| Chain sequence(s) |
A: SEAKERASDLKAEAAARALAIIDAARAAVAAADPALRPLALAASGEAASAIALGMQEGLEVGVERVREVAERAPPEMAAALREAARLLEEAGRRVEELL
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| Dynamic mode | No |
| Automated mutations | Yes |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] FoldX: Starting FoldX energy minimalization (00:00:00)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:00:38)
[INFO] Auto_mut: Residue number 39 from chain A and a score of 0.607 (leucine) selected for
automated muatation (00:00:38)
[INFO] Auto_mut: Residue number 41 from chain A and a score of 0.420 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 38 from chain A and a score of 0.126 (proline) selected for
automated muatation (00:00:38)
[INFO] Auto_mut: Residue number 42 from chain A and a score of 0.015 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 15 from chain A and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 40 from chain A and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 44 from chain A and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 50 from chain A and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 99 from chain A and a score of -0.051 (leucine) selected for
automated muatation (00:00:38)
[INFO] Auto_mut: Residue number 19 from chain A and a score of -0.150 omitted from automated
muatation (excluded by the user). (00:00:38)
[INFO] Auto_mut: Residue number 36 from chain A and a score of -0.157 (leucine) selected for
automated muatation (00:00:38)
[INFO] Auto_mut: Mutating residue number 39 from chain A (leucine) into glutamic acid (00:00:38)
[INFO] Auto_mut: Mutating residue number 39 from chain A (leucine) into aspartic acid (00:00:38)
[INFO] Auto_mut: Mutating residue number 38 from chain A (proline) into glutamic acid (00:00:38)
[INFO] Auto_mut: Mutating residue number 39 from chain A (leucine) into arginine (00:01:21)
[INFO] Auto_mut: Mutating residue number 38 from chain A (proline) into lysine (00:01:22)
[INFO] Auto_mut: Mutating residue number 39 from chain A (leucine) into lysine (00:01:23)
[INFO] Auto_mut: Mutating residue number 38 from chain A (proline) into aspartic acid (00:02:14)
[INFO] Auto_mut: Mutating residue number 99 from chain A (leucine) into glutamic acid (00:02:19)
[INFO] Auto_mut: Mutating residue number 99 from chain A (leucine) into aspartic acid (00:02:22)
[INFO] Auto_mut: Mutating residue number 38 from chain A (proline) into arginine (00:02:59)
[INFO] Auto_mut: Mutating residue number 99 from chain A (leucine) into arginine (00:03:14)
[INFO] Auto_mut: Mutating residue number 99 from chain A (leucine) into lysine (00:03:14)
[INFO] Auto_mut: Mutating residue number 36 from chain A (leucine) into glutamic acid (00:03:45)
[INFO] Auto_mut: Mutating residue number 36 from chain A (leucine) into aspartic acid (00:04:13)
[INFO] Auto_mut: Mutating residue number 36 from chain A (leucine) into lysine (00:04:31)
[INFO] Auto_mut: Mutating residue number 36 from chain A (leucine) into arginine (00:04:58)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (leucine) into glutamic
acid: Energy difference: 0.9941 kcal/mol, Difference in average score from
the base case: -0.1191 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (leucine) into lysine:
Energy difference: 0.1278 kcal/mol, Difference in average score from the
base case: -0.1048 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (leucine) into aspartic
acid: Energy difference: 1.6699 kcal/mol, Difference in average score from
the base case: -0.1251 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (leucine) into arginine:
Energy difference: -0.3826 kcal/mol, Difference in average score from the
base case: -0.1191 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (proline) into glutamic
acid: Energy difference: 1.4400 kcal/mol, Difference in average score from
the base case: -0.0818 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (proline) into lysine:
Energy difference: 1.5372 kcal/mol, Difference in average score from the
base case: -0.0888 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (proline) into aspartic
acid: Energy difference: 1.6749 kcal/mol, Difference in average score from
the base case: -0.0863 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (proline) into arginine:
Energy difference: 1.1298 kcal/mol, Difference in average score from the
base case: -0.0812 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 99 from chain A (leucine) into glutamic
acid: Energy difference: 0.9354 kcal/mol, Difference in average score from
