| Chain sequence(s) |
A: EVQLVESGGGLVQPGGSLRLSCAASGFSFSDFWMSWVRQAPGKGLEWVATISQAGSEKDYVDSVKGRFTISRDNAKKSLYLQMNSLRAEDTAVYYCASGVYSFDYRGQGTLVTVSS
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | No |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | Yes |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:02:02)
[INFO] AutoMut: Residue number 111 from chain A and a score of 1.589 (leucine) selected for
automated mutation (00:02:04)
[INFO] AutoMut: Residue number 11 from chain A and a score of 1.348 (leucine) selected for
automated mutation (00:02:04)
[INFO] AutoMut: Residue number 101 from chain A and a score of 1.346 (tyrosine) selected
for automated mutation (00:02:04)
[INFO] AutoMut: Residue number 100 from chain A and a score of 1.081 (valine) selected for
automated mutation (00:02:04)
[INFO] AutoMut: Residue number 5 from chain A and a score of 0.764 (valine) selected for
automated mutation (00:02:04)
[INFO] AutoMut: Residue number 93 from chain A and a score of 0.750 (valine) selected for
automated mutation (00:02:04)
[INFO] AutoMut: Mutating residue number 111 from chain A (leucine) into glutamic acid (00:02:04)
[INFO] AutoMut: Mutating residue number 11 from chain A (leucine) into glutamic acid (00:02:04)
[INFO] AutoMut: Mutating residue number 111 from chain A (leucine) into aspartic acid (00:02:04)
[INFO] AutoMut: Mutating residue number 111 from chain A (leucine) into arginine (00:02:21)
[INFO] AutoMut: Mutating residue number 11 from chain A (leucine) into lysine (00:02:22)
[INFO] AutoMut: Mutating residue number 111 from chain A (leucine) into lysine (00:02:26)
[INFO] AutoMut: Mutating residue number 11 from chain A (leucine) into aspartic acid (00:02:46)
[INFO] AutoMut: Mutating residue number 101 from chain A (tyrosine) into glutamic acid (00:02:56)
[INFO] AutoMut: Mutating residue number 11 from chain A (leucine) into arginine (00:03:00)
[INFO] AutoMut: Mutating residue number 101 from chain A (tyrosine) into lysine (00:03:16)
[INFO] AutoMut: Mutating residue number 101 from chain A (tyrosine) into aspartic acid (00:03:26)
[INFO] AutoMut: Mutating residue number 100 from chain A (valine) into glutamic acid (00:03:28)
[INFO] AutoMut: Mutating residue number 101 from chain A (tyrosine) into arginine (00:03:40)
[INFO] AutoMut: Mutating residue number 100 from chain A (valine) into lysine (00:03:42)
[INFO] AutoMut: Mutating residue number 100 from chain A (valine) into aspartic acid (00:03:48)
[INFO] AutoMut: Mutating residue number 5 from chain A (valine) into glutamic acid (00:04:01)
[INFO] AutoMut: Mutating residue number 100 from chain A (valine) into arginine (00:04:02)
[INFO] AutoMut: Mutating residue number 5 from chain A (valine) into aspartic acid (00:04:04)
[INFO] AutoMut: Mutating residue number 93 from chain A (valine) into glutamic acid (00:04:16)
[INFO] AutoMut: Mutating residue number 5 from chain A (valine) into lysine (00:04:20)
[INFO] AutoMut: Mutating residue number 5 from chain A (valine) into arginine (00:04:21)
[INFO] AutoMut: Mutating residue number 93 from chain A (valine) into lysine (00:04:34)
[INFO] AutoMut: Mutating residue number 93 from chain A (valine) into aspartic acid (00:05:03)
[INFO] AutoMut: Mutating residue number 93 from chain A (valine) into arginine (00:05:18)
[INFO] AutoMut: Effect of mutation residue number 111 from chain A (leucine) into glutamic
acid: Energy difference: 0.3796 kcal/mol, Difference in average score from
the base case: -0.1045 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 111 from chain A (leucine) into lysine:
Energy difference: -0.5045 kcal/mol, Difference in average score from the
base case: -0.1004 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 111 from chain A (leucine) into aspartic
acid: Energy difference: 0.7142 kcal/mol, Difference in average score from
the base case: -0.1008 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 111 from chain A (leucine) into arginine:
Energy difference: -0.7113 kcal/mol, Difference in average score from the
