| Chain sequence(s) |
A: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
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 (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] FoldX: Starting FoldX energy minimalization (00:00:01)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:01:06)
[INFO] Auto_mut: Residue number 40 from chain A and a score of 4.077 (valine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 39 from chain A and a score of 4.000 (valine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 36 from chain A and a score of 3.784 (valine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 41 from chain A and a score of 3.491 (isoleucine) selected
for automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 38 from chain A and a score of 2.691 (glycine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Residue number 37 from chain A and a score of 2.680 (glycine) selected for
automated muatation (00:01:07)
[INFO] Auto_mut: Mutating residue number 40 from chain A (valine) into glutamic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 40 from chain A (valine) into aspartic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 39 from chain A (valine) into glutamic acid (00:01:07)
[INFO] Auto_mut: Mutating residue number 40 from chain A (valine) into arginine (00:01:42)
[INFO] Auto_mut: Mutating residue number 40 from chain A (valine) into lysine (00:01:43)
[INFO] Auto_mut: Mutating residue number 39 from chain A (valine) into lysine (00:01:44)
[INFO] Auto_mut: Mutating residue number 39 from chain A (valine) into aspartic acid (00:02:21)
[INFO] Auto_mut: Mutating residue number 36 from chain A (valine) into glutamic acid (00:02:23)
[INFO] Auto_mut: Mutating residue number 36 from chain A (valine) into aspartic acid (00:02:28)
[INFO] Auto_mut: Mutating residue number 36 from chain A (valine) into lysine (00:02:55)
[INFO] Auto_mut: Mutating residue number 39 from chain A (valine) into arginine (00:02:57)
[INFO] Auto_mut: Mutating residue number 36 from chain A (valine) into arginine (00:02:58)
[INFO] Auto_mut: Mutating residue number 41 from chain A (isoleucine) into glutamic acid (00:03:30)
[INFO] Auto_mut: Mutating residue number 41 from chain A (isoleucine) into aspartic acid (00:03:45)
[INFO] Auto_mut: Mutating residue number 38 from chain A (glycine) into glutamic acid (00:03:47)
[INFO] Auto_mut: Mutating residue number 41 from chain A (isoleucine) into lysine (00:04:07)
[INFO] Auto_mut: Mutating residue number 41 from chain A (isoleucine) into arginine (00:04:17)
[INFO] Auto_mut: Mutating residue number 38 from chain A (glycine) into lysine (00:04:22)
[INFO] Auto_mut: Mutating residue number 38 from chain A (glycine) into aspartic acid (00:04:49)
[INFO] Auto_mut: Mutating residue number 37 from chain A (glycine) into glutamic acid (00:04:53)
[INFO] Auto_mut: Mutating residue number 37 from chain A (glycine) into aspartic acid (00:05:05)
[INFO] Auto_mut: Mutating residue number 38 from chain A (glycine) into arginine (00:05:25)
[INFO] Auto_mut: Mutating residue number 37 from chain A (glycine) into lysine (00:05:30)
[INFO] Auto_mut: Mutating residue number 37 from chain A (glycine) into arginine (00:05:41)
[INFO] Auto_mut: Effect of mutation residue number 40 from chain A (valine) into glutamic
acid: Energy difference: -0.0614 kcal/mol, Difference in average score from
the base case: -0.2293 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 40 from chain A (valine) into lysine:
Energy difference: -0.5107 kcal/mol, Difference in average score from the
base case: -0.2110 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 40 from chain A (valine) into aspartic
acid: Energy difference: 0.3002 kcal/mol, Difference in average score from
the base case: -0.2420 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 40 from chain A (valine) into arginine:
Energy difference: -0.5125 kcal/mol, Difference in average score from the
base case: -0.2290 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (valine) into glutamic
acid: Energy difference: -0.3614 kcal/mol, Difference in average score from
the base case: -0.2874 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (valine) into lysine:
Energy difference: -0.8140 kcal/mol, Difference in average score from the
base case: -0.3364 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (valine) into aspartic
acid: Energy difference: 0.0461 kcal/mol, Difference in average score from
the base case: -0.2697 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 39 from chain A (valine) into arginine:
Energy difference: -0.4931 kcal/mol, Difference in average score from the
base case: -0.3065 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (valine) into glutamic
