| Chain sequence(s) |
A: PVTLEQSPKELTAKEGEKVELNCVLRDSSCPLPSASTYWLRQKPGATKKESLSNGGRFVLTTNKTSKSSTLTITSAKPEDTATYICKAYPGGYCDGIYYYEGGGTKLTVKA
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] (00:00:00)
[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 minimization (00:00:00)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:01:29)
[INFO] AutoMut: Residue number 98 from chain A and a score of 2.219 omitted from automated
mutation (excluded by the user). (00:01:30)
[INFO] AutoMut: Residue number 99 from chain A and a score of 1.608 omitted from automated
mutation (excluded by the user). (00:01:30)
[INFO] AutoMut: Residue number 97 from chain A and a score of 1.456 omitted from automated
mutation (excluded by the user). (00:01:30)
[INFO] AutoMut: Residue number 93 from chain A and a score of 1.374 (tyrosine) selected for
automated mutation (00:01:30)
[INFO] AutoMut: Residue number 89 from chain A and a score of 1.010 (tyrosine) selected for
automated mutation (00:01:30)
[INFO] AutoMut: Residue number 38 from chain A and a score of 0.554 omitted from automated
mutation (excluded by the user). (00:01:30)
[INFO] AutoMut: Residue number 92 from chain A and a score of 0.398 omitted from automated
mutation (excluded by the user). (00:01:30)
[INFO] AutoMut: Residue number 59 from chain A and a score of 0.305 (valine) selected for
automated mutation (00:01:30)
[INFO] AutoMut: Residue number 60 from chain A and a score of 0.209 (leucine) selected for
automated mutation (00:01:30)
[INFO] AutoMut: Residue number 91 from chain A and a score of 0.045 (glycine) selected for
automated mutation (00:01:30)
[INFO] AutoMut: Residue number 37 from chain A and a score of 0.042 (threonine) selected
for automated mutation (00:01:30)
[INFO] AutoMut: Mutating residue number 93 from chain A (tyrosine) into glutamic acid (00:01:30)
[INFO] AutoMut: Mutating residue number 93 from chain A (tyrosine) into aspartic acid (00:01:30)
[INFO] AutoMut: Mutating residue number 89 from chain A (tyrosine) into glutamic acid (00:01:30)
[INFO] AutoMut: Mutating residue number 93 from chain A (tyrosine) into arginine (00:01:34)
[INFO] AutoMut: Mutating residue number 93 from chain A (tyrosine) into lysine (00:01:34)
[INFO] AutoMut: Mutating residue number 89 from chain A (tyrosine) into lysine (00:01:37)
[INFO] AutoMut: Mutating residue number 89 from chain A (tyrosine) into aspartic acid (00:01:40)
[INFO] AutoMut: Mutating residue number 59 from chain A (valine) into glutamic acid (00:01:42)
[INFO] AutoMut: Mutating residue number 89 from chain A (tyrosine) into arginine (00:01:46)
[INFO] AutoMut: Mutating residue number 59 from chain A (valine) into lysine (00:01:50)
[INFO] AutoMut: Mutating residue number 59 from chain A (valine) into aspartic acid (00:01:56)
[INFO] AutoMut: Mutating residue number 60 from chain A (leucine) into glutamic acid (00:01:59)
[INFO] AutoMut: Mutating residue number 59 from chain A (valine) into arginine (00:02:01)
[INFO] AutoMut: Mutating residue number 60 from chain A (leucine) into aspartic acid (00:02:05)
[INFO] AutoMut: Mutating residue number 60 from chain A (leucine) into lysine (00:02:09)
[INFO] AutoMut: Mutating residue number 60 from chain A (leucine) into arginine (00:02:09)
[INFO] AutoMut: Mutating residue number 91 from chain A (glycine) into glutamic acid (00:02:15)
[INFO] AutoMut: Mutating residue number 91 from chain A (glycine) into aspartic acid (00:02:17)
[INFO] AutoMut: Mutating residue number 37 from chain A (threonine) into glutamic acid (00:02:25)
[INFO] AutoMut: Mutating residue number 91 from chain A (glycine) into lysine (00:02:30)
[INFO] AutoMut: Mutating residue number 91 from chain A (glycine) into arginine (00:02:32)
[INFO] AutoMut: Mutating residue number 37 from chain A (threonine) into lysine (00:02:34)
[INFO] AutoMut: Mutating residue number 37 from chain A (threonine) into aspartic acid (00:02:42)
[INFO] AutoMut: Mutating residue number 37 from chain A (threonine) into arginine (00:02:52)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (tyrosine) into glutamic
