| Chain sequence(s) |
H: QVQLQESGGGLVQAGGSLRLSCAASGYISKYRFMGWYRQAPGKEREFVAGISRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAALLIGAGDSDDLLYYWGQGTQVTVSS
input PDB |
| Selected Chain(s) | H |
| Distance of aggregation | 5 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 H 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 (00:01:27)
[INFO] Auto_mut: Residue number 64 from chain H and a score of 1.970 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 12 from chain H and a score of 1.556 (leucine) selected for
automated muatation (00:01:29)
[INFO] Auto_mut: Residue number 114 from chain H and a score of 1.358 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 28 from chain H and a score of 1.295 (tyrosine) selected for
automated muatation (00:01:29)
[INFO] Auto_mut: Residue number 116 from chain H and a score of 1.141 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 66 from chain H and a score of 1.015 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 52 from chain H and a score of 0.831 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 38 from chain H and a score of 0.523 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 65 from chain H and a score of 0.512 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 67 from chain H and a score of 0.441 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 117 from chain H and a score of 0.412 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 108 from chain H and a score of 0.385 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 107 from chain H and a score of 0.368 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 13 from chain H and a score of 0.358 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 101 from chain H and a score of 0.355 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 118 from chain H and a score of 0.333 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 42 from chain H and a score of 0.329 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 103 from chain H and a score of 0.217 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 88 from chain H and a score of 0.162 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 125 from chain H and a score of 0.159 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 27 from chain H and a score of 0.095 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 63 from chain H and a score of 0.064 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 24 from chain H and a score of 0.033 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 11 from chain H and a score of 0.010 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 4 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 6 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 21 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 23 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 29 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 36 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 39 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 40 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 41 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 43 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 53 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 54 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 55 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 56 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 57 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 71 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 76 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 78 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 86 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 87 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 89 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 91 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 94 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 98 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 100 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 102 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 104 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 105 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 106 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 109 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 115 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 124 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 126 from chain H and a score of 0.000 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 99 from chain H and a score of -0.016 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 22 from chain H and a score of -0.016 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 25 from chain H and a score of -0.025 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 77 from chain H and a score of -0.051 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 19 from chain H and a score of -0.091 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 111 from chain H and a score of -0.107 omitted from
automated muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 45 from chain H and a score of -0.134 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 122 from chain H and a score of -0.161 omitted from
automated muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 79 from chain H and a score of -0.179 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 18 from chain H and a score of -0.197 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Residue number 7 from chain H and a score of -0.198 omitted from automated
muatation (excluded by the user). (00:01:29)
[INFO] Auto_mut: Mutating residue number 12 from chain H (leucine) into glutamic acid (00:01:29)
