 | 0.07 | -0.06 | -0.07 | -0.03 | -0.03 | -0.11 | -0.06 | -0.05 | -0.11 | -0.08 | -0.05 | -0.10 | -0.10 | -0.05 | -0.06 | -0.11 | -0.13 | -0.16 | -0.15 | -0.17 | -0.18 | -0.21 | -0.21 | -0.25 | -0.22 | -0.17 | -0.17 | -0.20 | -0.18 | -0.07 | -0.07 | -0.13 | -0.01 | 0.08 | 0.04 | -0.02 | 0.03 | 0.02 | 0.08 | 0.13 | 0.14 | 0.11 | 0.07 | 0.11 | 0.13 | 0.00 | -0.04 | 0.02 | 0.01 | -0.04 | -0.07 | 0.01 | -0.08 | -0.13 | -0.10 | -0.08 | -0.05 | -0.08 | -0.13 | -0.08 | -0.05 | -0.08 | -0.12 | -0.08 | -0.06 | -0.18 | -0.20 | -0.10 | -0.10 | -0.19 | -0.25 | -0.15 | -0.12 | -0.23 | -0.23 | -0.17 | -0.21 | -0.26 | -0.24 | -0.19 | -0.21 | -0.27 | -0.22 | -0.13 | -0.22 | -0.26 | -0.22 | -0.20 | -0.23 | -0.27 | -0.26 | -0.21 | -0.23 | -0.26 | -0.24 | -0.22 | -0.19 | -0.25 | -0.23 | -0.26 | -0.27 | -0.25 | -0.23 | -0.26 | -0.26 | -0.24 | -0.25 | -0.25 | -0.24 | -0.25 | -0.26 | -0.27 | -0.27 | -0.27 | -0.29 | -0.28 | -0.29 | -0.25 | -0.31 | -0.29 | -0.16 | -0.20 | -0.20 | -0.13 | -0.08 | -0.08 | -0.10 | -0.13 | -0.13 | -0.16 | -0.16 | -0.09 | -0.02 | 0.01 | -0.02 | -0.05 | -0.09 | -0.05 | -0.15 | -0.20 | -0.12 | -0.12 | -0.17 | -0.01 | 0.01 | -0.19 | -0.16 | 0.07 | -0.05 | -0.21 | -0.12 | 0.06 | -0.08 | -0.21 | -0.12 | -0.05 | -0.16 | -0.18 | -0.11 | -0.09 | -0.15 | -0.21 | -0.19 | -0.18 | -0.23 | -0.25 | -0.23 | -0.25 | -0.27 | -0.21 | -0.20 | -0.26 | -0.25 | -0.21 | -0.22 | -0.17 | -0.13 | -0.18 | -0.14 | -0.02 | -0.07 | -0.11 | -0.11 | -0.17 | -0.13 | -0.11 | -0.15 | -0.11 | -0.06 | -0.02 | 0.03 | 0.03 | 0.03 | 0.07 | 0.07 | 0.11 | 0.16 | 0.15 | 0.16 | 0.16 | 0.16 | 0.14 | 0.15 | 0.14 | 0.16 | 0.17 | 0.13 | 0.10 | -0.12 | -0.15 | -0.18 | -0.05 | 0.01 | -0.01 | -0.04 | -0.00 | 0.02 | 0.01 | 0.02 | 0.08 | 0.07 | 0.01 | 0.00 | -0.05 | -0.06 | -0.10 | -0.16 | -0.15 | -0.17 | -0.19 | -0.19 | -0.11 | -0.05 | -0.10 | -0.13 | -0.24 | -0.26 | -0.31 | -0.14 | -0.02 | -0.08 | -0.11 | -0.10 | -0.15 | -0.12 | -0.08 | -0.07 | -0.09 | -0.07 | -0.00 | 0.02 | -0.02 | 0.02 | 0.08 | 0.08 | 0.05 | 0.00 | 0.10 | 0.11 | 0.00 | 0.04 | 0.16 | 0.04 | -0.03 | 0.11 | 0.16 | -0.03 | 0.03 | 0.30 | 0.11 | 0.00 | 0.18 | 0.31 | 0.20 | 0.14 | 0.51 | 0.64 | 0.58 | 0.48 | 0.56 | 0.61 | 0.51 | 0.47 | 0.53 | 0.49 | 0.37 | 0.36 | 0.39 | 0.32 | 0.23 | 0.22 | 0.23 | 0.18 | 0.10 | 0.09 | 0.10 | 0.03 | 0.01 | 0.06 | -0.01 | -0.01 | -0.01 | 0.02 | -0.01 | -0.03 | -0.00 | -0.01 | -0.07 | -0.24 | -0.20 | -0.12 | -0.23 | -0.30 | -0.21 | -0.10 | -0.19 | -0.14 | 0.11 | 0.15 | 0.08 | 0.11 |