acid: Energy difference: 0.1570 kcal/mol, Difference in average score from
the base case: -0.0915 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (tyrosine) into lysine:
Energy difference: 0.1462 kcal/mol, Difference in average score from the
base case: -0.0873 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (tyrosine) into aspartic
acid: Energy difference: -0.0941 kcal/mol, Difference in average score from
the base case: -0.0901 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 93 from chain A (tyrosine) into arginine:
Energy difference: 0.3035 kcal/mol, Difference in average score from the
base case: -0.0910 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 89 from chain A (tyrosine) into glutamic
acid: Energy difference: 1.4056 kcal/mol, Difference in average score from
the base case: -0.0289 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 89 from chain A (tyrosine) into lysine:
Energy difference: 0.5923 kcal/mol, Difference in average score from the
base case: -0.0387 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 89 from chain A (tyrosine) into aspartic
acid: Energy difference: 1.8484 kcal/mol, Difference in average score from
the base case: -0.0217 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 89 from chain A (tyrosine) into arginine:
Energy difference: 1.1713 kcal/mol, Difference in average score from the
base case: -0.0433 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (valine) into glutamic
acid: Energy difference: 0.3474 kcal/mol, Difference in average score from
the base case: -0.1129 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (valine) into lysine:
Energy difference: -0.1823 kcal/mol, Difference in average score from the
base case: -0.0670 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (valine) into aspartic
acid: Energy difference: 0.4740 kcal/mol, Difference in average score from
the base case: -0.0903 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 59 from chain A (valine) into arginine:
Energy difference: -0.3731 kcal/mol, Difference in average score from the
base case: -0.0787 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 60 from chain A (leucine) into glutamic
acid: Energy difference: 2.5705 kcal/mol, Difference in average score from
the base case: -0.0255 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 60 from chain A (leucine) into lysine:
Energy difference: 2.5919 kcal/mol, Difference in average score from the
base case: -0.0279 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 60 from chain A (leucine) into aspartic
acid: Energy difference: 3.1027 kcal/mol, Difference in average score from
the base case: -0.0254 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 60 from chain A (leucine) into arginine:
Energy difference: 2.5879 kcal/mol, Difference in average score from the
base case: -0.0260 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 91 from chain A (glycine) into glutamic
acid: Energy difference: -0.7777 kcal/mol, Difference in average score from
the base case: -0.0386 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 91 from chain A (glycine) into lysine:
Energy difference: -1.1726 kcal/mol, Difference in average score from the
base case: -0.0318 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 91 from chain A (glycine) into aspartic
acid: Energy difference: -1.0214 kcal/mol, Difference in average score from
the base case: -0.0385 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 91 from chain A (glycine) into arginine:
Energy difference: -1.2120 kcal/mol, Difference in average score from the
base case: -0.0392 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 37 from chain A (threonine) into glutamic
acid: Energy difference: 3.5450 kcal/mol, Difference in average score from
the base case: -0.0036 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 37 from chain A (threonine) into lysine:
Energy difference: 0.3589 kcal/mol, Difference in average score from the
base case: -0.0036 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 37 from chain A (threonine) into aspartic
