| Chain sequence(s) |
A: QVQLVESGGGLVQPGGSLRLSCAASGGSEYSYSTFSLGWFRQAPGQGLEAVAAIASMGGLTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAAVRGYFMRLPSSHNFRYWGQGTLVTVS
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:29)
[INFO] AutoMut: Residue number 123 from chain A and a score of 1.621 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 11 from chain A and a score of 1.363 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 57 from chain A and a score of 1.063 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 105 from chain A and a score of 0.953 (tyrosine) selected
for automated mutation (00:04:32)
[INFO] AutoMut: Residue number 60 from chain A and a score of 0.878 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 10 from chain A and a score of 0.853 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 96 from chain A and a score of 0.795 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 5 from chain A and a score of 0.682 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 107 from chain A and a score of 0.671 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 122 from chain A and a score of 0.525 (threonine) selected
for automated mutation (00:04:32)
[INFO] AutoMut: Residue number 125 from chain A and a score of 0.370 (threonine) selected
for automated mutation (00:04:32)
[INFO] AutoMut: Residue number 58 from chain A and a score of 0.334 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 59 from chain A and a score of 0.313 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 98 from chain A and a score of 0.310 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 61 from chain A and a score of 0.286 (threonine) selected
for automated mutation (00:04:32)
[INFO] AutoMut: Residue number 9 from chain A and a score of 0.064 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 121 from chain A and a score of 0.016 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 4 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 6 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 20 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 22 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 35 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 36 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 37 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 38 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 39 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 40 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 41 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 51 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 52 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 53 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 54 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 55 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 56 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 67 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 71 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 73 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 81 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 82 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 83 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 84 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 86 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 89 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 93 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 95 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 97 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 99 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 100 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 101 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 106 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 110 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 115 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 117 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 124 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 126 from chain A and a score of 0.000 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 12 from chain A and a score of -0.046 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Residue number 34 from chain A and a score of -0.147 omitted from automated
mutation (excluded by the user). (00:04:32)
