| Chain sequence(s) |
B: KRKLSKDEQENYKKVLESKKDVEKALEEAGGKDVSKLTPYWQIVKEEVEMALKYFEEKLK
input PDB |
| Selected Chain(s) | B |
| 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 B 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 (00:01:50)
[INFO] AutoMut: Residue number 40 from chain B and a score of 1.648 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 43 from chain B and a score of 1.082 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 39 from chain B and a score of 0.586 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 41 from chain B and a score of 0.414 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 38 from chain B and a score of 0.134 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 42 from chain B and a score of 0.037 (glutamine) selected
for automated mutation (00:01:50)
[INFO] AutoMut: Residue number 15 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Residue number 48 from chain B and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:01:50)
[INFO] AutoMut: Mutating residue number 42 from chain B (glutamine) into glutamic acid (00:01:50)
[INFO] AutoMut: Mutating residue number 42 from chain B (glutamine) into lysine (00:01:51)
[INFO] AutoMut: Mutating residue number 42 from chain B (glutamine) into aspartic acid (00:01:51)
[INFO] AutoMut: Mutating residue number 42 from chain B (glutamine) into arginine (00:01:59)
[INFO] AutoMut: Effect of mutation residue number 42 from chain B (glutamine) into glutamic
acid: Energy difference: 0.3800 kcal/mol, Difference in average score from
the base case: -0.0666 (00:02:08)
[INFO] AutoMut: Effect of mutation residue number 42 from chain B (glutamine) into lysine:
Energy difference: -1.4120 kcal/mol, Difference in average score from the
base case: -0.0103 (00:02:08)
[INFO] AutoMut: Effect of mutation residue number 42 from chain B (glutamine) into aspartic
acid: Energy difference: 0.9570 kcal/mol, Difference in average score from
the base case: -0.0559 (00:02:08)
[INFO] AutoMut: Effect of mutation residue number 42 from chain B (glutamine) into
arginine: Energy difference: -1.0570 kcal/mol, Difference in average score
from the base case: -0.0414 (00:02:08)
[INFO] Main: Simulation completed successfully. (00:02:09)
|
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 | K | B | -3.9502 | |
| 2 | R | B | -4.3029 | |
| 3 | K | B | -3.4696 | |
| 4 | L | B | 0.0000 | |
| 5 | S | B | -2.8363 | |
| 6 | K | B | -3.6922 | |
| 7 | D | B | -4.0385 | |
| 8 | E | B | -3.6978 | |
| 9 | Q | B | -4.0827 | |
| 10 | E | B | -4.2148 | |
| 11 | N | B | -3.6214 | |
| 12 | Y | B | -2.7404 | |
| 13 | K | B | -3.8323 | |
| 14 | K | B | -3.8591 | |
| 15 | V | B | 0.0000 | |
| 16 | L | B | -2.5926 | |
| 17 | E | B | -3.9377 | |
| 18 | S | B | -3.5867 | |
| 19 | K | B | -3.9757 | |
| 20 | K | B | -4.2692 | |
| 21 | D | B | -4.1101 | |
| 22 | V | B | 0.0000 | |
| 23 | E | B | -4.2166 | |
| 24 | K | B | -4.5546 | |
| 25 | A | B | 0.0000 | |
| 26 | L | B | 0.0000 | |
| 27 | E | B | -4.5167 | |
| 28 | E | B | -3.8586 | |
| 29 | A | B | -3.1433 | |
| 30 | G | B | -2.6687 | |
| 31 | G | B | -3.2486 | |
| 32 | K | B | -3.8069 | |
| 33 | D | B | -3.2701 | |
| 34 | V | B | -1.7018 | |
| 35 | S | B | -1.6911 | |
| 36 | K | B | -2.8151 | |
| 37 | L | B | 0.0000 | |
| 38 | T | B | 0.1335 | |
| 39 | P | B | 0.5861 | |
| 40 | Y | B | 1.6483 | |
| 41 | W | B | 0.4143 | |
| 42 | Q | B | 0.0373 | |
| 43 | I | B | 1.0816 | |
| 44 | V | B | -0.5492 | |
| 45 | K | B | -1.9309 | |
| 46 | E | B | -2.6629 | |
| 47 | E | B | -2.8834 | |
| 48 | V | B | 0.0000 | |
| 49 | E | B | -2.9267 | |
| 50 | M | B | -1.7215 | |
| 51 | A | B | -1.3332 | |
| 52 | L | B | -1.7049 | |
| 53 | K | B | -1.8211 | |
| 54 | Y | B | -0.3474 | |
| 55 | F | B | -1.5536 | |
| 56 | E | B | -3.1633 | |
| 57 | E | B | -3.5564 | |
| 58 | K | B | -3.1302 | |
| 59 | L | B | -3.6398 | |
| 60 | K | B | -3.8141 |
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 |
|||
| QR42B | -1.057 | -0.0414 | View | CSV | PDB |
| QK42B | -1.412 | -0.0103 | 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