| Chain sequence(s) |
A: STKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQNFHLRPRDLISNINVIVLELKGFMCEYADETATIVEFLNRWITFCQSIISTLT
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] (00:00:01)
[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 (00:00:14)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:14)
[INFO] FoldX: Starting FoldX energy minimalization (00:00:15)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:02:06)
[CRITICAL] pyMol: Pymol encountered an error: /bin/sh: pymol: command not found Movie
creation failed. (00:02:06)
[INFO] Auto_mut: Residue number 103 from chain A and a score of 2.017 (phenylalanine)
selected for automated muatation (00:02:13)
[INFO] Auto_mut: Residue number 104 from chain A and a score of 1.477 (methionine) selected
for automated muatation (00:02:13)
[INFO] Auto_mut: Residue number 91 from chain A and a score of 0.985 (valine) selected for
automated muatation (00:02:13)
[INFO] Auto_mut: Residue number 19 from chain A and a score of 0.862 (leucine) selected for
automated muatation (00:02:13)
[INFO] Auto_mut: Residue number 72 from chain A and a score of 0.575 (leucine) selected for
automated muatation (00:02:13)
[INFO] Auto_mut: Residue number 94 from chain A and a score of 0.404 (leucine) selected for
automated muatation (00:02:13)
[INFO] Auto_mut: Mutating residue number 104 from chain A (methionine) into glutamic acid (00:02:13)
[INFO] Auto_mut: Mutating residue number 103 from chain A (phenylalanine) into aspartic acid
Mutating residue number 103 from chain A (phenylalanine) into aspartic acid (00:02:13)
[INFO] Auto_mut: Mutating residue number 103 from chain A (phenylalanine) into glutamic acid
Mutating residue number 103 from chain A (phenylalanine) into glutamic acid (00:02:13)
[INFO] Auto_mut: Mutating residue number 104 from chain A (methionine) into lysine (00:03:41)
[INFO] Auto_mut: Mutating residue number 103 from chain A (phenylalanine) into arginine (00:03:58)
[INFO] Auto_mut: Mutating residue number 103 from chain A (phenylalanine) into lysine (00:04:08)
[INFO] Auto_mut: Mutating residue number 104 from chain A (methionine) into aspartic acid (00:05:10)
[INFO] Auto_mut: Mutating residue number 91 from chain A (valine) into glutamic acid (00:05:32)
[INFO] Auto_mut: Mutating residue number 91 from chain A (valine) into aspartic acid (00:05:37)
[INFO] Auto_mut: Mutating residue number 104 from chain A (methionine) into arginine (00:06:39)
[INFO] Auto_mut: Mutating residue number 91 from chain A (valine) into arginine (00:06:58)
[INFO] Auto_mut: Mutating residue number 91 from chain A (valine) into lysine (00:07:01)
[INFO] Auto_mut: Mutating residue number 19 from chain A (leucine) into glutamic acid (00:08:04)
[INFO] Auto_mut: Mutating residue number 19 from chain A (leucine) into aspartic acid (00:08:08)
[INFO] Auto_mut: Mutating residue number 72 from chain A (leucine) into glutamic acid (00:08:20)
[INFO] Auto_mut: Mutating residue number 72 from chain A (leucine) into lysine (00:09:19)
[INFO] Auto_mut: Mutating residue number 19 from chain A (leucine) into arginine (00:09:28)