[INFO] AutoMut: Mutating residue number 105 from chain A (tyrosine) into glutamic acid (00:04:32)
[INFO] AutoMut: Mutating residue number 105 from chain A (tyrosine) into aspartic acid (00:04:32)
[INFO] AutoMut: Mutating residue number 122 from chain A (threonine) into glutamic acid (00:04:32)
[INFO] AutoMut: Mutating residue number 122 from chain A (threonine) into lysine (00:04:59)
[INFO] AutoMut: Mutating residue number 105 from chain A (tyrosine) into lysine (00:05:03)
[INFO] AutoMut: Mutating residue number 105 from chain A (tyrosine) into arginine (00:05:11)
[INFO] AutoMut: Mutating residue number 122 from chain A (threonine) into aspartic acid (00:05:26)
[INFO] AutoMut: Mutating residue number 125 from chain A (threonine) into glutamic acid (00:05:40)
[INFO] AutoMut: Mutating residue number 122 from chain A (threonine) into arginine (00:05:54)
[INFO] AutoMut: Mutating residue number 125 from chain A (threonine) into aspartic acid (00:06:13)
[INFO] AutoMut: Mutating residue number 125 from chain A (threonine) into lysine (00:06:21)
[INFO] AutoMut: Mutating residue number 61 from chain A (threonine) into glutamic acid (00:06:23)
[INFO] AutoMut: Mutating residue number 125 from chain A (threonine) into arginine (00:06:43)
[INFO] AutoMut: Mutating residue number 61 from chain A (threonine) into lysine (00:07:16)
[INFO] AutoMut: Mutating residue number 61 from chain A (threonine) into aspartic acid (00:08:23)
[INFO] AutoMut: Mutating residue number 61 from chain A (threonine) into arginine (00:09:14)
[INFO] AutoMut: Effect of mutation residue number 105 from chain A (tyrosine) into glutamic
acid: Energy difference: 1.2267 kcal/mol, Difference in average score from
the base case: -0.0606 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 105 from chain A (tyrosine) into lysine:
Energy difference: 0.7862 kcal/mol, Difference in average score from the
base case: -0.0654 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 105 from chain A (tyrosine) into aspartic
acid: Energy difference: 1.0635 kcal/mol, Difference in average score from
the base case: -0.0732 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 105 from chain A (tyrosine) into
arginine: Energy difference: 1.1159 kcal/mol, Difference in average score
from the base case: -0.0721 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 122 from chain A (threonine) into
glutamic acid: Energy difference: 1.5264 kcal/mol, Difference in average
score from the base case: -0.0181 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 122 from chain A (threonine) into lysine:
Energy difference: 0.7501 kcal/mol, Difference in average score from the
base case: -0.0219 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 122 from chain A (threonine) into
aspartic acid: Energy difference: 1.0949 kcal/mol, Difference in average
score from the base case: -0.0103 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 122 from chain A (threonine) into
arginine: Energy difference: 0.9137 kcal/mol, Difference in average score
from the base case: -0.0358 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 125 from chain A (threonine) into
glutamic acid: Energy difference: -0.3467 kcal/mol, Difference in average
score from the base case: -0.0512 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 125 from chain A (threonine) into lysine:
Energy difference: -1.1476 kcal/mol, Difference in average score from the
base case: -0.0226 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 125 from chain A (threonine) into
aspartic acid: Energy difference: 0.2195 kcal/mol, Difference in average
score from the base case: -0.0224 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 125 from chain A (threonine) into
arginine: Energy difference: -1.0998 kcal/mol, Difference in average score
from the base case: -0.0321 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 61 from chain A (threonine) into glutamic
acid: Energy difference: -0.0921 kcal/mol, Difference in average score from
the base case: -0.0291 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 61 from chain A (threonine) into lysine:
Energy difference: -0.3333 kcal/mol, Difference in average score from the
base case: -0.0344 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 61 from chain A (threonine) into aspartic