acid: Energy difference: -0.1934 kcal/mol, Difference in average score from
the base case: -0.3132 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (valine) into lysine:
Energy difference: -0.5770 kcal/mol, Difference in average score from the
base case: -0.3293 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (valine) into aspartic
acid: Energy difference: 0.6220 kcal/mol, Difference in average score from
the base case: -0.2959 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 36 from chain A (valine) into arginine:
Energy difference: -0.3088 kcal/mol, Difference in average score from the
base case: -0.3356 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 41 from chain A (isoleucine) into
glutamic acid: Energy difference: -0.2903 kcal/mol, Difference in average
score from the base case: -0.2255 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 41 from chain A (isoleucine) into lysine:
Energy difference: -1.2488 kcal/mol, Difference in average score from the
base case: -0.1990 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 41 from chain A (isoleucine) into
aspartic acid: Energy difference: -0.3668 kcal/mol, Difference in average
score from the base case: -0.2337 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 41 from chain A (isoleucine) into
arginine: Energy difference: -1.5394 kcal/mol, Difference in average score
from the base case: -0.1919 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (glycine) into glutamic
acid: Energy difference: 0.1377 kcal/mol, Difference in average score from
the base case: -0.0951 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (glycine) into lysine:
Energy difference: 0.1278 kcal/mol, Difference in average score from the
base case: -0.0860 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (glycine) into aspartic
acid: Energy difference: 0.1145 kcal/mol, Difference in average score from
the base case: -0.0888 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 38 from chain A (glycine) into arginine:
Energy difference: -0.1850 kcal/mol, Difference in average score from the
base case: -0.0990 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 37 from chain A (glycine) into glutamic
acid: Energy difference: -0.7024 kcal/mol, Difference in average score from
the base case: -0.1015 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 37 from chain A (glycine) into lysine:
Energy difference: -1.1573 kcal/mol, Difference in average score from the
base case: -0.0993 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 37 from chain A (glycine) into aspartic
acid: Energy difference: -0.4770 kcal/mol, Difference in average score from
the base case: -0.0886 (00:06:20)
[INFO] Auto_mut: Effect of mutation residue number 37 from chain A (glycine) into arginine:
Energy difference: -1.0713 kcal/mol, Difference in average score from the
base case: -0.0847 (00:06:20)
[INFO] Main: Simulation completed successfully. (00:06:24)
|
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 | D | A | -2.2949 | |
| 2 | A | A | -1.7139 | |
| 3 | E | A | -2.4638 | |
| 4 | F | A | -1.0030 | |
| 5 | R | A | -2.8663 | |
| 6 | H | A | -3.1119 | |
| 7 | D | A | -2.8255 | |
| 8 | S | A | -1.7206 | |
| 9 | G | A | -1.4577 | |
| 10 | Y | A | -1.2905 | |
| 11 | E | A | -2.4403 | |
| 12 | V | A | -0.7243 | |
| 13 | H | A | -0.7609 | |
| 14 | H | A | -1.3262 | |
| 15 | Q | A | -0.5180 | |
| 16 | K | A | 0.0461 | |
| 17 | L | A | 1.8027 | |
| 18 | V | A | 2.0240 | |
| 19 | F | A | 2.0307 | |
| 20 | F | A | 2.0490 | |
| 21 | A | A | 0.7435 | |
| 22 | E | A | -1.0774 | |
| 23 | D | A | -1.2418 | |
| 24 | V | A | -0.9012 | |
| 25 | G | A | -1.6193 | |
| 26 | S | A | -2.0251 | |
| 27 | N | A | -2.4739 | |
| 28 | K | A | -2.0342 | |
| 29 | G | A | -1.2115 | |
| 30 | A | A | -0.4081 | |
| 31 | I | A | 0.3574 | |
| 32 | I | A | 1.1593 | |
| 33 | G | A | 1.3614 | |
| 34 | L | A | 2.6191 | |
| 35 | M | A | 2.6730 | |
| 36 | V | A | 3.7842 | |
| 37 | G | A | 2.6801 | |
| 38 | G | A | 2.6910 | |
| 39 | V | A | 3.9997 | |
| 40 | V | A | 4.0765 | |
| 41 | I | A | 3.4914 | |
| 42 | A | A | 1.7603 |
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 |
|||
| VK39A | -0.814 | -0.3364 | View | CSV | PDB |
| IR41A | -1.5394 | -0.1919 | View | CSV | PDB |
| VK36A | -0.577 | -0.3293 | View | CSV | PDB |
| IK41A | -1.2488 | -0.199 | View | CSV | PDB |
| VR39A | -0.4931 | -0.3065 | View | CSV | PDB |
| VR36A | -0.3088 | -0.3356 | View | CSV | PDB |
| VR40A | -0.5125 | -0.229 | View | CSV | PDB |
| VK40A | -0.5107 | -0.211 | View | CSV | PDB |
| GK37A | -1.1573 | -0.0993 | View | CSV | PDB |
| GR37A | -1.0713 | -0.0847 | View | CSV | PDB |
| GR38A | -0.185 | -0.099 | View | CSV | PDB |
| GD38A | 0.1145 | -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