| Chain sequence(s) |
A: SPSAPVNVTVRHLKANSAVVSWDVLEDEVVIGFAISQQKKDVRMLRFIQEVNTTTRSCALWDLEEDTEYIVHVQAISIQGQSPASEPVLFKTPR
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 (00:01:07)
[INFO] Auto_mut: Residue number 78 from chain A and a score of 1.588 (isoleucine) selected
for automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 29 from chain A and a score of 1.488 (valine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 47 from chain A and a score of 1.123 (phenylalanine)
selected for automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 30 from chain A and a score of 1.100 (valine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 89 from chain A and a score of 0.935 (leucine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 31 from chain A and a score of 0.837 (isoleucine) selected
for automated muatation (00:01:07)
[INFO] Auto_mut: Mutating residue number 78 from chain A (isoleucine) into glutamic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 78 from chain A (isoleucine) into aspartic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 29 from chain A (valine) into glutamic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 78 from chain A (isoleucine) into arginine (00:01:39)
[INFO] Auto_mut: Mutating residue number 78 from chain A (isoleucine) into lysine (00:01:40)
[INFO] Auto_mut: Mutating residue number 29 from chain A (valine) into lysine (00:01:41)
[INFO] Auto_mut: Mutating residue number 29 from chain A (valine) into aspartic acid (00:02:14)
[INFO] Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into glutamic acid
Mutating residue number 47 from chain A (phenylalanine) into glutamic acid (00:02:16)
[INFO] Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into aspartic acid
Mutating residue number 47 from chain A (phenylalanine) into aspartic acid (00:02:23)
[INFO] Auto_mut: Mutating residue number 29 from chain A (valine) into arginine (00:02:45)
[INFO] Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into lysine (00:02:51)
[INFO] Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into arginine (00:02:56)
[INFO] Auto_mut: Mutating residue number 30 from chain A (valine) into glutamic acid (00:03:21)
[INFO] Auto_mut: Mutating residue number 30 from chain A (valine) into aspartic acid (00:03:31)
[INFO] Auto_mut: Mutating residue number 89 from chain A (leucine) into glutamic acid (00:03:43)
[INFO] Auto_mut: Mutating residue number 30 from chain A (valine) into lysine (00:03:55)
[INFO] Auto_mut: Mutating residue number 30 from chain A (valine) into arginine (00:04:04)
[INFO] Auto_mut: Mutating residue number 89 from chain A (leucine) into lysine (00:04:23)
[INFO] Auto_mut: Mutating residue number 89 from chain A (leucine) into aspartic acid (00:04:28)
[INFO] Auto_mut: Mutating residue number 31 from chain A (isoleucine) into glutamic acid (00:04:36)
[INFO] Auto_mut: Mutating residue number 89 from chain A (leucine) into arginine (00:05:05)
[INFO] Auto_mut: Mutating residue number 31 from chain A (isoleucine) into aspartic acid (00:05:10)
[INFO] Auto_mut: Mutating residue number 31 from chain A (isoleucine) into lysine (00:05:10)
[INFO] Auto_mut: Mutating residue number 31 from chain A (isoleucine) into arginine (00:05:44)
[INFO] Auto_mut: Effect of mutation residue number 78 from chain A (isoleucine) into
glutamic acid: Energy difference: -0.0305 kcal/mol, Difference in average
score from the base case: -0.1018 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 78 from chain A (isoleucine) into lysine:
Energy difference: -0.2377 kcal/mol, Difference in average score from the
