| Chain sequence(s) |
A: QVQLQQSGSELKKPGASVKVSCKASGYTFTNYGMNWVKQAPGQGLKWMGWINTYTGEPTYTDDFKGRFAFSLDTSVSTAYLQISSLKADDTAVYFCARGGFGSSYWYFDVWGQGSLVTVSSGGGSGGGGSGGGGSGGGGSDIQLTQSPSSLSASVGDRVSITCKASQDVSIAVAWYQQKPGKAPKLLIYSASYRYTGVPDRFSGSGSGTDFTLTISSLQPEDFAVYYCQQHYITPLTFGAGTKVEIK
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 (00:02:42)
[INFO] Auto_mut: Residue number 105 from chain A and a score of 1.517 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 76 from chain A and a score of 1.162 (valine) selected for
automated muatation (00:02:43)
[INFO] Auto_mut: Residue number 106 from chain A and a score of 1.079 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 232 from chain A and a score of 1.024 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 193 from chain A and a score of 0.965 (tyrosine) selected
for automated muatation (00:02:43)
[INFO] Auto_mut: Residue number 190 from chain A and a score of 0.930 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 171 from chain A and a score of 0.896 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 101 from chain A and a score of 0.890 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 189 from chain A and a score of 0.884 (tyrosine) selected
for automated muatation (00:02:43)
[INFO] Auto_mut: Residue number 104 from chain A and a score of 0.833 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 233 from chain A and a score of 0.729 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 116 from chain A and a score of 0.684 (leucine) selected for
automated muatation (00:02:43)
[INFO] Auto_mut: Residue number 54 from chain A and a score of 0.679 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 11 from chain A and a score of 0.658 (leucine) selected for
automated muatation (00:02:43)
[INFO] Auto_mut: Residue number 100 from chain A and a score of 0.652 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 107 from chain A and a score of 0.620 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 103 from chain A and a score of 0.534 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 102 from chain A and a score of 0.525 omitted from automated
muatation (excluded by the user). (00:02:43)
[INFO] Auto_mut: Residue number 75 from chain A and a score of 0.361 (serine) selected for
automated muatation (00:02:43)
[INFO] Auto_mut: Mutating residue number 76 from chain A (valine) into glutamic acid (00:02:43)
[INFO] Auto_mut: Mutating residue number 76 from chain A (valine) into aspartic acid (00:02:43)
[INFO] Auto_mut: Mutating residue number 193 from chain A (tyrosine) into glutamic acid (00:02:43)
[INFO] Auto_mut: Mutating residue number 76 from chain A (valine) into arginine (00:04:04)
[INFO] Auto_mut: Mutating residue number 193 from chain A (tyrosine) into lysine (00:04:13)
[INFO] Auto_mut: Mutating residue number 76 from chain A (valine) into lysine (00:04:16)
[INFO] Auto_mut: Mutating residue number 193 from chain A (tyrosine) into aspartic acid (00:05:32)
[INFO] Auto_mut: Mutating residue number 189 from chain A (tyrosine) into glutamic acid (00:05:42)
[INFO] Auto_mut: Mutating residue number 189 from chain A (tyrosine) into aspartic acid (00:05:55)
[INFO] Auto_mut: Mutating residue number 193 from chain A (tyrosine) into arginine (00:06:56)
[INFO] Auto_mut: Mutating residue number 189 from chain A (tyrosine) into lysine (00:07:06)
[INFO] Auto_mut: Mutating residue number 189 from chain A (tyrosine) into arginine (00:07:21)
[INFO] Auto_mut: Mutating residue number 116 from chain A (leucine) into glutamic acid (00:08:24)
[INFO] Auto_mut: Mutating residue number 116 from chain A (leucine) into aspartic acid (00:08:36)
[INFO] Auto_mut: Mutating residue number 11 from chain A (leucine) into glutamic acid (00:08:47)
[INFO] Auto_mut: Mutating residue number 116 from chain A (leucine) into lysine (00:09:52)
[INFO] Auto_mut: Mutating residue number 116 from chain A (leucine) into arginine (00:09:59)
[INFO] Auto_mut: Mutating residue number 11 from chain A (leucine) into lysine (00:10:13)
[INFO] Auto_mut: Mutating residue number 11 from chain A (leucine) into aspartic acid (00:11:39)
[INFO] Auto_mut: Mutating residue number 75 from chain A (serine) into glutamic acid (00:11:39)
[INFO] Auto_mut: Mutating residue number 75 from chain A (serine) into aspartic acid (00:11:43)
[INFO] Auto_mut: Mutating residue number 11 from chain A (leucine) into arginine (00:12:59)
[INFO] Auto_mut: Mutating residue number 75 from chain A (serine) into arginine (00:13:05)
[INFO] Auto_mut: Mutating residue number 75 from chain A (serine) into lysine (00:13:05)
[INFO] Auto_mut: Effect of mutation residue number 76 from chain A (valine) into glutamic
acid: Energy difference: 0.3830 kcal/mol, Difference in average score from
the base case: -0.0392 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 76 from chain A (valine) into lysine:
Energy difference: -1.1255 kcal/mol, Difference in average score from the
base case: -0.0353 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 76 from chain A (valine) into aspartic
acid: Energy difference: -0.0068 kcal/mol, Difference in average score from
the base case: -0.0380 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 76 from chain A (valine) into arginine:
Energy difference: -0.7146 kcal/mol, Difference in average score from the
base case: -0.0347 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 193 from chain A (tyrosine) into glutamic
acid: Energy difference: -0.2178 kcal/mol, Difference in average score from
the base case: -0.0387 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 193 from chain A (tyrosine) into lysine:
Energy difference: -0.6801 kcal/mol, Difference in average score from the
base case: -0.0430 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 193 from chain A (tyrosine) into aspartic
acid: Energy difference: -0.4244 kcal/mol, Difference in average score from
the base case: -0.0329 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 193 from chain A (tyrosine) into
arginine: Energy difference: -0.5424 kcal/mol, Difference in average score
from the base case: -0.0454 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 189 from chain A (tyrosine) into glutamic
acid: Energy difference: 1.3901 kcal/mol, Difference in average score from
the base case: -0.0099 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 189 from chain A (tyrosine) into lysine:
Energy difference: 0.3060 kcal/mol, Difference in average score from the
base case: -0.0108 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 189 from chain A (tyrosine) into aspartic
acid: Energy difference: 3.3033 kcal/mol, Difference in average score from
the base case: -0.0041 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 189 from chain A (tyrosine) into
arginine: Energy difference: 0.1039 kcal/mol, Difference in average score
from the base case: -0.0140 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 116 from chain A (leucine) into glutamic
acid: Energy difference: 0.5114 kcal/mol, Difference in average score from
the base case: -0.0221 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 116 from chain A (leucine) into lysine:
Energy difference: 0.3972 kcal/mol, Difference in average score from the
base case: -0.0193 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 116 from chain A (leucine) into aspartic
acid: Energy difference: 1.4372 kcal/mol, Difference in average score from
the base case: -0.0255 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 116 from chain A (leucine) into arginine:
Energy difference: 0.6647 kcal/mol, Difference in average score from the
base case: -0.0412 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into glutamic
acid: Energy difference: 0.4024 kcal/mol, Difference in average score from
the base case: -0.0420 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into lysine:
Energy difference: 0.2455 kcal/mol, Difference in average score from the
base case: -0.0402 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into aspartic
acid: Energy difference: 0.7925 kcal/mol, Difference in average score from
the base case: -0.0428 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 11 from chain A (leucine) into arginine:
Energy difference: 0.3271 kcal/mol, Difference in average score from the
base case: -0.0420 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 75 from chain A (serine) into glutamic
acid: Energy difference: 0.3928 kcal/mol, Difference in average score from
the base case: -0.0240 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 75 from chain A (serine) into lysine:
Energy difference: -0.0051 kcal/mol, Difference in average score from the
base case: -0.0122 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 75 from chain A (serine) into aspartic
acid: Energy difference: 0.2449 kcal/mol, Difference in average score from
the base case: -0.0188 (00:14:40)
[INFO] Auto_mut: Effect of mutation residue number 75 from chain A (serine) into arginine:
Energy difference: -1.2720 kcal/mol, Difference in average score from the
base case: -0.0073 (00:14:40)
[INFO] Main: Simulation completed successfully. (00:14:47)
|
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 | A | -1.3474 | |
| 2 | V | A | -0.7433 | |
| 3 | Q | A | -1.3809 | |
| 4 | L | A | 0.0000 | |
| 5 | Q | A | -1.7869 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -1.0467 | |
| 8 | G | A | -0.8475 | |
| 9 | S | A | -0.0914 | |
| 10 | E | A | -0.3210 | |
| 11 | L | A | 0.6576 | |
| 12 | K | A | -1.1002 | |
| 13 | K | A | -2.1837 | |
| 14 | P | A | -2.0025 | |
| 15 | G | A | -1.4247 | |
| 16 | A | A | -1.1833 | |
| 17 | S | A | -1.2539 | |
| 18 | V | A | 0.0000 | |
| 19 | K | A | -1.9214 | |
| 20 | V | A | 0.0000 | |
| 21 | S | A | -0.8964 | |
| 22 | C | A | 0.0000 | |
| 23 | K | A | -1.2694 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -0.7851 | |
| 26 | G | A | -0.8376 | |