[INFO] Auto_mut: Mutating residue number 19 from chain A (leucine) into lysine (00:09:33)
[INFO] Auto_mut: Mutating residue number 72 from chain A (leucine) into aspartic acid (00:10:51)
[INFO] Auto_mut: Mutating residue number 94 from chain A (leucine) into glutamic acid (00:10:53)
[INFO] Auto_mut: Mutating residue number 94 from chain A (leucine) into aspartic acid (00:11:27)
[INFO] Auto_mut: Mutating residue number 94 from chain A (leucine) into lysine (00:12:17)
[INFO] Auto_mut: Mutating residue number 72 from chain A (leucine) into arginine (00:12:17)
[INFO] Auto_mut: Mutating residue number 94 from chain A (leucine) into arginine (00:12:46)
[INFO] Auto_mut: Effect of mutation residue number 103 from chain A (phenylalanine) into
glutamic acid: Energy difference: 1.9543 kcal/mol, Difference in average
score from the base case: -0.0843 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 103 from chain A (phenylalanine) into
lysine: Energy difference: 2.0537 kcal/mol, Difference in average score
from the base case: -0.0708 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 103 from chain A (phenylalanine) into
aspartic acid: Energy difference: 2.3168 kcal/mol, Difference in average
score from the base case: -0.0705 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 103 from chain A (phenylalanine) into
arginine: Energy difference: 1.8756 kcal/mol, Difference in average score
from the base case: -0.0769 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 104 from chain A (methionine) into
glutamic acid: Energy difference: -0.4543 kcal/mol, Difference in average
score from the base case: -0.0671 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 104 from chain A (methionine) into
lysine: Energy difference: -0.1353 kcal/mol, Difference in average score
from the base case: -0.0636 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 104 from chain A (methionine) into
aspartic acid: Energy difference: -0.0515 kcal/mol, Difference in average
score from the base case: -0.0671 (00:14:11)
[INFO] Auto_mut: Effect of mutation residue number 104 from chain A (methionine) into
arginine: Energy difference: -0.0864 kcal/mol, Difference in average score
from the base case: -0.0676 (00:14:14)
[INFO] Auto_mut: Effect of mutation residue number 91 from chain A (valine) into glutamic
acid: Energy difference: 0.1158 kcal/mol, Difference in average score from
the base case: -0.0823 (00:14:14)
[INFO] Auto_mut: Effect of mutation residue number 91 from chain A (valine) into lysine:
Energy difference: -0.6340 kcal/mol, Difference in average score from the
base case: -0.0724 (00:14:14)
[INFO] Auto_mut: Effect of mutation residue number 91 from chain A (valine) into aspartic
acid: Energy difference: 0.4708 kcal/mol, Difference in average score from
the base case: -0.0853 (00:14:14)
[INFO] Auto_mut: Effect of mutation residue number 91 from chain A (valine) into arginine:
Energy difference: -0.8309 kcal/mol, Difference in average score from the
base case: -0.0714 (00:14:15)
[INFO] Auto_mut: Effect of mutation residue number 19 from chain A (leucine) into glutamic
acid: Energy difference: 0.6869 kcal/mol, Difference in average score from