the base case: -0.1363 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 99 from chain A (leucine) into lysine:
Energy difference: 0.8245 kcal/mol, Difference in average score from the
base case: -0.1187 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 99 from chain A (leucine) into aspartic
acid: Energy difference: 1.4481 kcal/mol, Difference in average score from
the base case: -0.1329 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 99 from chain A (leucine) into arginine:
Energy difference: 1.0234 kcal/mol, Difference in average score from the
base case: -0.1145 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into glutamic
acid: Energy difference: 2.1054 kcal/mol, Difference in average score from
the base case: -0.0506 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into lysine:
Energy difference: 0.8390 kcal/mol, Difference in average score from the
base case: -0.0772 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into aspartic
acid: Energy difference: 2.2695 kcal/mol, Difference in average score from
the base case: -0.0632 (00:05:53)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into arginine:
Energy difference: -0.0369 kcal/mol, Difference in average score from the
base case: -0.0115 (00:05:53)
[INFO] Main: Simulation completed successfully. (00:05:55)
|
The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan3D score | mutation |
|---|---|---|---|---|
| residue index | residue name | chain | Aggrescan3D score | |
| 1 | S | A | -2.2326 | |
| 2 | E | A | -3.4963 | |
| 3 | A | A | -2.7702 | |
| 4 | K | A | -3.6557 | |
| 5 | E | A | -4.7965 | |
| 6 | R | A | -4.2292 | |
| 7 | A | A | 0.0000 | |
| 8 | S | A | -3.2439 | |
| 9 | D | A | -3.8567 | |
| 10 | L | A | 0.0000 | |
| 11 | K | A | -2.5277 | |
| 12 | A | A | -2.0014 | |
| 13 | E | A | -2.7279 | |
| 14 | A | A | 0.0000 | |
| 15 | A | A | 0.0000 | |
| 16 | A | A | -1.0719 | |
| 17 | R | A | -1.8694 | |
| 18 | A | A | 0.0000 | |
| 19 | L | A | -0.1504 | |
| 20 | A | A | -0.4302 | |
| 21 | I | A | -0.2026 | |
| 22 | I | A | 0.0000 | |
| 23 | D | A | -1.1250 | |
| 24 | A | A | -0.4062 | |
| 25 | A | A | -0.6723 | |
| 26 | R | A | -0.8377 | |
| 27 | A | A | -0.4582 | |
| 28 | A | A | -0.7695 | |
| 29 | V | A | 0.0000 | |
| 30 | A | A | -0.5444 | |
| 31 | A | A | -0.4175 | |
| 32 | A | A | -0.5599 | |
| 33 | D | A | -1.1659 | |
| 34 | P | A | -0.8719 | |
| 35 | A | A | -0.4204 | |
| 36 | L | A | -0.1574 | |
| 37 | R | A | -0.7458 | |
| 38 | P | A | 0.1258 | |
| 39 | L | A | 0.6069 | |
| 40 | A | A | 0.0000 | |
| 41 | L | A | 0.4197 | |
| 42 | A | A | 0.0153 | |
| 43 | A | A | 0.0000 | |
| 44 | S | A | 0.0000 | |
| 45 | G | A | -1.1168 | |
| 46 | E | A | -2.2934 | |
| 47 | A | A | 0.0000 | |
| 48 | A | A | -0.7341 | |
| 49 | S | A | -1.0023 | |
| 50 | A | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | A | A | -0.4495 | |
| 53 | L | A | -0.8283 | |
| 54 | G | A | 0.0000 | |
| 55 | M | A | -0.9399 | |
| 56 | Q | A | -1.7873 | |
| 57 | E | A | -2.4129 | |
| 58 | G | A | -1.5981 | |
| 59 | L | A | 0.0000 | |
| 60 | E | A | -3.2653 | |
| 61 | V | A | -1.9534 | |
| 62 | G | A | 0.0000 | |
| 63 | V | A | 0.0000 | |
| 64 | E | A | -3.9263 | |
| 65 | R | A | -3.7995 | |
| 66 | V | A | 0.0000 | |
| 67 | R | A | -4.6892 | |
| 68 | E | A | -4.6844 | |
| 69 | V | A | -3.5320 | |
| 70 | A | A | 0.0000 | |
| 71 | E | A | -3.7958 | |
| 72 | R | A | -3.1076 | |
| 73 | A | A | -1.6652 | |
| 74 | P | A | 0.0000 | |
| 75 | P | A | -1.5053 | |
| 76 | E | A | -1.8200 | |
| 77 | M | A | 0.0000 | |
| 78 | A | A | -2.2500 | |
| 79 | A | A | -1.5587 | |
| 80 | A | A | 0.0000 | |
| 81 | L | A | 0.0000 | |
| 82 | R | A | -3.3083 | |
| 83 | E | A | -2.2909 | |
| 84 | A | A | 0.0000 | |
| 85 | A | A | 0.0000 | |
| 86 | R | A | -3.6021 | |
| 87 | L | A | -2.6673 | |
| 88 | L | A | 0.0000 | |
| 89 | E | A | -4.3974 | |
| 90 | E | A | -4.3368 | |
| 91 | A | A | 0.0000 | |
| 92 | G | A | -3.9257 | |
| 93 | R | A | -4.9213 | |
| 94 | R | A | -4.2471 | |
| 95 | V | A | 0.0000 | |
| 96 | E | A | -3.3611 | |
| 97 | E | A | -2.9791 | |
| 98 | L | A | -1.4543 | |
| 99 | L | A | -0.0510 |
Automated mutations analysis
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 |
|||
| LR39A | -0.3826 | -0.1191 | View | CSV | PDB |
| LR36A | -0.0369 | -0.0115 | View | CSV | PDB |
| LK39A | 0.1278 | -0.1048 | View | CSV | PDB |
| LE99A | 0.9354 | -0.1363 | View | CSV | PDB |
| LK99A | 0.8245 | -0.1187 | View | CSV | PDB |
| LK36A | 0.839 | -0.0772 | View | CSV | PDB |
| PR38A | 1.1298 | -0.0812 | View | CSV | PDB |
| PK38A | 1.5372 | -0.0888 | 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