base case: -0.1024 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 78 from chain A (isoleucine) into
aspartic acid: Energy difference: 0.1757 kcal/mol, Difference in average
score from the base case: -0.0970 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 78 from chain A (isoleucine) into
arginine: Energy difference: -0.2562 kcal/mol, Difference in average score
from the base case: -0.1099 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 29 from chain A (valine) into glutamic
acid: Energy difference: 0.1502 kcal/mol, Difference in average score from
the base case: -0.1288 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 29 from chain A (valine) into lysine:
Energy difference: -0.2891 kcal/mol, Difference in average score from the
base case: -0.1267 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 29 from chain A (valine) into aspartic
acid: Energy difference: 0.3456 kcal/mol, Difference in average score from
the base case: -0.1257 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 29 from chain A (valine) into arginine:
Energy difference: -0.4161 kcal/mol, Difference in average score from the
base case: -0.1320 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into
glutamic acid: Energy difference: 0.9633 kcal/mol, Difference in average
score from the base case: -0.1105 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into
lysine: Energy difference: 0.4502 kcal/mol, Difference in average score
from the base case: -0.0896 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into
aspartic acid: Energy difference: 1.3660 kcal/mol, Difference in average
score from the base case: -0.0768 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into
arginine: Energy difference: 0.0798 kcal/mol, Difference in average score
from the base case: -0.1103 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 30 from chain A (valine) into glutamic
acid: Energy difference: 1.4003 kcal/mol, Difference in average score from
the base case: -0.0114 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 30 from chain A (valine) into lysine:
Energy difference: 1.8422 kcal/mol, Difference in average score from the
base case: -0.0103 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 30 from chain A (valine) into aspartic
acid: Energy difference: 2.4137 kcal/mol, Difference in average score from
the base case: -0.0174 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 30 from chain A (valine) into arginine:
Energy difference: 2.8104 kcal/mol, Difference in average score from the
base case: -0.0141 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 89 from chain A (leucine) into glutamic
acid: Energy difference: 0.8232 kcal/mol, Difference in average score from
the base case: -0.1271 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 89 from chain A (leucine) into lysine:
Energy difference: 0.5920 kcal/mol, Difference in average score from the
base case: -0.1309 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 89 from chain A (leucine) into aspartic
acid: Energy difference: 0.2679 kcal/mol, Difference in average score from
the base case: -0.1318 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 89 from chain A (leucine) into arginine:
Energy difference: 0.4522 kcal/mol, Difference in average score from the
base case: -0.1301 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into
glutamic acid: Energy difference: 1.7593 kcal/mol, Difference in average
score from the base case: -0.0339 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into lysine:
Energy difference: 0.7139 kcal/mol, Difference in average score from the
base case: -0.0475 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into