[INFO] Auto_mut: Mutating residue number 12 from chain H (leucine) into aspartic acid (00:01:29)
[INFO] Auto_mut: Mutating residue number 12 from chain H (leucine) into lysine (00:01:29)
[INFO] Auto_mut: Mutating residue number 12 from chain H (leucine) into arginine (00:02:38)
[INFO] Auto_mut: Mutating residue number 28 from chain H (tyrosine) into glutamic acid (00:02:39)
[INFO] Auto_mut: Mutating residue number 28 from chain H (tyrosine) into lysine (00:02:47)
[INFO] Auto_mut: Mutating residue number 28 from chain H (tyrosine) into aspartic acid (00:03:55)
[INFO] Auto_mut: Mutating residue number 28 from chain H (tyrosine) into arginine (00:03:56)
[INFO] Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into glutamic
acid: Energy difference: 0.1564 kcal/mol, Difference in average score from
the base case: -0.0420 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into lysine:
Energy difference: 0.2516 kcal/mol, Difference in average score from the
base case: -0.0409 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into aspartic
acid: Energy difference: 1.1332 kcal/mol, Difference in average score from
the base case: -0.0423 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into arginine:
Energy difference: 0.2185 kcal/mol, Difference in average score from the
base case: -0.0424 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain H (tyrosine) into glutamic
acid: Energy difference: -0.5936 kcal/mol, Difference in average score from
the base case: -0.0338 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain H (tyrosine) into lysine:
Energy difference: -0.3478 kcal/mol, Difference in average score from the
base case: -0.0278 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain H (tyrosine) into aspartic
acid: Energy difference: -1.1865 kcal/mol, Difference in average score from
the base case: -0.0347 (00:05:20)
[INFO] Auto_mut: Effect of mutation residue number 28 from chain H (tyrosine) into arginine:
Energy difference: -0.2269 kcal/mol, Difference in average score from the
base case: -0.0298 (00:05:20)
[INFO] Main: Simulation completed successfully. (00:05:23)
|
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 | Q | H | -1.1669 | |
| 2 | V | H | -0.2611 | |
| 3 | Q | H | -1.1667 | |
| 4 | L | H | 0.0000 | |
| 5 | Q | H | -1.1983 | |
| 6 | E | H | 0.0000 | |
| 7 | S | H | -0.1980 | |
| 8 | G | H | -0.4769 | |
| 9 | G | H | -0.2991 | |
| 11 | G | H | 0.0102 | |
| 12 | L | H | 1.5555 | |
| 13 | V | H | 0.3584 | |
| 14 | Q | H | -1.1489 | |
| 15 | A | H | -0.2666 | |
| 16 | G | H | -0.5084 | |
| 17 | G | H | -0.2285 | |
| 18 | S | H | -0.1966 | |
| 19 | L | H | -0.0914 | |
| 20 | R | H | -1.7700 | |
| 21 | L | H | 0.0000 | |
| 22 | S | H | -0.0163 | |
| 23 | C | H | 0.0000 | |
| 24 | A | H | 0.0330 | |
| 25 | A | H | -0.0250 | |
| 26 | S | H | -0.2314 | |
| 27 | G | H | 0.0952 | |
| 28 | Y | H | 1.2949 | |
| 29 | I | H | 0.0000 | |
| 30 | S | H | -0.5121 | |
| 35 | K | H | -1.7375 | |
| 36 | Y | H | 0.0000 | |
| 37 | R | H | -0.9893 | |
| 38 | F | H | 0.5227 | |
| 39 | M | H | 0.0000 | |
| 40 | G | H | 0.0000 | |
| 41 | W | H | 0.0000 | |
| 42 | Y | H | 0.3288 | |
| 43 | R | H | 0.0000 | |
| 44 | Q | H | -0.6213 | |
| 45 | A | H | -0.1340 | |
| 46 | P | H | -0.3374 | |
| 47 | G | H | -0.6757 | |
| 48 | K | H | -1.3492 | |
| 49 | E | H | -2.1224 | |
| 50 | R | H | -1.1868 | |
| 51 | E | H | -0.3026 | |
| 52 | F | H | 0.8309 | |
| 53 | V | H | 0.0000 | |
| 54 | A | H | 0.0000 | |
| 55 | G | H | 0.0000 | |
| 56 | I | H | 0.0000 | |
| 57 | S | H | 0.0000 | |
| 58 | R | H | -2.0224 | |
| 59 | G | H | -0.8327 | |
| 63 | S | H | 0.0637 | |
| 64 | I | H | 1.9698 | |
| 65 | T | H | 0.5124 | |
| 66 | Y | H | 1.0148 | |
| 67 | Y | H | 0.4413 | |
| 68 | A | H | -0.2568 | |
| 69 | D | H | -2.0098 | |
| 70 | S | H | -0.5304 | |
| 71 | V | H | 0.0000 | |
| 72 | K | H | -1.9787 | |
| 74 | G | H | -0.8403 | |
| 75 | R | H | -0.4688 | |
| 76 | F | H | 0.0000 | |
| 77 | T | H | -0.0511 | |
| 78 | I | H | 0.0000 | |
| 79 | S | H | -0.1795 | |
| 80 | R | H | -0.3675 | |
| 81 | D | H | -1.0190 | |
| 82 | N | H | -1.4199 | |
| 83 | A | H | -0.4695 | |
| 84 | K | H | -1.7232 | |
| 85 | N | H | -0.6310 | |
| 86 | T | H | 0.0000 | |
| 87 | V | H | 0.0000 | |
| 88 | Y | H | 0.1616 | |
| 89 | L | H | 0.0000 | |
| 90 | Q | H | -0.6440 | |
| 91 | M | H | 0.0000 | |
| 92 | N | H | -0.5703 | |
| 93 | S | H | -0.3479 | |
| 94 | L | H | 0.0000 | |
| 95 | K | H | -1.4014 | |
| 96 | P | H | -0.6874 | |
| 97 | E | H | -1.8410 | |
| 98 | D | H | 0.0000 | |
| 99 | T | H | -0.0161 | |
| 100 | A | H | 0.0000 | |
| 101 | V | H | 0.3549 | |
| 102 | Y | H | 0.0000 | |
| 103 | Y | H | 0.2172 | |
| 104 | C | H | 0.0000 | |
| 105 | A | H | 0.0000 | |
| 106 | A | H | 0.0000 | |
| 107 | L | H | 0.3680 | |
| 108 | L | H | 0.3849 | |
| 109 | I | H | 0.0000 | |
| 110 | G | H | -0.3959 | |
| 111 | A | H | -0.1067 | |
| 111A | G | H | -0.7821 | |
| 112B | D | H | -1.9132 | |
| 112A | S | H | -0.9994 | |
| 112 | D | H | -1.9073 | |
| 113 | D | H | -1.1215 | |
| 114 | L | H | 1.3576 | |
| 115 | L | H | 0.0000 | |
| 116 | Y | H | 1.1413 | |
| 117 | Y | H | 0.4120 | |
| 118 | W | H | 0.3326 | |
| 119 | G | H | -0.2174 | |
| 120 | Q | H | -1.2233 | |
| 121 | G | H | -0.2639 | |
| 122 | T | H | -0.1613 | |
| 123 | Q | H | -0.6924 | |
| 124 | V | H | 0.0000 | |
| 125 | T | H | 0.1585 | |
| 126 | V | H | 0.0000 | |
| 127 | S | H | -0.2642 | |
| 128 | S | H | -0.2299 |
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 |
|||
| YD28H | -1.1865 | -0.0347 | View | CSV | PDB |
| YE28H | -0.5936 | -0.0338 | View | CSV | PDB |
| LE12H | 0.1564 | -0.042 | View | CSV | PDB |
| LR12H | 0.2185 | -0.0424 | 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