A | Gln 30.70 | 0.79 | 1.00 | 0.65 | 0.58 | 0.49 | 0.34 | 0.17 | 0.14 | 0.22 | 0.05 | 0.11 | 0.09 | 0.09 | 0.06 | 0.13 | 0.16 | 0.17 | 0.15 | 0.15 | 0.17 | 0.13 | 0.07 | 0.09 | 0.13 | 0.05 | -0.06 | -0.03 | -0.03 | -0.04 | -0.11 | -0.07 | -0.08 | -0.13 | -0.10 | -0.09 | -0.13 | -0.13 | -0.08 | -0.10 | -0.15 | -0.18 | -0.19 | -0.19 | -0.20 | -0.20 | -0.21 | -0.22 | -0.25 | -0.21 | -0.18 | -0.21 | -0.23 | -0.19 | -0.13 | -0.15 | -0.18 | -0.08 | -0.02 | -0.06 | -0.09 | -0.05 | -0.05 | 0.01 | 0.07 | 0.06 | 0.05 | 0.06 | 0.07 | 0.08 | -0.02 | -0.02 | 0.03 | 0.00 | -0.08 | -0.13 | -0.08 | -0.16 | -0.16 | -0.14 | -0.15 | -0.15 | -0.13 | -0.17 | -0.16 | -0.16 | -0.12 | -0.16 | -0.14 | -0.11 | -0.19 | -0.23 | -0.13 | -0.10 | -0.20 | -0.23 | -0.12 | -0.09 | -0.18 | -0.17 | -0.11 | -0.14 | -0.18 | -0.15 | -0.12 | -0.13 | -0.17 | -0.15 | -0.11 | -0.17 | -0.19 | -0.16 | -0.13 | -0.17 | -0.20 | -0.22 | -0.21 | -0.22 | -0.22 | -0.23 | -0.23 | -0.17 | -0.20 | -0.18 | -0.22 | -0.25 | -0.23 | -0.21 | -0.25 | -0.25 | -0.24 | -0.25 | -0.26 | -0.25 | -0.26 | -0.26 | -0.26 | -0.27 | -0.27 | -0.27 | -0.26 | -0.28 | -0.25 | -0.26 | -0.27 | -0.24 | -0.23 | -0.22 | -0.15 | -0.07 | -0.10 | -0.09 | -0.13 | -0.10 | -0.15 | -0.15 | -0.09 | -0.01 | 0.01 | -0.03 | -0.07 | -0.12 | -0.05 | -0.21 | -0.26 | -0.19 | -0.17 | -0.27 | -0.14 | -0.18 | -0.36 | -0.28 | -0.09 | -0.23 | -0.34 | -0.24 | -0.10 | -0.22 | -0.29 | -0.17 | -0.13 | -0.22 | -0.23 | -0.15 | -0.12 | -0.17 | -0.22 | -0.17 | -0.15 | -0.21 | -0.21 | -0.15 | -0.16 | -0.18 | -0.14 | -0.11 | -0.16 | -0.17 | -0.13 | -0.12 | -0.08 | -0.06 | -0.13 | -0.09 | -0.02 | -0.07 | -0.09 | -0.05 | -0.14 | -0.11 | -0.12 | -0.16 | -0.13 | -0.06 | 0.04 | 0.07 | 0.09 | 0.09 | 0.14 | 0.12 | 0.17 | 0.20 | 0.18 | 0.17 | 0.17 | 0.16 | 0.12 | 0.14 | 0.13 | 0.17 | 0.20 | 0.16 | 0.09 | -0.12 | -0.15 | -0.20 | -0.08 | -0.04 | -0.06 | -0.10 | -0.05 | -0.03 | -0.04 | -0.02 | 0.06 | 0.05 | -0.03 | -0.04 | -0.10 | -0.11 | -0.15 | -0.21 | -0.19 | -0.19 | -0.20 | -0.17 | -0.09 | -0.04 | -0.06 | -0.04 | -0.09 | -0.12 | -0.17 | -0.04 | 0.06 | -0.01 | -0.05 | -0.04 | -0.10 | -0.06 | -0.01 | 0.00 | -0.02 | -0.02 | 0.04 | 0.07 | 0.04 | 0.04 | 0.09 | 0.10 | 0.07 | 0.03 | 0.12 | 0.11 | 0.03 | 0.08 | 0.18 | 0.08 | 0.03 | 0.13 | 0.14 | -0.00 | 0.04 | 0.16 | 0.02 | 0.12 | 0.24 | 0.26 | 0.14 | 0.25 | 0.60 | 0.66 | 0.60 | 0.53 | 0.60 | 0.60 | 0.50 | 0.47 | 0.50 | 0.44 | 0.36 | 0.34 | 0.30 | 0.27 | 0.21 | 0.18 | 0.18 | 0.17 | 0.09 | 0.07 | 0.14 | 0.10 | 0.06 | 0.08 | 0.05 | 0.06 | 0.02 | 0.06 | 0.03 | 0.00 | 0.03 | 0.03 | -0.04 | -0.17 | -0.10 | -0.04 | -0.10 | -0.16 | -0.12 | -0.07 | -0.12 | -0.12 | 0.00 | 0.02 | -0.01 | 0.02 |
A | Lys 40.21 | 0.39 | 0.65 | 1.00 | 0.82 | 0.67 | 0.43 | 0.12 | 0.10 | 0.22 | 0.14 | 0.18 | 0.18 | 0.12 | 0.13 | 0.23 | 0.19 | 0.17 | 0.14 | 0.11 | 0.10 | 0.04 | -0.02 | -0.02 | -0.01 | -0.08 | -0.18 | -0.19 | -0.23 | -0.17 | -0.27 | -0.32 | -0.33 | -0.34 | -0.33 | -0.36 | -0.38 | -0.34 | -0.29 | -0.34 | -0.38 | -0.39 | -0.37 | -0.37 | -0.36 | -0.37 | -0.39 | -0.43 | -0.45 | -0.41 | -0.39 | -0.42 | -0.44 | -0.38 | -0.33 | -0.35 | -0.37 | -0.25 | -0.18 | -0.23 | -0.22 | -0.14 | -0.15 | -0.08 | -0.00 | 0.02 | 0.01 | 0.06 | 0.12 | 0.11 | 