base case: -0.1044 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 11 from chain A (leucine) into glutamic
acid: Energy difference: 0.6329 kcal/mol, Difference in average score from
the base case: -0.1020 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 11 from chain A (leucine) into lysine:
Energy difference: 0.2086 kcal/mol, Difference in average score from the
base case: -0.0885 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 11 from chain A (leucine) into aspartic
acid: Energy difference: 0.2510 kcal/mol, Difference in average score from
the base case: -0.1023 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 11 from chain A (leucine) into arginine:
Energy difference: -0.0900 kcal/mol, Difference in average score from the
base case: -0.1008 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (tyrosine) into glutamic
acid: Energy difference: -0.0167 kcal/mol, Difference in average score from
the base case: -0.0733 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (tyrosine) into lysine:
Energy difference: 0.0267 kcal/mol, Difference in average score from the
base case: -0.0731 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (tyrosine) into aspartic
acid: Energy difference: 0.4366 kcal/mol, Difference in average score from
the base case: -0.0561 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 101 from chain A (tyrosine) into
arginine: Energy difference: -0.0370 kcal/mol, Difference in average score
from the base case: -0.0798 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (valine) into glutamic
acid: Energy difference: 0.2226 kcal/mol, Difference in average score from
the base case: -0.0362 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (valine) into lysine:
Energy difference: -0.4386 kcal/mol, Difference in average score from the
base case: -0.0310 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (valine) into aspartic
acid: Energy difference: 0.1458 kcal/mol, Difference in average score from
the base case: -0.0243 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 100 from chain A (valine) into arginine:
Energy difference: -1.6756 kcal/mol, Difference in average score from the
base case: -0.0430 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (valine) into glutamic
acid: Energy difference: 0.0177 kcal/mol, Difference in average score from
the base case: -0.0878 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (valine) into lysine:
Energy difference: -0.6963 kcal/mol, Difference in average score from the
base case: -0.0827 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (valine) into aspartic
acid: Energy difference: 0.7468 kcal/mol, Difference in average score from
the base case: -0.0869 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 5 from chain A (valine) into arginine:
Energy difference: -0.4299 kcal/mol, Difference in average score from the
base case: -0.0866 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (valine) into glutamic
acid: Energy difference: 0.5059 kcal/mol, Difference in average score from
the base case: -0.0345 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (valine) into lysine:
Energy difference: -0.2332 kcal/mol, Difference in average score from the
base case: -0.0347 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (valine) into aspartic
acid: Energy difference: 1.5810 kcal/mol, Difference in average score from
the base case: -0.0248 (00:05:39)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (valine) into arginine:
Energy difference: -0.1471 kcal/mol, Difference in average score from the
base case: -0.0386 (00:05:39)
[INFO] Main: Simulation completed successfully. (00:05:47)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 1 | E | A | -2.0639 | |
| 2 | V | A | -1.1002 | |
| 3 | Q | A | -1.3220 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.7645 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.1860 | |
| 8 | G | A | -0.7546 | |
| 9 | G | A | 0.1445 | |
| 10 | G | A | 0.6512 | |