acid: Energy difference: 3.2311 kcal/mol, Difference in average score from
the base case: -0.0104 (00:03:29)
[INFO] AutoMut: Effect of mutation residue number 37 from chain A (threonine) into
arginine: Energy difference: 5.8488 kcal/mol, Difference in average score
from the base case: -0.0087 (00:03:29)
[INFO] Main: Simulation completed successfully. (00:03:33)
|
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 | P | A | -0.8890 | |
| 2 | V | A | -1.1516 | |
| 3 | T | A | -1.2735 | |
| 4 | L | A | 0.0000 | |
| 5 | E | A | -2.1039 | |
| 6 | Q | A | -1.6083 | |
| 7 | S | A | -1.9860 | |
| 8 | P | A | -2.3233 | |
| 9 | K | A | -3.3509 | |
| 10 | E | A | -3.1974 | |
| 11 | L | A | -1.5620 | |
| 12 | T | A | -1.1515 | |
| 13 | A | A | 0.0000 | |
| 14 | K | A | -3.6966 | |
| 15 | E | A | -3.8470 | |
| 16 | G | A | -2.9466 | |
| 17 | E | A | -3.8297 | |
| 18 | K | A | -3.4587 | |
| 19 | V | A | 0.0000 | |
| 20 | E | A | -2.3308 | |
| 21 | L | A | 0.0000 | |
| 22 | N | A | -1.3077 | |
| 23 | C | A | 0.0000 | |
| 24 | V | A | -0.8993 | |
| 25 | L | A | 0.0000 | |
| 26 | R | A | -2.3296 | |
| 27 | D | A | -1.5290 | |
| 28 | S | A | -0.9807 | |
| 29 | S | A | -0.8903 | |
| 30 | C | A | 0.0000 | |
| 31 | P | A | -0.8648 | |
| 32 | L | A | 0.0000 | |
| 33 | P | A | -0.8991 | |
| 34 | S | A | -0.9154 | |
| 35 | A | A | -0.1924 | |
| 36 | S | A | 0.0000 | |
| 37 | T | A | 0.0421 | |
| 38 | Y | A | 0.5540 | |
| 39 | W | A | 0.0000 | |
| 40 | L | A | -1.0751 | |
| 41 | R | A | -1.7699 | |
| 42 | Q | A | -2.2516 | |
| 43 | K | A | -2.0744 | |
| 44 | P | A | -1.0278 | |
| 45 | G | A | -0.9992 | |
| 46 | A | A | -1.5109 | |
| 47 | T | A | -1.5475 | |
| 48 | K | A | -2.8563 | |
| 49 | K | A | -2.8777 | |
| 50 | E | A | -2.5278 | |
| 51 | S | A | -1.1344 | |
| 52 | L | A | -0.4759 | |
| 53 | S | A | -0.6898 | |
| 54 | N | A | -1.2372 | |
| 55 | G | A | -1.1185 | |
| 56 | G | A | -0.9670 | |
| 57 | R | A | -0.9447 | |
| 58 | F | A | -0.1538 | |
| 59 | V | A | 0.3050 | |
| 60 | L | A | 0.2090 | |
| 61 | T | A | -0.2289 | |
| 62 | T | A | -0.8946 | |
| 63 | N | A | -1.8404 | |
| 64 | K | A | -2.3536 | |
| 65 | T | A | -1.3546 | |
| 66 | S | A | -1.2084 | |
| 67 | K | A | -1.6184 | |
| 68 | S | A | -1.2269 | |
| 69 | S | A | 0.0000 | |
| 70 | T | A | -0.4324 | |
| 71 | L | A | 0.0000 | |
| 72 | T | A | -0.9036 | |
| 73 | I | A | 0.0000 | |
| 74 | T | A | -1.4323 | |
| 75 | S | A | -2.1282 | |
| 76 | A | A | 0.0000 | |
| 77 | K | A | -2.8844 | |
| 78 | P | A | -2.4007 | |
| 79 | E | A | -2.4988 | |
| 80 | D | A | 0.0000 | |
| 81 | T | A | -1.5214 | |
| 82 | A | A | 0.0000 | |
| 83 | T | A | -1.7330 | |
| 84 | Y | A | 0.0000 | |
| 85 | I | A | 0.0000 | |
| 86 | C | A | 0.0000 | |
| 87 | K | A | -0.3694 | |
| 88 | A | A | 0.0000 | |
| 89 | Y | A | 1.0103 | |
| 90 | P | A | 0.0000 | |
| 91 | G | A | 0.0450 | |
| 92 | G | A | 0.3981 | |
| 93 | Y | A | 1.3738 | |
| 94 | C | A | 0.0000 | |
| 95 | D | A | -1.2838 | |
| 96 | G | A | -0.1524 | |
| 97 | I | A | 1.4560 | |
| 98 | Y | A | 2.2193 | |
| 99 | Y | A | 1.6079 | |
| 100 | Y | A | 0.0000 | |
| 101 | E | A | -1.4782 | |
| 102 | G | A | -1.6272 | |
| 103 | G | A | -1.7141 | |
| 104 | G | A | -1.9337 | |
| 105 | T | A | 0.0000 | |
| 106 | K | A | -3.0245 | |
| 107 | L | A | 0.0000 | |
| 108 | T | A | -1.7367 | |
| 109 | V | A | 0.0000 | |
| 110 | K | A | -3.1383 | |
| 111 | A | A | -1.8430 |
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 |
|||
| VR59A | -0.3731 | -0.0787 | View | CSV | PDB |
| GR91A | -1.212 | -0.0392 | View | CSV | PDB |
| GD91A | -1.0214 | -0.0385 | View | CSV | PDB |
| YD93A | -0.0941 | -0.0901 | View | CSV | PDB |
| VK59A | -0.1823 | -0.067 | View | CSV | PDB |
| YK93A | 0.1462 | -0.0873 | View | CSV | PDB |
| YK89A | 0.5923 | -0.0387 | View | CSV | PDB |
| YR89A | 1.1713 | -0.0433 | View | CSV | PDB |
| LK60A | 2.5919 | -0.0279 | View | CSV | PDB |
| LR60A | 2.5879 | -0.026 | View | CSV | PDB |
| TK37A | 0.3589 | -0.0036 | View | CSV | PDB |
| TD37A | 3.2311 | -0.0104 | 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