| 27 | Y | A | -0.4360 | |
| 28 | T | A | -0.3781 | |
| 29 | F | A | 0.0000 | |
| 30 | T | A | -0.1241 | |
| 31 | N | A | -0.7163 | |
| 32 | Y | A | 0.2836 | |
| 33 | G | A | 0.0000 | |
| 34 | M | A | 0.0000 | |
| 35 | N | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | K | A | -0.7161 | |
| 39 | Q | A | -0.8480 | |
| 40 | A | A | -1.0859 | |
| 41 | P | A | -1.1093 | |
| 42 | G | A | -1.3233 | |
| 43 | Q | A | -1.8433 | |
| 44 | G | A | -1.1186 | |
| 45 | L | A | 0.0000 | |
| 46 | K | A | -1.5461 | |
| 47 | W | A | 0.0000 | |
| 48 | M | A | 0.0000 | |
| 49 | G | A | 0.0000 | |
| 50 | W | A | -0.1380 | |
| 51 | I | A | 0.0000 | |
| 52 | N | A | -0.4075 | |
| 53 | T | A | 0.0000 | |
| 54 | Y | A | 0.6791 | |
| 55 | T | A | -0.1670 | |
| 56 | G | A | -0.9103 | |
| 57 | E | A | -1.8320 | |
| 58 | P | A | -0.9900 | |
| 59 | T | A | -0.7468 | |
| 60 | Y | A | -0.9725 | |
| 61 | T | A | -1.7942 | |
| 62 | D | A | -3.2295 | |
| 63 | D | A | -3.2012 | |
| 64 | F | A | 0.0000 | |
| 65 | K | A | -3.0525 | |
| 66 | G | A | -1.9622 | |
| 67 | R | A | -1.5059 | |
| 68 | F | A | 0.0000 | |
| 69 | A | A | -0.7656 | |
| 70 | F | A | 0.0000 | |
| 71 | S | A | -0.5074 | |
| 72 | L | A | -0.2143 | |
| 73 | D | A | -0.3926 | |
| 74 | T | A | 0.1035 | |
| 75 | S | A | 0.3613 | |
| 76 | V | A | 1.1616 | |
| 77 | S | A | 0.2088 | |
| 78 | T | A | 0.0000 | |
| 79 | A | A | 0.0000 | |
| 80 | Y | A | -0.5454 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.1455 | |
| 83 | I | A | 0.0000 | |
| 84 | S | A | -1.0017 | |
| 85 | S | A | -1.0889 | |
| 86 | L | A | 0.0000 | |
| 87 | K | A | -2.2505 | |
| 88 | A | A | -1.7738 | |
| 89 | D | A | -2.1695 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.6238 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.3421 | |
| 94 | Y | A | 0.0000 | |
| 95 | F | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | 0.6520 | |
| 101 | F | A | 0.8900 | |
| 102 | G | A | 0.5251 | |
| 103 | S | A | 0.5342 | |
| 104 | S | A | 0.8328 | |
| 105 | Y | A | 1.5172 | |
| 106 | W | A | 1.0786 | |
| 107 | Y | A | 0.6196 | |
| 108 | F | A | 0.0000 | |
| 109 | D | A | -0.1711 | |
| 110 | V | A | -0.3970 | |
| 111 | W | A | 0.0000 | |
| 112 | G | A | 0.0000 | |
| 113 | Q | A | -1.7674 | |
| 114 | G | A | -0.9121 | |
| 115 | S | A | 0.0000 | |
| 116 | L | A | 0.6836 | |
| 117 | V | A | 0.0000 | |
| 118 | T | A | -0.1684 | |
| 119 | V | A | 0.0000 | |
| 120 | S | A | -1.0623 | |
| 121 | S | A | -1.4823 | |
| 122 | G | A | -1.3253 | |
| 123 | G | A | -1.0893 | |
| 124 | G | A | -1.0971 | |
| 125 | S | A | -0.9193 | |
| 126 | G | A | -1.1512 | |
| 127 | G | A | -1.1855 | |
| 128 | G | A | -1.1443 | |
| 129 | G | A | -1.2375 | |
| 130 | S | A | -1.0386 | |
| 131 | G | A | -1.3693 | |
| 132 | G | A | -1.2174 | |
| 133 | G | A | -1.1919 | |
| 134 | G | A | -1.1833 | |
| 135 | S | A | -1.0243 | |
| 136 | G | A | -1.4500 | |
| 137 | G | A | -1.2703 | |
| 138 | G | A | -1.2626 | |
| 139 | G | A | -1.4432 | |
| 140 | S | A | -1.4238 | |
| 141 | D | A | -1.7771 | |
| 142 | I | A | 0.0000 | |
| 143 | Q | A | -1.9080 | |
| 144 | L | A | -1.2599 | |
| 145 | T | A | -0.9527 | |
| 146 | Q | A | -0.6485 | |
| 147 | S | A | -0.5651 | |
| 148 | P | A | -0.4305 | |
| 149 | S | A | -0.4814 | |
| 150 | S | A | -0.7144 | |
| 151 | L | A | -0.6246 | |
| 152 | S | A | -1.0182 | |