0.00 | 0.06 | 0.10 | 0.06 | -0.06 | -0.06 | -0.00 | -0.07 | -0.06 | -0.02 | -0.09 | -0.06 | -0.03 | -0.08 | -0.16 | -0.14 | -0.07 | -0.16 | -0.19 | -0.15 | -0.24 | -0.33 | -0.26 | -0.20 | -0.30 | -0.35 | -0.21 | -0.16 | -0.28 | -0.29 | -0.19 | -0.23 | -0.27 | -0.21 | -0.21 | -0.21 | -0.21 | -0.27 | -0.21 | -0.20 | -0.22 | -0.18 | -0.16 | -0.22 | -0.27 | -0.30 | -0.34 | -0.38 | -0.34 | -0.32 | -0.37 | -0.35 | -0.36 | -0.33 | -0.34 | -0.39 | -0.39 | -0.37 | -0.39 | -0.41 | -0.43 | -0.39 | -0.38 | -0.41 | -0.41 | -0.36 | -0.37 | -0.38 | -0.34 | -0.31 | -0.31 | -0.30 | -0.26 | -0.23 | -0.11 | -0.14 | -0.13 | -0.05 | -0.01 | 0.06 | 0.05 | 0.06 | 0.03 | 0.04 | -0.00 | -0.01 | 0.03 | 0.08 | 0.07 | 0.05 | 0.02 | 0.03 | 0.08 | -0.01 | -0.04 | 0.01 | 0.04 | -0.07 | -0.04 | -0.13 | -0.23 | -0.14 | -0.08 | -0.21 | -0.25 | -0.18 | -0.17 | -0.26 | -0.25 | -0.23 | -0.20 | -0.28 | -0.29 | -0.19 | -0.15 | -0.21 | -0.27 | -0.18 | -0.15 | -0.22 | -0.21 | -0.12 | -0.11 | -0.18 | -0.13 | -0.03 | -0.07 | -0.12 | -0.06 | -0.02 | -0.01 | -0.07 | -0.15 | -0.11 | -0.11 | -0.22 | -0.22 | -0.09 | -0.19 | -0.15 | -0.16 | -0.23 | -0.18 | -0.07 | 0.05 | 0.15 | 0.16 | 0.19 | 0.27 | 0.26 | 0.31 | 0.35 | 0.32 | 0.29 | 0.30 | 0.26 | 0.20 | 0.24 | 0.24 | 0.29 | 0.34 | 0.30 | 0.21 | -0.10 | -0.13 | -0.21 | -0.04 | 0.00 | -0.05 | -0.11 | -0.05 | -0.01 | -0.02 | 0.02 | 0.15 | 0.13 | -0.00 | -0.02 | -0.12 | -0.14 | -0.18 | -0.27 | -0.26 | -0.26 | -0.30 | -0.27 | -0.19 | -0.14 | -0.11 | -0.03 | -0.03 | -0.03 | -0.10 | 0.02 | 0.16 | 0.08 | -0.07 | -0.08 | -0.13 | -0.06 | -0.03 | -0.02 | -0.03 | -0.02 | 0.00 | 0.03 | 0.02 | 0.02 | 0.04 | 0.05 | 0.01 | -0.00 | 0.10 | 0.09 | -0.00 | 0.07 | 0.18 | 0.15 | 0.09 | 0.21 | 0.26 | 0.11 | 0.13 | 0.28 | 0.12 | 0.20 | 0.37 | 0.35 | 0.32 | 0.24 | 0.62 | 0.65 | 0.67 | 0.62 | 0.59 | 0.61 | 0.57 | 0.50 | 0.45 | 0.47 | 0.41 | 0.27 | 0.25 | 0.31 | 0.21 | 0.12 | 0.15 | 0.15 | 0.03 | 0.01 | 0.09 | 0.04 | -0.02 | 0.07 | 0.08 | -0.02 | -0.13 | -0.05 | -0.07 | -0.11 | -0.09 | -0.08 | -0.13 | -0.22 | -0.04 | 0.03 | -0.07 | -0.09 | -0.03 | -0.04 | -0.06 | 0.01 | 0.05 | 0.10 | 0.16 | 0.15 |
A | Ile 50.13 | 0.36 | 0.58 | 0.82 | 1.00 | 0.85 | 0.62 | 0.43 | 0.38 | 0.43 | 0.07 | 0.17 | 0.15 | 0.09 | 0.10 | 0.22 | 0.20 | 0.16 | 0.15 | 0.17 | 0.13 | 0.06 | 0.04 | 0.05 | 0.01 | -0.08 | -0.15 | -0.17 | -0.19 | -0.19 | -0.24 | -0.25 | -0.27 | -0.28 | -0.25 | -0.27 | -0.31 | -0.25 | -0.20 | -0.24 | -0.30 | -0.30 | -0.31 | -0.31 | -0.34 | -0.36 | -0.42 | -0.42 | -0.41 | -0.40 | -0.39 | -0.37 | -0.37 | -0.37 | -0.28 | -0.24 | -0.30 | -0.21 | -0.05 | -0.11 | -0.16 | -0.07 | -0.03 | 0.03 | 0.07 | 0.10 | 0.11 | 0.12 | 0.14 | 0.17 | 0.06 | 0.06 | 0.12 | 0.09 | -0.01 | -0.04 | 0.03 | -0.04 | 0.06 | 0.08 | 0.05 | 0.04 | 0.05 | 0.02 | -0.05 | -0.06 | 0.02 | -0.06 | -0.08 | -0.08 | -0.22 | -0.25 | -0.18 | -0.23 | -0.37 | -0.36 | -0.26 | -0.27 | -0.37 | -0.37 | -0.31 | -0.36 | -0.38 | -0.34 | -0.35 | -0.35 | -0.36 | -0.37 | -0.33 | -0.34 | -0.34 | -0.31 | -0.29 | -0.33 | -0.35 | -0.35 | -0.42 | -0.47 | -0.35 | -0.36 | -0.42 | -0.38 | -0.36 | -0.31 | -0.32 | -0.37 | -0.37 | -0.32 | -0.35 | -0.39 | -0.38 | -0.33 | -0.34 | -0.38 | -0.34 | -0.31 | -0.36 | -0.37 | -0.27 | -0.30 | -0.36 | -0.29 | -0.20 | -0.24 | -0.15 | -0.05 | -0.03 | -0.01 | 0.07 | 0.13 | 0.09 | 0.08 | 0.04 | 0.05 | 0.01 | -0.02 | 0.03 | 0.09 | 0.12 | 0.13 | 0.09 | 0.09 | 0.13 | 0.01 | -0.02 | 0.04 | 0.07 | -0.04 | 0.02 | -0.06 | -0.21 | -0.18 | -0.10 | -0.26 | -0.33 | -0.27 | -0.28 | -0.41 | -0.42 | -0.38 | -0.34 | -0.42 | -0.42 | -0.33 | -0.30 | -0.38 | -0.41 | -0.33 | -0.32 | -0.38 | -0.37 | -0.30 | -0.29 | -0.34 | -0.30 | -0.23 | -0.25 | -0.28 | -0.24 | -0.19 | -0.16 | -0.20 | -0.30 | -0.24 | -0.19 | -0.27 | -0.28 | -0.21 | -0.18 | -0.16 | -0.09 | -0.17 | -0.10 | -0.05 | -0.00 | 0.08 | 0.03 | 0.14 | 0.09 | 0.18 | 0.13 | 0.22 | 0.30 | 0.32 | 0.32 | 0.32 | 0.32 | 0.33 | 0.33 | 0.32 | 0.28 | 0.24 | 0.29 | 0.07 | 0.06 | 0.00 | 0.17 | 0.20 | 0.15 | 0.10 | 0.14 | 0.17 | 0.15 | 0.15 | 0.22 | 0.18 | 0.11 | 0.13 | 0.05 | 0.05 | 0.02 | -0.06 | -0.10 | -0.12 | -0.21 | -0.24 | -0.27 | -0.22 | -0.26 | -0.23 | -0.25 | -0.18 | -0.26 | -0.21 | -0.05 | -0.01 | -0.19 | -0.19 | -0.24 | -0.23 | -0.20 | -0.18 | -0.21 | -0.23 | -0.19 | -0.14 | -0.17 | -0.18 | -0.13 | -0.11 | -0.16 | -0.20 | -0.09 | -0.09 | -0.19 | -0.13 | 0.01 | -0.03 | -0.09 | 0.02 | 0.11 | -0.02 | -0.07 | 0.16 | 0.29 | 0.30 | 0.27 | 0.37 | 0.32 | 0.27 | 0.60 | 0.65 | 0.60 | 0.53 | 0.57 | 0.57 | 0.48 | 0.42 | 0.44 | 0.41 | 0.29 | 0.21 | 0.23 | 0.21 | 0.07 | 0.03 | 0.08 | 0.03 | -0.08 | -0.03 | 0.05 | -0.03 | -0.04 | 0.03 | -0.02 | -0.09 | -0.08 | -0.05 | -0.13 | -0.09 | 0.01 | -0.07 | -0.18 | -0.25 | -0.10 | -0.04 | -0.21 | -0.11 | 0.08 | 0.06 | -0.02 | 0.11 | 0.18 | 0.17 | 0.20 | 0.19 |
A | Asn 60.10 | 0.35 | 0.49 | 0.67 | 0.85 | 1.00 | 0.71 | 0.59 | 0.54 | 0.56 | 0.06 | 0.21 | 0.20 | 0.15 | 0.17 | 0.29 | 0.26 | 0.21 | 0.22 | 0.23 | 0.17 | 0.10 | 0.09 | 0.09 | 0.00 | -0.08 | -0.15 | -0.20 | -0.21 | -0.25 | -0.28 | -0.28 | -0.31 | -0.33 | -0.30 | -0.32 | -0.34 | -0.29 | -0.25 | -0.30 | -0.35 | -0.34 | -0.34 | -0.33 | -0.36 | -0.36 | -0.42 | -0.44 | -0.42 | -0.39 | -0.39 | -0.38 | -0.35 | -0.35 | -0.26 | -0.20 | -0.25 | -0.17 | 0.01 | -0.05 | -0.11 | -0.01 | 0.02 | 0.08 | 0.13 | 0.17 | 0.17 | 0.17 | 0.21 | 0.23 | 0.13 | 0.13 | 0.18 | 0.15 | 0.06 | 0.01 | 0.08 | -0.04 | 0.04 | 0.09 | 0.08 | 0.05 | 0.07 | 0.04 | -0.03 | -0.03 | 0.04 | -0.04 | -0.07 | -0.06 | -0.20 | -0.25 | -0.19 | -0.23 | -0.37 | -0.36 | -0.29 | -0.29 | -0.38 | -0.38 | -0.33 | -0.37 | -0.40 | -0.36 | -0.36 | -0.35 | -0.36 | -0.35 | -0.30 | -0.31 | -0.32 | -0.30 | -0.30 | -0.34 | -0.36 | -0.39 | -0.46 | -0.44 | -0.33 | -0.34 | -0.38 | -0.38 | -0.37 | -0.32 | -0.32 | -0.37 | -0.37 | -0.32 | -0.33 | -0.36 | -0.36 | -0.31 | -0.31 | -0.34 | -0.30 | -0.27 | -0.32 | -0.33 | -0.24 | -0.26 | -0.31 | -0.26 | -0.16 | -0.20 | -0.11 | 0.00 | 0.01 | 0.02 | 0.10 | 0.16 | 0.12 | 0.14 | 0.09 | 0.10 | 0.04 | 0.02 | 0.07 | 0.14 | 0.17 | 0.17 | 0.14 | 0.11 | 0.11 | 0.02 | 0.00 | 0.09 | 0.10 | 0.01 | 0.06 | -0.02 | -0.15 | -0.13 | -0.07 | -0.20 | -0.26 | -0.27 | -0.28 | -0.34 | -0.37 | -0.35 | -0.31 | -0.40 | -0.40 | -0.31 | -0.29 | -0.37 | -0.41 | -0.34 | -0.33 | -0.41 | -0.40 | -0.32 | -0.34 | -0.39 | -0.32 | -0.23 | -0.30 | -0.33 | -0.24 | -0.20 | -0.18 | -0.21 | -0.30 | -0.23 | -0.18 | -0.29 | -0.30 | -0.29 | -0.22 | -0.21 | -0.11 | -0.18 | -0.10 | -0.09 | -0.08 | 0.01 | -0.06 | 0.06 | -0.01 | 0.14 | 0.07 | 0.15 | 0.27 | 0.30 | 0.31 | 0.31 | 0.34 | 0.36 | 0.36 | 0.34 | 0.26 | 0.24 | 0.33 | 0.14 | 0.13 | 0.08 | 0.25 | 0.27 | 0.22 | 0.16 | 0.20 | 0.23 | 0.20 | 0.17 | 0.23 | 0.16 | 0.11 | 0.16 | 0.09 | 0.10 | 0.08 | -0.02 | -0.07 | -0.11 | -0.22 | -0.26 | -0.33 | -0.27 | -0.34 | -0.33 | -0.34 | -0.29 | -0.32 | -0.27 | -0.16 | -0.10 | -0.22 | -0.21 | -0.25 | -0.26 | -0.21 | -0.19 | -0.21 | -0.22 | -0.17 | -0.15 | -0.15 | -0.15 | -0.12 | -0.11 | -0.16 | -0.21 | -0.11 | -0.10 | -0.21 | -0.15 | -0.03 | -0.07 | -0.09 | 0.03 | 0.11 | 0.00 | -0.02 | 0.07 | 0.18 | 0.22 | 0.13 | 0.13 | 0.15 | 0.05 | 0.43 | 0.55 | 0.50 | 0.39 | 0.44 | 0.52 | 0.41 | 0.32 | 0.41 | 0.42 | 0.26 | 0.20 | 0.28 | 0.23 | 0.07 | 0.07 | 0.14 | 0.06 | -0.04 | 0.02 | 0.09 | -0.03 | -0.04 | 0.03 | -0.03 | -0.11 | -0.08 | -0.07 | -0.16 | -0.13 | -0.03 | -0.12 | -0.20 | -0.29 | -0.19 | -0.16 | -0.28 | -0.13 | 0.08 | 0.08 | 0.04 | 0.19 | 0.24 | 0.26 | 0.27 | 0.24 |
A | Val 70.24 | 0.43 | 0.34 | 0.43 | 0.62 | 0.71 | 1.00 | 0.79 | 0.79 | 0.72 | 0.08 | 0.36 | 0.44 | 0.34 | 0.28 | 0.46 | 0.49 | 0.35 | 0.37 | 0.47 | 0.36 | 0.21 | 0.29 | 0.30 | 0.12 | 0.04 | 0.05 | -0.03 | -0.07 | -0.15 | -0.09 | -0.13 | -0.24 | -0.24 | -0.15 | -0.22 | -0.33 | -0.24 | -0.15 | -0.22 | -0.32 | -0.31 | -0.38 | -0.39 | -0.48 | -0.54 | -0.59 | -0.55 | -0.54 | -0.55 | -0.50 | -0.44 | -0.44 | -0.47 | -0.26 | -0.18 | -0.29 | -0.13 | 0.13 | 0.03 | -0.03 | 0.19 | 0.22 | 0.31 | 0.37 | 0.43 | 0.42 | 0.37 | 0.44 | 0.47 | 0.33 | 0.31 | 0.38 | 0.32 | 0.22 | 0.22 | 0.31 | 0.28 | 0.30 | 0.28 | 0.26 | 0.32 | 0.31 | 0.20 | 0.18 | 0.26 | 0.24 | 0.07 | 0.11 | 0.11 | -0.20 | -0.24 | -0.13 | -0.28 | -0.49 | -0.51 | -0.45 | -0.46 | -0.62 | -0.62 | -0.56 | -0.60 | -0.64 | -0.61 | -0.58 | -0.58 | -0.62 | -0.59 | -0.51 | -0.52 | -0.55 | -0.53 | -0.53 | -0.56 | -0.58 | -0.54 | -0.50 | -0.58 | -0.52 | -0.50 | -0.55 | -0.60 | -0.55 | -0.48 | -0.48 | -0.55 | -0.54 | -0.46 | -0.48 | -0.55 | -0.51 | -0.43 | -0.47 | -0.51 | -0.43 | -0.42 | -0.52 | -0.48 | -0.35 | -0.44 | -0.50 | -0.36 | -0.26 | -0.35 | -0.18 | 0.09 | 0.01 | 