the base case: -0.1012 (00:14:17)
[INFO] Auto_mut: Effect of mutation residue number 19 from chain A (leucine) into lysine:
Energy difference: 0.3628 kcal/mol, Difference in average score from the
base case: -0.0766 (00:14:17)
[INFO] Auto_mut: Effect of mutation residue number 19 from chain A (leucine) into aspartic
acid: Energy difference: 1.2198 kcal/mol, Difference in average score from
the base case: -0.1073 (00:14:17)
[INFO] Auto_mut: Effect of mutation residue number 19 from chain A (leucine) into arginine:
Energy difference: 0.5323 kcal/mol, Difference in average score from the
base case: -0.0933 (00:14:17)
[INFO] Auto_mut: Effect of mutation residue number 72 from chain A (leucine) into glutamic
acid: Energy difference: 0.7162 kcal/mol, Difference in average score from
the base case: -0.0803 (00:14:19)
[INFO] Auto_mut: Effect of mutation residue number 72 from chain A (leucine) into lysine:
Energy difference: 0.1238 kcal/mol, Difference in average score from the
base case: -0.0625 (00:14:19)
[INFO] Auto_mut: Effect of mutation residue number 72 from chain A (leucine) into aspartic
acid: Energy difference: 1.1793 kcal/mol, Difference in average score from
the base case: -0.0791 (00:14:21)
[INFO] Auto_mut: Effect of mutation residue number 72 from chain A (leucine) into arginine:
Energy difference: 0.5213 kcal/mol, Difference in average score from the
base case: -0.0638 (00:14:21)
[INFO] Auto_mut: Effect of mutation residue number 94 from chain A (leucine) into glutamic
acid: Energy difference: 0.9640 kcal/mol, Difference in average score from
the base case: -0.0856 (00:14:21)
[INFO] Auto_mut: Effect of mutation residue number 94 from chain A (leucine) into lysine:
Energy difference: 0.1514 kcal/mol, Difference in average score from the
base case: -0.0837 (00:14:21)
[INFO] Auto_mut: Effect of mutation residue number 94 from chain A (leucine) into aspartic
acid: Energy difference: 1.4879 kcal/mol, Difference in average score from
the base case: -0.0871 (00:14:21)
[INFO] Auto_mut: Effect of mutation residue number 94 from chain A (leucine) into arginine:
Energy difference: 0.3494 kcal/mol, Difference in average score from the
base case: -0.0962 (00:14:21)
[INFO] Main: Simulation completed successfully. (00:21:04)
|
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 | |
| 6 | S | A | -1.4156 | |
| 7 | T | A | -1.4083 | |
| 8 | K | A | -2.4525 | |
| 9 | K | A | -2.5886 | |
| 10 | T | A | -1.6288 | |
| 11 | Q | A | -1.4473 | |
| 12 | L | A | -0.9776 | |
| 13 | Q | A | -1.2410 | |
| 14 | L | A | 0.0000 | |
| 15 | E | A | -1.2001 | |
| 16 | H | A | -0.8041 | |
| 17 | L | A | 0.0000 | |
| 18 | L | A | 0.0000 | |
| 19 | L | A | 0.8620 | |
| 20 | D | A | 0.0683 | |
| 21 | L | A | 0.0000 | |
| 22 | Q | A | -0.3151 | |
| 23 | M | A | -0.1676 | |
| 24 | I | A | 0.0000 | |
| 25 | L | A | -1.1434 | |
| 26 | N | A | -1.9144 | |
| 27 | G | A | -1.7347 | |
| 28 | I | A | 0.0000 | |
| 29 | N | A | -2.5745 | |
| 30 | N | A | -2.8490 | |
| 31 | Y | A | -2.6425 | |
| 32 | K | A | -2.9657 | |
| 33 | N | A | -2.9334 | |
| 34 | P | A | -2.0194 | |
| 35 | K | A | -2.0911 | |
| 36 | L | A | -1.9142 | |