| 153 | A | A | 0.0000 | |
| 154 | S | A | -0.8240 | |
| 155 | V | A | -0.0988 | |
| 156 | G | A | -0.9320 | |
| 157 | D | A | -1.7332 | |
| 158 | R | A | -2.3687 | |
| 159 | V | A | 0.0000 | |
| 160 | S | A | -0.7520 | |
| 161 | I | A | 0.0000 | |
| 162 | T | A | -0.7568 | |
| 163 | C | A | 0.0000 | |
| 164 | K | A | -2.3611 | |
| 165 | A | A | 0.0000 | |
| 166 | S | A | -2.0874 | |
| 167 | Q | A | -2.8179 | |
| 168 | D | A | -2.5673 | |
| 169 | V | A | 0.0000 | |
| 170 | S | A | -0.3560 | |
| 171 | I | A | 0.8960 | |
| 172 | A | A | 0.0000 | |
| 173 | V | A | 0.0000 | |
| 174 | A | A | 0.0000 | |
| 175 | W | A | 0.0000 | |
| 176 | Y | A | 0.0000 | |
| 177 | Q | A | 0.0000 | |
| 178 | Q | A | 0.0000 | |
| 179 | K | A | -1.5576 | |
| 180 | P | A | -1.1182 | |
| 181 | G | A | -1.6468 | |
| 182 | K | A | -2.6223 | |
| 183 | A | A | -1.6962 | |
| 184 | P | A | 0.0000 | |
| 185 | K | A | -1.5927 | |
| 186 | L | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | I | A | 0.0000 | |
| 189 | Y | A | 0.8842 | |
| 190 | S | A | 0.9303 | |
| 191 | A | A | 0.0000 | |
| 192 | S | A | 0.3412 | |
| 193 | Y | A | 0.9646 | |
| 194 | R | A | -0.6624 | |
| 195 | Y | A | -0.1135 | |
| 196 | T | A | -0.2526 | |
| 197 | G | A | -0.8206 | |
| 198 | V | A | 0.0000 | |
| 199 | P | A | -1.3082 | |
| 200 | D | A | -2.2527 | |
| 201 | R | A | -1.5080 | |
| 202 | F | A | 0.0000 | |
| 203 | S | A | -0.7112 | |
| 204 | G | A | 0.0000 | |
| 205 | S | A | -0.2763 | |
| 206 | G | A | -0.7152 | |
| 207 | S | A | -0.7760 | |
| 208 | G | A | -1.4626 | |
| 209 | T | A | -2.0005 | |
| 210 | D | A | -2.1872 | |
| 211 | F | A | 0.0000 | |
| 212 | T | A | -0.7204 | |
| 213 | L | A | 0.0000 | |
| 214 | T | A | -0.6298 | |
| 215 | I | A | 0.0000 | |
| 216 | S | A | -1.5663 | |
| 217 | S | A | -1.3862 | |
| 218 | L | A | 0.0000 | |
| 219 | Q | A | -0.7602 | |
| 220 | P | A | -0.8286 | |
| 221 | E | A | -1.4994 | |
| 222 | D | A | 0.0000 | |
| 223 | F | A | -0.4200 | |
| 224 | A | A | 0.0000 | |
| 225 | V | A | -0.1876 | |
| 226 | Y | A | 0.0000 | |
| 227 | Y | A | 0.0000 | |
| 228 | C | A | 0.0000 | |
| 229 | Q | A | 0.0000 | |
| 230 | Q | A | 0.0000 | |
| 231 | H | A | 0.0000 | |
| 232 | Y | A | 1.0235 | |
| 233 | I | A | 0.7291 | |
| 234 | T | A | 0.2495 | |
| 235 | P | A | -0.1948 | |
| 236 | L | A | 0.0000 | |
| 237 | T | A | -0.4433 | |
| 238 | F | A | -0.3083 | |
| 239 | G | A | 0.0000 | |
| 240 | A | A | -0.4102 | |
| 241 | G | A | 0.0000 | |
| 242 | T | A | 0.0000 | |
| 243 | K | A | -0.8099 | |
| 244 | V | A | 0.0000 | |
| 245 | E | A | -1.3004 | |
| 246 | I | A | -0.7608 | |
| 247 | K | A | -1.5462 |
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 |
|||
| VK76A | -1.1255 | -0.0353 | View | CSV | PDB |
| YK193A | -0.6801 | -0.043 | View | CSV | PDB |
| YR193A | -0.5424 | -0.0454 | View | CSV | PDB |
| VR76A | -0.7146 | -0.0347 | View | CSV | PDB |
| SR75A | -1.272 | -0.0073 | View | CSV | PDB |
| SK75A | -0.0051 | -0.0122 | View | CSV | PDB |
| LK11A | 0.2455 | -0.0402 | View | CSV | PDB |
| YR189A | 0.1039 | -0.014 | View | CSV | PDB |
| LR11A | 0.3271 | -0.042 | View | CSV | PDB |
| LR116A | 0.6647 | -0.0412 | View | CSV | PDB |
| LK116A | 0.3972 | -0.0193 | View | CSV | PDB |
| YK189A | 0.306 | -0.0108 | 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