0.05 | 0.20 | 0.29 | 0.30 | 0.24 | 0.17 | 0.14 | 0.08 | 0.06 | 0.16 | 0.26 | 0.34 | 0.37 | 0.28 | 0.21 | 0.21 | 0.10 | 0.08 | 0.16 | 0.13 | 0.04 | 0.13 | 0.05 | -0.13 | -0.12 | -0.01 | -0.19 | -0.32 | -0.25 | -0.22 | -0.38 | -0.48 | -0.47 | -0.42 | -0.54 | -0.53 | -0.44 | -0.45 | -0.54 | -0.57 | -0.53 | -0.53 | -0.58 | -0.59 | -0.53 | -0.54 | -0.59 | -0.55 | -0.44 | -0.47 | -0.52 | -0.46 | -0.41 | -0.44 | -0.46 | -0.48 | -0.46 | -0.40 | -0.44 | -0.51 | -0.49 | -0.37 | -0.32 | -0.14 | -0.25 | -0.13 | -0.11 | -0.24 | -0.02 | -0.14 | 0.10 | 0.01 | 0.24 | 0.13 | 0.27 | 0.44 | 0.49 | 0.50 | 0.51 | 0.54 | 0.55 | 0.55 | 0.52 | 0.41 | 0.35 | 0.49 | 0.20 | 0.21 | 0.14 | 0.39 | 0.46 | 0.41 | 0.32 | 0.39 | 0.42 | 0.37 | 0.32 | 0.40 | 0.30 | 0.24 | 0.31 | 0.20 | 0.22 | 0.18 | 0.03 | -0.05 | -0.12 | -0.33 | -0.45 | -0.53 | -0.48 | -0.55 | -0.58 | -0.59 | -0.55 | -0.59 | -0.51 | -0.38 | -0.36 | -0.44 | -0.44 | -0.43 | -0.47 | -0.45 | -0.42 | -0.40 | -0.41 | -0.36 | -0.32 | -0.33 | -0.29 | -0.24 | -0.22 | -0.30 | -0.35 | -0.20 | -0.19 | -0.36 | -0.30 | -0.12 | -0.24 | -0.35 | -0.18 | -0.04 | -0.26 | -0.29 | 0.15 | 0.22 | 0.02 | 0.09 | 0.33 | 0.14 | 0.15 | 0.52 | 0.64 | 0.57 | 0.47 | 0.56 | 0.62 | 0.48 | 0.42 | 0.55 | 0.49 | 0.29 | 0.27 | 0.39 | 0.26 | 0.06 | 0.07 | 0.17 | 0.03 | -0.12 | -0.03 | 0.00 | -0.16 | -0.15 | -0.00 | -0.11 | -0.22 | -0.11 | -0.09 | -0.26 | -0.19 | -0.04 | -0.16 | -0.33 | -0.43 | -0.30 | -0.24 | -0.37 | -0.21 | 0.03 | 0.09 | 0.06 | 0.24 | 0.40 | 0.44 | 0.42 | 0.40 |
A | Lys 80.10 | 0.25 | 0.17 | 0.12 | 0.43 | 0.59 | 0.79 | 1.00 | 0.89 | 0.65 | -0.08 | 0.23 | 0.27 | 0.16 | 0.11 | 0.31 | 0.33 | 0.18 | 0.22 | 0.38 | 0.25 | 0.12 | 0.25 | 0.29 | 0.08 | 0.02 | 0.11 | 0.06 | 0.01 | -0.14 | 0.04 | 0.02 | -0.10 | -0.09 | 0.02 | -0.05 | -0.13 | -0.04 | 0.02 | -0.05 | -0.14 | -0.09 | -0.15 | -0.18 | -0.27 | -0.32 | -0.39 | -0.33 | -0.26 | -0.31 | -0.32 | -0.21 | -0.17 | -0.27 | -0.12 | 0.03 | -0.08 | -0.05 | 0.23 | 0.17 | 0.05 | 0.23 | 0.30 | 0.34 | 0.35 | 0.40 | 0.42 | 0.35 | 0.36 | 0.40 | 0.33 | 0.26 | 0.33 | 0.30 | 0.27 | 0.23 | 0.31 | 0.29 | 0.35 | 0.32 | 0.35 | 0.35 | 0.33 | 0.28 | 0.28 | 0.33 | 0.28 | 0.19 | 0.21 | 0.15 | -0.11 | -0.07 | -0.03 | -0.25 | -0.40 | -0.35 | -0.39 | -0.40 | -0.50 | -0.49 | -0.51 | -0.53 | -0.54 | -0.56 | -0.53 | -0.51 | -0.55 | -0.49 | -0.46 | -0.48 | -0.50 | -0.50 | -0.52 | -0.50 | -0.47 | -0.41 | -0.39 | -0.42 | -0.32 | -0.33 | -0.34 | -0.40 | -0.31 | -0.25 | -0.23 | -0.28 | -0.28 | -0.18 | -0.20 | -0.27 | -0.21 | -0.12 | -0.19 | -0.24 | -0.13 | -0.13 | -0.27 | -0.24 | -0.08 | -0.19 | -0.32 | -0.17 | -0.04 | -0.14 | -0.09 | 0.19 | 0.17 | 0.13 | 0.25 | 0.31 | 0.31 | 0.27 | 0.23 | 0.25 | 0.21 | 0.17 | 0.21 | 0.24 | 0.33 | 0.36 | 0.25 | 0.18 | 0.19 | 0.11 | 0.14 | 0.18 | 0.12 | 0.08 | 0.13 | 0.06 | -0.07 | -0.10 | -0.07 | -0.21 | -0.28 | -0.30 | -0.31 | -0.40 | -0.46 | -0.46 | -0.46 | -0.52 | -0.49 | -0.44 | -0.49 | -0.56 | -0.55 | -0.53 | -0.57 | -0.59 | -0.59 | -0.57 | -0.59 | -0.60 | -0.58 | -0.55 | -0.56 | -0.57 | -0.54 | -0.52 | -0.53 | -0.51 | -0.50 | -0.49 | -0.38 | -0.32 | -0.38 | -0.46 | -0.18 | -0.16 | 0.06 | -0.02 | 0.09 | 0.01 | -0.21 | -0.06 | -0.23 | -0.00 | -0.25 | 0.00 | -0.20 | -0.05 | 0.21 | 0.31 | 0.31 | 0.36 | 0.46 | 0.44 | 0.43 | 0.32 | 0.14 | 0.09 | 0.38 | 0.35 | 0.38 | 0.38 | 0.51 | 0.55 | 0.55 | 0.51 | 0.54 | 0.53 | 0.49 | 0.41 | 0.38 | 0.29 | 0.34 | 0.44 | 0.40 | 0.44 | 0.41 | 0.32 | 0.24 | 0.15 | -0.06 | -0.21 | -0.42 | -0.39 | -0.52 | -0.64 | -0.66 | -0.62 | -0.58 | -0.63 | -0.61 | -0.50 | -0.48 | -0.47 | -0.43 | -0.52 | -0.53 | -0.50 | -0.47 | -0.50 | -0.47 | -0.46 | -0.46 | -0.42 | -0.37 | -0.39 | -0.45 | -0.51 | -0.44 | -0.41 | -0.51 | -0.49 | -0.37 | -0.41 | -0.48 | -0.39 | -0.24 | -0.32 | -0.40 | -0.12 | 0.17 | 0.04 | -0.08 | 0.09 | -0.00 | 0.09 | 0.21 | 0.32 | 0.17 | 0.05 | 0.21 | 0.25 | 0.05 | 0.03 | 0.24 | 0.13 | -0.09 | 0.00 | 0.14 | -0.05 | -0.22 | -0.13 | -0.03 | -0.18 | -0.26 | -0.11 | -0.10 | -0.27 | -0.20 | -0.09 | -0.19 | -0.25 | -0.07 | -0.13 | -0.30 | -0.19 | -0.06 | -0.21 | -0.36 | -0.36 | -0.37 | -0.36 | -0.44 | -0.20 | 0.06 | 0.14 | 0.11 | 0.29 | 0.42 | 0.42 | 0.36 | 0.33 |
A | Gln 90.12 | 0.26 | 0.14 | 0.10 | 0.38 | 0.54 | 0.79 | 0.89 | 1.00 | 0.81 | -0.00 | 0.34 | 0.42 | 0.30 | 0.24 | 0.44 | 0.47 | 0.31 | 0.34 | 0.49 | 0.35 | 0.19 | 0.32 | 0.35 | 0.11 | 0.05 | 0.12 | 0.02 | -0.03 | -0.16 | -0.02 | -0.07 | -0.19 | -0.18 | -0.08 | -0.17 | -0.26 | -0.15 | -0.08 | -0.16 | -0.26 | -0.21 | -0.29 | -0.31 | -0.42 | -0.46 | -0.52 | -0.46 | -0.40 | -0.44 | -0.44 | -0.33 | -0.30 | -0.38 | -0.20 | -0.06 | -0.17 | -0.08 | 0.22 | 0.14 | 0.04 | 0.26 | 0.33 | 0.39 | 0.42 | 0.49 | 0.49 | 0.42 | 0.47 | 0.51 | 0.39 | 0.34 | 0.43 | 0.36 | 0.31 | 0.28 | 0.35 | 0.29 | 0.37 | 0.34 | 0.36 | 0.39 | 0.38 | 0.30 | 0.30 | 0.36 | 0.33 | 0.19 | 0.22 | 0.18 | -0.12 | -0.12 | -0.06 | -0.27 | -0.48 | -0.44 | -0.47 | -0.51 | -0.60 | -0.59 | -0.61 | -0.62 | -0.62 | -0.65 | -0.61 | -0.57 | -0.61 | -0.58 | -0.51 | -0.51 | -0.55 | -0.56 | -0.59 | -0.57 | -0.55 | -0.50 | -0.46 | -0.47 | -0.39 | -0.40 | -0.41 | -0.51 | -0.44 | -0.37 | -0.34 | -0.41 | -0.42 | -0.31 | -0.32 | -0.40 | -0.35 | -0.25 | -0.31 | -0.37 | -0.25 | -0.24 | -0.38 | -0.35 | -0.18 | -0.29 | -0.41 | -0.24 | -0.12 | -0.22 | -0.10 | 0.20 | 0.13 | 0.12 | 0.27 | 0.35 | 0.35 | 0.30 | 0.24 | 0.26 | 0.19 | 0.15 | 0.22 | 0.29 | 0.41 | 0.44 | 0.33 | 0.23 | 0.22 | 0.11 | 0.13 | 0.20 | 0.13 | 0.07 | 0.14 | 0.06 | -0.09 | -0.11 | -0.06 | -0.21 | -0.30 | -0.32 | -0.31 | -0.42 | -0.49 | -0.50 | -0.50 | -0.59 | -0.55 | -0.49 | -0.55 | -0.63 | -0.63 | -0.60 | -0.63 | -0.67 | -0.66 | -0.63 | -0.65 | -0.68 | -0.64 | -0.56 | -0.60 | -0.62 | -0.55 | -0.52 | -0.57 | -0.56 | -0.53 | -0.54 | -0.47 | -0.42 | -0.47 | -0.53 | -0.26 | -0.24 | 0.00 | -0.10 | 0.03 | -0.02 | -0.26 | -0.04 | -0.21 | 0.07 | -0.16 | 0.14 | -0.08 | 0.08 | 0.36 | 0.45 | 0.45 | 0.49 | 0.58 | 0.58 | 0.57 | 0.48 | 0.28 | 0.23 | 0.52 | 0.39 | 0.43 | 0.40 | 0.59 | 0.64 | 0.61 | 0.54 | 0.59 | 0.60 | 0.55 | 0.47 | 0.47 | 0.35 | 0.37 | 0.48 | 0.41 | 0.45 | 0.41 | 0.28 | 0.18 | 0.09 | -0.16 | -0.34 | -0.54 | -0.52 | -0.64 | -0.74 | -0.73 | -0.70 | -0.66 | -0.69 | -0.65 | -0.57 | -0.56 | -0.56 | -0.51 | -0.59 | -0.58 | -0.56 | -0.52 | -0.54 | -0.51 | -0.48 | -0.48 | -0.43 | -0.39 | -0.40 | -0.47 | -0.53 | -0.43 | -0.40 | -0.52 | -0.50 | -0.37 | -0.40 | -0.47 | -0.38 | -0.22 | -0.29 | -0.38 | -0.11 | 0.18 | 0.01 | -0.09 | 0.06 | -0.10 | 0.11 | 0.28 | 0.39 | 0.26 | 0.14 | 0.27 | 0.33 | 0.15 | 0.09 | 0.30 | 0.22 | -0.02 | 0.04 | 0.21 | 0.02 | -0.18 | -0.08 | 0.05 | -0.14 | -0.23 | -0.07 | -0.08 | -0.27 | -0.21 | -0.06 | -0.18 | -0.29 | -0.11 | -0.15 | -0.34 | -0.26 | -0.10 | -0.24 | -0.44 | -0.46 | -0.41 | -0.41 | -0.44 | -0.18 | 0.07 | 0.18 | 0.20 | 0.38 | 0.51 | 0.52 | 0.47 | 0.43 |
The following additional files have been created:
The main table contains all collected data in a single file. The column names match the names used above for graphs in plots and columns in tables. You can find a more detailed explanation of this table in the user manual at Recipes > Run a molecular dynamics simulation > Analyzing a trajectory. If you parse this file automatically, keep in mind that the number of columns can change any time, so you have to use the names in the first table row to find the columns of interest: 4mbs_analysis.tab
Data of the per-residue plots:
4mbs_plotres_secstrMolA.tab
4mbs_plotres_conMolA.tab
4mbs_plotres_ligconMolA.tab
The time averaged structure in PDB format: 4mbs_average.pdb
The snapshot with the minimum solute energy. Either just the solute in PDB format 4mbs_energymin.pdb, or the complete system including solvent as a YASARA scene 4mbs_energymin.sce.
The last snapshot of the simulation. Either just the solute in PDB format 4mbs_last.pdb, or the complete system including solvent as a YASARA scene 4mbs_last.sce
A table that lists the Root Mean Square Fluctuations [RMSFs] of all atoms in [A] is available here: 4mbs_rmsf.tab. The RMSFs have also been converted to B-factors and stored in the B-factor field of the time-average structure above.
To facilitate publication, high resolution versions of the plots above have been created with a 4:3 aspect ratio suited for printing in a single column of a typical journal article. Just look at the figure number above to find the right file:
4mbs_report_figure10_hires.png
4mbs_report_figure11_hires.png
4mbs_report_figure12_hires.png
4mbs_report_figure13_hires.png
4mbs_report_figure14_hires.png
4mbs_report_figure15_hires.png
4mbs_report_figure16_hires.png