| 37 | T | A | -1.4898 | |
| 38 | R | A | -1.9778 | |
| 39 | M | A | 0.0000 | |
| 40 | L | A | -0.2918 | |
| 41 | T | A | -0.4901 | |
| 42 | F | A | -0.5070 | |
| 43 | K | A | -1.3819 | |
| 44 | F | A | 0.0000 | |
| 45 | Y | A | -0.5328 | |
| 46 | M | A | 0.0000 | |
| 47 | P | A | 0.0000 | |
| 48 | K | A | -2.7602 | |
| 49 | K | A | -2.7104 | |
| 50 | A | A | -1.8478 | |
| 51 | T | A | -1.1130 | |
| 52 | E | A | -1.5744 | |
| 53 | L | A | -1.1226 | |
| 54 | K | A | -0.7888 | |
| 55 | H | A | -1.2292 | |
| 56 | L | A | 0.0000 | |
| 57 | Q | A | -0.5414 | |
| 58 | C | A | 0.0000 | |
| 59 | L | A | 0.0000 | |
| 60 | E | A | -1.1629 | |
| 61 | E | A | -1.8461 | |
| 62 | E | A | -1.3543 | |
| 63 | L | A | 0.0000 | |
| 64 | K | A | -2.8279 | |
| 65 | P | A | -1.8409 | |
| 66 | L | A | 0.0000 | |
| 67 | E | A | -2.2787 | |
| 68 | E | A | -1.9922 | |
| 69 | V | A | 0.0000 | |
| 70 | L | A | 0.0000 | |
| 71 | N | A | -1.2556 | |
| 72 | L | A | 0.5748 | |
| 73 | A | A | 0.0000 | |
| 74 | Q | A | -1.3298 | |
| 77 | N | A | -1.8767 | |
| 78 | F | A | -1.4830 | |
| 79 | H | A | -1.2472 | |
| 80 | L | A | -1.2330 | |
| 81 | R | A | -2.8814 | |
| 82 | P | A | -2.4301 | |
| 83 | R | A | -3.2494 | |
| 84 | D | A | -2.1654 | |
| 85 | L | A | 0.0000 | |
| 86 | I | A | 0.0000 | |
| 87 | S | A | -1.1359 | |
| 88 | N | A | -0.8381 | |
| 89 | I | A | 0.0000 | |
| 90 | N | A | -0.2098 | |
| 91 | V | A | 0.9848 | |
| 92 | I | A | 0.0000 | |
| 93 | V | A | 0.0000 | |
| 94 | L | A | 0.4036 | |
| 95 | E | A | -1.0569 | |
| 96 | L | A | -0.6680 | |
| 97 | K | A | -1.2761 | |
| 98 | G | A | -1.0230 | |
| 103 | F | A | 2.0169 | |
| 104 | M | A | 1.4766 | |
| 105 | C | A | -0.5038 | |
| 106 | E | A | -1.8899 | |
| 107 | Y | A | -1.5670 | |
| 108 | A | A | -2.1964 | |
| 109 | D | A | -2.8300 | |
| 110 | E | A | -2.8056 | |
| 111 | T | A | -1.6065 | |
| 112 | A | A | -1.2183 | |
| 113 | T | A | -0.5654 | |
| 114 | I | A | 0.0000 | |
| 115 | V | A | -0.8440 | |
| 116 | E | A | -1.7720 | |
| 117 | F | A | 0.0000 | |
| 118 | L | A | 0.0000 | |
| 119 | N | A | -1.7589 | |
| 120 | R | A | -1.5896 | |
| 121 | W | A | 0.0000 | |
| 122 | I | A | 0.0000 | |
| 123 | T | A | -0.9891 | |
| 124 | F | A | 0.0000 | |
| 125 | C | A | 0.0000 | |
| 126 | Q | A | -1.3929 | |
| 127 | S | A | -0.7893 | |
| 128 | I | A | 0.0000 | |
| 129 | I | A | -0.6131 | |
| 130 | S | A | -0.4097 | |
| 131 | T | A | -0.1495 | |
| 132 | L | A | -0.0345 | |
| 133 | T | A | -0.2343 |
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 |
|||
| VR91A | -0.8309 | -0.0714 | View | CSV | PDB |
| VK91A | -0.634 | -0.0724 | View | CSV | PDB |
| ME104A | -0.4543 | -0.0671 | View | CSV | PDB |
| MK104A | -0.1353 | -0.0636 | View | CSV | PDB |
| LK94A | 0.1514 | -0.0837 | View | CSV | PDB |
| LK72A | 0.1238 | -0.0625 | View | CSV | PDB |
| LR94A | 0.3494 | -0.0962 | View | CSV | PDB |
| LK19A | 0.3628 | -0.0766 | View | CSV | PDB |
| LR19A | 0.5323 | -0.0933 | View | CSV | PDB |
| LR72A | 0.5213 | -0.0638 | View | CSV | PDB |
| FE103A | 1.9543 | -0.0843 | View | CSV | PDB |
| FR103A | 1.8756 | -0.0769 | 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