acid: Energy difference: 0.9637 kcal/mol, Difference in average score from
the base case: -0.0414 (00:10:36)
[INFO] AutoMut: Effect of mutation residue number 61 from chain A (threonine) into
arginine: Energy difference: 0.2235 kcal/mol, Difference in average score
from the base case: -0.0346 (00:10:36)
[INFO] Main: Simulation completed successfully. (00:10:52)
|
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 | Q | A | -1.5509 | |
| 2 | V | A | -1.3151 | |
| 3 | Q | A | -1.3700 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.6817 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.3384 | |
| 8 | G | A | -0.7355 | |
| 9 | G | A | 0.0637 | |
| 10 | G | A | 0.8532 | |
| 11 | L | A | 1.3626 | |
| 12 | V | A | -0.0461 | |
| 13 | Q | A | -1.2938 | |
| 14 | P | A | -1.6163 | |
| 15 | G | A | -1.4049 | |
| 16 | G | A | -1.1086 | |
| 17 | S | A | -1.3363 | |
| 18 | L | A | -1.1632 | |
| 19 | R | A | -2.3599 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.6255 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -0.3122 | |
| 24 | A | A | -0.5603 | |
| 25 | S | A | -1.0336 | |
| 26 | G | A | -1.4112 | |
| 27 | G | A | -1.3441 | |
| 28 | S | A | -1.2529 | |
| 29 | E | A | -1.7761 | |
| 30 | Y | A | -0.8986 | |
| 31 | S | A | -0.7556 | |
| 32 | Y | A | -1.0925 | |
| 33 | S | A | -0.6025 | |
| 34 | T | A | -0.1473 | |
| 35 | F | A | 0.0000 | |
| 36 | S | A | 0.0000 | |
| 37 | L | A | 0.0000 | |
| 38 | G | A | 0.0000 | |
| 39 | W | A | 0.0000 | |
| 40 | F | A | 0.0000 | |
| 41 | R | A | 0.0000 | |
| 42 | Q | A | -0.7684 | |
| 43 | A | A | -1.0534 | |
| 44 | P | A | -1.1205 | |
| 45 | G | A | -1.3585 | |
| 46 | Q | A | -1.8422 | |
| 47 | G | A | -1.2170 | |
| 48 | L | A | -0.3346 | |
| 49 | E | A | -0.9751 | |
| 50 | A | A | -0.4663 | |
| 51 | V | A | 0.0000 | |
| 52 | A | A | 0.0000 | |
| 53 | A | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | A | A | 0.0000 | |
| 56 | S | A | 0.0000 | |
| 57 | M | A | 1.0633 | |
| 58 | G | A | 0.3341 | |
| 59 | G | A | 0.3134 | |
| 60 | L | A | 0.8778 | |
| 61 | T | A | 0.2856 | |
| 62 | Y | A | -0.2454 | |
| 63 | Y | A | -1.0164 | |
| 64 | A | A | -1.3783 | |
| 65 | D | A | -2.3548 | |
| 66 | S | A | -1.8397 | |
| 67 | V | A | 0.0000 | |
| 68 | K | A | -2.5215 | |
| 69 | G | A | -1.7288 | |
| 70 | R | A | -1.4050 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -1.0139 | |
| 73 | I | A | 0.0000 | |
| 74 | S | A | -0.6492 | |
| 75 | R | A | -1.2981 | |
| 76 | D | A | -1.9306 | |
| 77 | N | A | -2.1689 | |
| 78 | S | A | -1.8441 | |
| 79 | K | A | -2.5929 | |
| 80 | N | A | -2.0200 | |
| 81 | T | A | 0.0000 | |
| 82 | L | A | 0.0000 | |
| 83 | Y | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | Q | A | -1.7566 | |
| 86 | M | A | 0.0000 | |
| 87 | N | A | -1.4644 | |
| 88 | S | A | -1.1722 | |
| 89 | L | A | 0.0000 | |
| 90 | R | A | -2.3135 | |
| 91 | A | A | -1.7308 | |
| 92 | E | A | -2.2803 | |
| 93 | D | A | 0.0000 | |
| 94 | T | A | -0.4502 | |
| 95 | A | A | 0.0000 | |
| 96 | V | A | 0.7949 | |
| 97 | Y | A | 0.0000 | |
| 98 | Y | A | 0.3102 | |
| 99 | C | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | A | A | 0.0000 | |
| 102 | V | A | -1.2383 | |
| 103 | R | A | -1.9150 | |
| 104 | G | A | -0.6120 | |
| 105 | Y | A | 0.9529 | |
| 106 | F | A | 0.0000 | |
| 107 | M | A | 0.6713 | |
| 108 | R | A | -0.8652 | |
| 109 | L | A | -0.5289 | |
| 110 | P | A | 0.0000 | |
| 111 | S | A | -0.8768 | |
| 112 | S | A | -1.0196 | |
| 113 | H | A | -1.7074 | |
| 114 | N | A | -1.6108 | |
| 115 | F | A | 0.0000 | |
| 116 | R | A | -2.3281 | |
| 117 | Y | A | 0.0000 | |
| 118 | W | A | -0.3187 | |
| 119 | G | A | -0.2497 | |
| 120 | Q | A | -0.9414 | |
| 121 | G | A | 0.0157 | |
| 122 | T | A | 0.5248 | |
| 123 | L | A | 1.6205 | |
| 124 | V | A | 0.0000 | |
| 125 | T | A | 0.3702 | |
| 126 | V | A | 0.0000 | |
| 127 | S | A | -0.5764 |
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 |
|||
| TR125A | -1.0998 | -0.0321 | View | CSV | PDB |
| TE125A | -0.3467 | -0.0512 | View | CSV | PDB |
| TK61A | -0.3333 | -0.0344 | View | CSV | PDB |
| TE61A | -0.0921 | -0.0291 | View | CSV | PDB |
| YK105A | 0.7862 | -0.0654 | View | CSV | PDB |
| YD105A | 1.0635 | -0.0732 | View | CSV | PDB |
| TR122A | 0.9137 | -0.0358 | View | CSV | PDB |
| TK122A | 0.7501 | -0.0219 | 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