aspartic acid: Energy difference: 1.7120 kcal/mol, Difference in average
score from the base case: -0.0357 (00:06:19)
[INFO] Auto_mut: Effect of mutation residue number 31 from chain A (isoleucine) into
arginine: Energy difference: 0.9295 kcal/mol, Difference in average score
from the base case: -0.0545 (00:06:19)
[INFO] Main: Simulation completed successfully. (00:06:23)
|
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 | -0.6552 | |
| 2 | P | A | 0.0000 | |
| 3 | S | A | -0.3158 | |
| 4 | A | A | -0.3898 | |
| 5 | P | A | 0.0000 | |
| 6 | V | A | -0.1056 | |
| 7 | N | A | -1.1172 | |
| 8 | V | A | -0.6966 | |
| 9 | T | A | -0.2048 | |
| 10 | V | A | -0.1920 | |
| 11 | R | A | -1.5641 | |
| 12 | H | A | -1.6708 | |
| 13 | L | A | -1.6163 | |
| 14 | K | A | -3.1753 | |
| 15 | A | A | -3.4904 | |
| 16 | N | A | -3.0005 | |
| 17 | S | A | -1.6123 | |
| 18 | A | A | 0.0000 | |
| 19 | V | A | -0.2745 | |
| 20 | V | A | 0.0000 | |
| 21 | S | A | 0.0000 | |
| 22 | W | A | 0.0000 | |
| 23 | D | A | -0.8127 | |
| 24 | V | A | -0.1916 | |
| 25 | L | A | -0.4933 | |
| 26 | E | A | -2.3131 | |
| 27 | D | A | -2.2899 | |
| 28 | E | A | -0.6920 | |
| 29 | V | A | 1.4877 | |
| 30 | V | A | 1.0996 | |
| 31 | I | A | 0.8367 | |
| 32 | G | A | 0.0000 | |
| 33 | F | A | 0.0000 | |
| 34 | A | A | -0.4575 | |
| 35 | I | A | 0.0000 | |
| 36 | S | A | 0.2268 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | -0.8011 | |
| 39 | K | A | -2.1585 | |
| 40 | K | A | -2.4833 | |
| 41 | D | A | -2.4489 | |
| 42 | V | A | -0.8916 | |
| 43 | R | A | -1.4588 | |
| 44 | M | A | 0.1409 | |
| 45 | L | A | 0.6564 | |
| 46 | R | A | -0.3534 | |
| 47 | F | A | 1.1233 | |
| 48 | I | A | -0.0138 | |
| 49 | Q | A | -0.9988 | |
| 50 | E | A | -1.6017 | |
| 51 | V | A | -0.1647 | |
| 52 | N | A | -0.7942 | |
| 53 | T | A | -0.5739 | |
| 54 | T | A | -0.1855 | |
| 55 | T | A | -0.7748 | |
| 56 | R | A | -1.1812 | |
| 57 | S | A | -0.6107 | |
| 58 | C | A | -0.3864 | |
| 59 | A | A | 0.2609 | |
| 60 | L | A | 0.0000 | |
| 61 | W | A | -0.3174 | |
| 62 | D | A | -2.0793 | |
| 63 | L | A | 0.0000 | |
| 64 | E | A | -4.1396 | |
| 65 | E | A | -4.6105 | |
| 66 | D | A | -3.9520 | |
| 67 | T | A | -3.3776 | |
| 68 | E | A | -2.6030 | |
| 69 | Y | A | 0.0000 | |
| 70 | I | A | -0.0963 | |
| 71 | V | A | 0.0000 | |
| 72 | H | A | -0.2732 | |
| 73 | V | A | 0.0000 | |
| 74 | Q | A | -0.8634 | |
| 75 | A | A | 0.0000 | |
| 76 | I | A | 0.0000 | |
| 77 | S | A | 0.0000 | |
| 78 | I | A | 1.5879 | |
| 79 | Q | A | -0.3875 | |
| 80 | G | A | -0.6316 | |
| 81 | Q | A | -1.3623 | |
| 82 | S | A | 0.0000 | |
| 83 | P | A | -0.8433 | |
| 84 | A | A | -0.7657 | |
| 85 | S | A | 0.0000 | |
| 86 | E | A | -1.7685 | |
| 87 | P | A | -0.5461 | |
| 88 | V | A | 0.3814 | |
| 89 | L | A | 0.9349 | |
| 90 | F | A | -0.2127 | |
| 91 | K | A | -2.6939 | |
| 92 | T | A | 0.0000 | |
| 93 | P | A | -3.1090 | |
| 94 | R | A | -3.4791 |
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 |
|||
| VR29A | -0.4161 | -0.132 | View | CSV | PDB |
| VK29A | -0.2891 | -0.1267 | View | CSV | PDB |
| IR78A | -0.2562 | -0.1099 | View | CSV | PDB |
| IK78A | -0.2377 | -0.1024 | View | CSV | PDB |
| FR47A | 0.0798 | -0.1103 | View | CSV | PDB |
| LD89A | 0.2679 | -0.1318 | View | CSV | PDB |
| LR89A | 0.4522 | -0.1301 | View | CSV | PDB |
| FK47A | 0.4502 | -0.0896 | View | CSV | PDB |
| IK31A | 0.7139 | -0.0475 | View | CSV | PDB |
| IR31A | 0.9295 | -0.0545 | View | CSV | PDB |
| VE30A | 1.4003 | -0.0114 | View | CSV | PDB |
| VD30A | 2.4137 | -0.0174 | 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