| 11 | L | A | 1.3482 | |
| 12 | V | A | 0.0000 | |
| 13 | Q | A | -1.4288 | |
| 14 | P | A | -1.6158 | |
| 15 | G | A | -1.3778 | |
| 16 | G | A | -0.9609 | |
| 17 | S | A | -1.3435 | |
| 18 | L | A | -1.0301 | |
| 19 | R | A | -2.2815 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.4398 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -0.3796 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -1.1925 | |
| 26 | G | A | -1.1995 | |
| 27 | F | A | -0.6504 | |
| 28 | S | A | -0.7140 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | -1.2722 | |
| 31 | D | A | -1.4546 | |
| 32 | F | A | 0.2772 | |
| 33 | W | A | 0.1813 | |
| 34 | M | A | 0.0000 | |
| 35 | S | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.7965 | |
| 40 | A | A | -1.1383 | |
| 41 | P | A | -1.1203 | |
| 42 | G | A | -1.5687 | |
| 43 | K | A | -2.3227 | |
| 44 | G | A | -1.4219 | |
| 45 | L | A | -0.3876 | |
| 46 | E | A | -0.7683 | |
| 47 | W | A | 0.3275 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | T | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | S | A | 0.0000 | |
| 53 | Q | A | -1.0042 | |
| 54 | A | A | -0.8616 | |
| 55 | G | A | -1.2304 | |
| 56 | S | A | -1.4483 | |
| 57 | E | A | -2.8255 | |
| 58 | K | A | -2.7105 | |
| 59 | D | A | -2.7874 | |
| 60 | Y | A | -1.7297 | |
| 61 | V | A | -1.3422 | |
| 62 | D | A | -2.4972 | |
| 63 | S | A | -1.6354 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.7549 | |
| 66 | G | A | -1.7344 | |
| 67 | R | A | -1.3745 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -1.2861 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.5979 | |
| 72 | R | A | -1.1182 | |
| 73 | D | A | -1.6965 | |
| 74 | N | A | -2.2176 | |
| 75 | A | A | -1.6261 | |
| 76 | K | A | -2.6792 | |
| 77 | K | A | -2.5693 | |
| 78 | S | A | -1.4023 | |
| 79 | L | A | 0.0000 | |
| 80 | Y | A | -0.6289 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.6250 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.5019 | |
| 85 | S | A | -1.1974 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -2.2566 | |
| 88 | A | A | -1.7165 | |
| 89 | E | A | -2.2256 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.4101 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.7495 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | S | A | 0.3147 | |
| 99 | G | A | 0.5181 | |
| 100 | V | A | 1.0813 | |
| 101 | Y | A | 1.3458 | |
| 102 | S | A | 0.3044 | |
| 103 | F | A | 0.0698 | |
| 104 | D | A | -1.1298 | |
| 105 | Y | A | -0.0553 | |
| 106 | R | A | -0.9233 | |
| 107 | G | A | -0.7119 | |
| 108 | Q | A | -1.0346 | |
| 109 | G | A | 0.0000 | |
| 110 | T | A | 0.6142 | |
| 111 | L | A | 1.5887 | |
| 112 | V | A | 0.0000 | |
| 113 | T | A | 0.3291 | |
| 114 | V | A | 0.0000 | |
| 115 | S | A | -0.7191 | |
| 116 | S | A | -0.5216 |
Automated mutations analysis - charged mutations
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine.
The table below shows 2 best scored mutants for each mutated residue. Protein variants
are ordered according to the mutation effect they had on protein stability
(energetic effect) together with the difference in the average per-residue aggregation score
between the wild type and the mutant (in the table green values indicate a positive change,
grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this
CSV file .
Mutant |
Energetic effect |
Score comparison |
|||
| LR111A | -0.7113 | -0.1044 | View | CSV | PDB |
| LK111A | -0.5045 | -0.1004 | View | CSV | PDB |
| VK5A | -0.6963 | -0.0827 | View | CSV | PDB |
| VR100A | -1.6756 | -0.043 | View | CSV | PDB |
| VR5A | -0.4299 | -0.0866 | View | CSV | PDB |
| LR11A | -0.09 | -0.1008 | View | CSV | PDB |
| YR101A | -0.037 | -0.0798 | View | CSV | PDB |
| YE101A | -0.0167 | -0.0733 | View | CSV | PDB |
| VK100A | -0.4386 | -0.031 | View | CSV | PDB |
| VK93A | -0.2332 | -0.0347 | View | CSV | PDB |
| VR93A | -0.1471 | -0.0386 | View | CSV | PDB |
| LK11A | 0.2086 | -0.0885 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine