| Chain sequence(s) |
A: TSESGELHGLTTEEEFVEGTYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE
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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:48)
[INFO] AutoMutEv:Residue number 73 from chain A and a score of 2.123 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 66 from chain A and a score of 1.926 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 62 from chain A and a score of 1.722 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 74 from chain A and a score of 1.678 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 39 from chain A and a score of 1.545 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 63 from chain A and a score of 1.523 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 72 from chain A and a score of 1.434 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 67 from chain A and a score of 1.246 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 34 from chain A and a score of 1.191 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 10 from chain A and a score of 1.146 (leucine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Residue number 64 from chain A and a score of 1.096 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 68 from chain A and a score of 1.057 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 65 from chain A and a score of 1.036 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 59 from chain A and a score of 0.937 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 61 from chain A and a score of 0.839 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 71 from chain A and a score of 0.803 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 60 from chain A and a score of 0.672 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 69 from chain A and a score of 0.613 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 36 from chain A and a score of 0.578 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 58 from chain A and a score of 0.573 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 47 from chain A and a score of 0.551 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 46 from chain A and a score of 0.452 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 70 from chain A and a score of 0.412 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 37 from chain A and a score of 0.284 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 38 from chain A and a score of 0.281 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 57 from chain A and a score of 0.261 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 33 from chain A and a score of 0.152 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 35 from chain A and a score of 0.139 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 31 from chain A and a score of 0.053 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 30 from chain A and a score of 0.016 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 27 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 43 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 49 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 50 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:00:49)
[INFO] AutoMutEv:Residue number 7 from chain A and a score of -0.193 (leucine) selected for
automated mutation (00:00:49)
[INFO] AutoMutEv:Mutating residue number 10 from chain A (leucine) into methionine (00:00:49)
[INFO] AutoMutEv:Mutating residue number 7 from chain A (leucine) into methionine (00:00:49)
[INFO] AutoMutEv:Effect of mutation residue number 10 from chain A (leucine) into
methionine: Energy difference: -0.1687 kcal/mol, Difference in average
score from the base case: -0.0247 (00:00:55)
[INFO] AutoMutEv:Effect of mutation residue number 7 from chain A (leucine) into methionine:
Energy difference: -0.5090 kcal/mol, Difference in average score from the
base case: -0.0332 (00:00:55)
[INFO] Main: Simulation completed successfully. (00:00:56)
|
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 | T | A | -0.9991 | |
| 2 | S | A | -1.6027 | |
| 3 | E | A | -2.3090 | |
| 4 | S | A | -1.6968 | |
| 5 | G | A | -1.6020 | |
| 6 | E | A | -1.8889 | |
| 7 | L | A | -0.1930 | |
| 8 | H | A | -0.7190 | |
| 9 | G | A | -0.3141 | |
| 10 | L | A | 1.1457 | |
| 11 | T | A | -0.5194 | |
| 12 | T | A | -1.7497 | |
| 13 | E | A | -3.2383 | |
| 14 | E | A | -3.1008 | |
| 15 | E | A | -2.6101 | |
| 16 | F | A | -1.3506 | |
| 17 | V | A | -0.5160 | |
| 18 | E | A | -1.8251 | |
| 19 | G | A | -0.7969 | |
| 20 | T | A | -0.3883 | |
| 21 | Y | A | -0.2305 | |
| 22 | K | A | -1.4727 | |
| 23 | V | A | -1.1155 | |
| 24 | E | A | -2.7380 | |
| 25 | I | A | -2.2232 | |
| 26 | D | A | -2.8766 | |
| 27 | T | A | 0.0000 | |
| 28 | K | A | -2.1946 | |
| 29 | S | A | -1.3434 | |
| 30 | Y | A | 0.0164 | |
| 31 | W | A | 0.0532 | |
| 32 | K | A | -0.9278 | |
| 33 | A | A | 0.1521 | |
| 34 | L | A | 1.1907 | |
| 35 | G | A | 0.1393 | |
| 36 | I | A | 0.5783 | |
| 37 | S | A | 0.2836 | |
| 38 | P | A | 0.2809 | |
| 39 | F | A | 1.5449 | |
| 40 | H | A | -0.6616 | |
| 41 | E | A | -2.6820 | |
| 42 | H | A | -2.8283 | |
| 43 | A | A | 0.0000 | |
| 44 | E | A | -2.2706 | |
| 45 | V | A | -0.3724 | |
| 46 | V | A | 0.4521 | |
| 47 | F | A | 0.5510 | |
| 48 | T | A | -0.6166 | |
| 49 | A | A | 0.0000 | |
| 50 | N | A | 0.0000 | |
| 51 | D | A | -2.4094 | |
| 52 | S | A | -1.5238 | |
| 53 | G | A | -1.1814 | |
| 54 | P | A | -1.9848 | |
| 55 | R | A | -2.1425 | |
| 56 | R | A | -1.7805 | |
| 57 | Y | A | 0.2613 | |
| 58 | T | A | 0.5728 | |
| 59 | I | A | 0.9366 | |
| 60 | A | A | 0.6716 | |
| 61 | A | A | 0.8391 | |
| 62 | L | A | 1.7223 | |
| 63 | L | A | 1.5232 | |
| 64 | S | A | 1.0956 | |
| 65 | P | A | 1.0363 | |
| 66 | Y | A | 1.9264 | |
| 67 | S | A | 1.2462 | |
| 68 | Y | A | 1.0568 | |
| 69 | S | A | 0.6128 | |
| 70 | T | A | 0.4121 | |
| 71 | T | A | 0.8026 | |
| 72 | A | A | 1.4342 | |
| 73 | V | A | 2.1226 | |
| 74 | V | A | 1.6782 | |
| 75 | T | A | -0.3679 | |
| 76 | N | A | -1.8331 | |
| 77 | P | A | -2.0732 | |
| 78 | K | A | -3.0145 | |
| 79 | E | A | -2.7641 |
Automated mutations analysis - evolutionary conserved mutations
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated based off an evolutionary approach.
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 |
|||
| LM7A | -0.509 | -0.0332 | View | CSV | PDB |
| LM10A | -0.1687 | -0.0247 | 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