| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVKLVESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSSISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
B: AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALPDPPAASALP input PDB |
| Selected Chain(s) | A,B |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:06)
[INFO] FoldX: Starting FoldX energy minimization (00:00:06)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:16)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/568ee3fe22b58f1/tmp/folded.pdb (00:10:16)
[INFO] Main: Simulation completed successfully. (00:16:53)
|
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 | E | A | -1.5966 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7063 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6466 | |
| 6 | Q | A | -0.6842 | |
| 7 | S | A | -0.7382 | |
| 8 | P | A | -0.3073 | |
| 9 | A | A | -0.3005 | |
| 10 | T | A | -0.3855 | |
| 11 | L | A | -0.1836 | |
| 12 | S | A | -0.6341 | |
| 13 | L | A | -1.0905 | |
| 14 | S | A | -1.7582 | |
| 15 | P | A | -2.0472 | |
| 16 | G | A | -1.7750 | |
| 17 | E | A | -2.3843 | |
| 18 | R | A | -2.5837 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6678 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.9906 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.5246 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.2593 | |
| 27 | Q | A | -2.3261 | |
| 28 | N | A | -2.4847 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.2602 | |
| 31 | S | A | -0.9266 | |
| 32 | N | A | -0.9289 | |
| 33 | L | A | 0.0000 | |
| 34 | A | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | -0.7608 | |
| 39 | K | A | -1.1857 | |
| 40 | P | A | -0.7491 | |
| 41 | G | A | -1.1729 | |
| 42 | Q | A | -1.6371 | |
| 43 | A | A | -1.2290 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.5125 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | D | A | -1.0503 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.2289 | |
| 53 | N | A | -1.7084 | |
| 54 | R | A | -1.7278 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.7154 | |
| 57 | G | A | -0.8369 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.4813 | |
| 60 | A | A | -0.4036 | |
| 61 | R | A | -0.7506 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6901 | |
| 64 | G | A | 0.0000 | |
| 65 | S | A | -0.8420 | |
| 66 | G | A | -1.1123 | |
| 67 | S | A | -1.3415 | |
| 68 | G | A | -1.6676 | |
| 69 | T | A | -2.1351 | |
| 70 | D | A | -2.4559 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8284 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.5987 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3867 | |
| 77 | S | A | -1.7520 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.0498 | |
| 80 | P | A | -2.1995 | |
| 81 | E | A | -2.4751 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.7070 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.1547 | |
| 86 | Y | A | 0.0000 | |
| 87 | Y | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | R | A | 0.0000 | |
| 92 | R | A | -1.2053 | |
| 93 | N | A | -1.3565 | |
| 94 | W | A | -0.9522 | |
| 95 | P | A | -0.9090 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | -0.1685 | |
| 98 | F | A | 0.1848 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7497 | |
| 101 | G | A | -0.6933 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.7001 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.0468 | |
| 106 | I | A | -1.7622 | |
| 107 | K | A | -2.1292 | |
| 108 | G | A | -1.6712 | |
| 109 | G | A | -1.8063 | |
| 110 | G | A | -1.3282 | |
| 111 | G | A | -1.2562 | |
| 112 | S | A | -1.3390 | |
| 113 | G | A | -1.4532 | |
| 114 | G | A | -1.6040 | |
| 115 | G | A | -1.5168 | |
| 116 | G | A | -1.4948 | |
| 117 | S | A | -1.0487 | |
| 118 | G | A | -1.4860 | |
| 119 | G | A | -1.5328 | |
| 120 | G | A | -1.5431 | |
| 121 | G | A | -1.5582 | |
| 122 | S | A | -1.6958 | |
| 123 | E | A | -2.7016 | |
| 124 | V | A | -1.6065 | |
| 125 | K | A | -2.0880 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.1288 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.3986 | |
| 130 | G | A | -0.8187 | |
| 131 | G | A | 0.0363 | |
| 132 | G | A | 0.5582 | |
| 133 | L | A | 1.3014 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.5001 | |
| 136 | P | A | -1.8199 | |
| 137 | G | A | -1.5307 | |
| 138 | G | A | -1.0393 | |
| 139 | S | A | -1.3475 | |
| 140 | L | A | -1.0726 | |
| 141 | R | A | -2.1917 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.5391 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.4077 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -1.0993 | |
| 148 | G | A | -1.3438 | |
| 149 | F | A | -0.9208 | |
| 150 | T | A | -0.6606 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.5887 | |
| 153 | R | A | -2.0970 | |
| 154 | Y | A | -1.0677 | |
| 155 | A | A | 0.0000 | |
| 156 | M | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | R | A | 0.0000 | |
| 161 | Q | A | -0.6219 | |
| 162 | A | A | -1.0369 | |
| 163 | P | A | -0.8352 | |
| 164 | G | A | -1.4449 | |
| 165 | K | A | -2.2640 | |
| 166 | G | A | -1.3665 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9465 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | S | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.7815 | |
| 177 | G | A | -0.3951 | |
| 178 | A | A | -0.1138 | |
| 179 | T | A | 0.0000 | |
| 180 | T | A | 0.0928 | |
| 181 | Y | A | -0.1040 | |
| 182 | Y | A | -0.7327 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.5072 | |
| 185 | P | A | -1.8638 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.6153 | |
| 188 | G | A | -1.7495 | |
| 189 | R | A | -1.5332 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8480 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4204 | |
| 194 | R | A | -0.9887 | |
| 195 | D | A | -1.6240 | |
| 196 | N | A | -1.8914 | |
| 197 | S | A | -1.6012 | |
| 198 | K | A | -2.3877 | |
| 199 | N | A | -1.7496 | |
| 200 | T | A | -1.0952 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.5885 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.4086 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.4421 | |
| 207 | S | A | -1.3139 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.8903 | |
| 210 | A | A | -2.0209 | |
| 211 | E | A | -2.4466 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.5288 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.7223 | |
| 216 | Y | A | 0.0000 | |
| 217 | Y | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | K | A | 0.0000 | |
| 221 | D | A | 0.0000 | |
| 222 | Q | A | 0.0000 | |
| 223 | D | A | -1.7043 | |
| 224 | F | A | -1.4292 | |
| 225 | D | A | -1.5448 | |
| 226 | I | A | 0.5577 | |
| 227 | L | A | 0.0000 | |
| 228 | T | A | -0.4623 | |
| 229 | G | A | 0.0000 | |
| 230 | Y | A | 0.0000 | |
| 231 | L | A | 0.0000 | |
| 232 | N | A | 0.0000 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -1.0221 | |
| 236 | P | A | -1.3184 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.3855 | |
| 240 | G | A | 0.0000 | |
| 241 | T | A | 0.4163 | |
| 242 | L | A | 1.4693 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.1886 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.8165 | |
| 247 | S | A | -0.7732 | |
| 1 | A | B | -0.4010 | |
| 2 | Q | B | -1.3001 | |
| 3 | E | B | -2.1125 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.8459 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9674 | |
| 8 | P | B | -0.8993 | |
| 9 | H | B | -0.8016 | |
| 10 | C | B | -0.4998 | |
| 11 | T | B | -0.4872 | |
| 12 | T | B | 0.0630 | |
| 13 | V | B | -0.1206 | |
| 14 | P | B | -0.9651 | |
| 15 | V | B | -0.5548 | |
| 16 | G | B | -0.8606 | |
| 17 | A | B | -0.5713 | |
| 18 | S | B | -0.9935 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.4038 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -1.1131 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.8212 | |
| 25 | T | B | -1.7342 | |
| 26 | S | B | -1.6291 | |
| 27 | G | B | -1.2319 | |
| 28 | G | B | -1.3802 | |
| 29 | L | B | -1.6748 | |
| 30 | R | B | -2.4256 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1819 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.4959 | |
| 36 | Q | B | -0.6800 | |
| 37 | L | B | -0.1536 | |
| 38 | G | B | -0.9571 | |
| 39 | P | B | -1.0705 | |
| 40 | Q | B | -1.5889 | |
| 41 | P | B | -1.2055 | |
| 42 | Q | B | -1.3367 | |
| 43 | D | B | -1.1135 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.1514 | |
| 47 | Y | B | -0.4403 | |
| 48 | E | B | -1.4222 | |
| 49 | D | B | -2.3235 | |
| 50 | G | B | -1.4590 | |
| 51 | V | B | 0.0000 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.3149 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -2.4043 | |
| 58 | R | B | -2.2200 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | 0.0000 | |
| 61 | G | B | -1.4340 | |
| 62 | R | B | -1.5376 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.8257 | |
| 67 | G | B | -1.2532 | |
| 68 | S | B | -1.6013 | |
| 69 | Q | B | -1.9548 | |
| 70 | D | B | -2.2367 | |
| 71 | N | B | -2.2672 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0536 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6777 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.4324 | |
| 78 | R | B | -2.0776 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.8479 | |
| 81 | L | B | 0.3461 | |
| 82 | S | B | -0.0475 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2322 | |
| 85 | G | B | 0.2064 | |
| 86 | T | B | 0.1592 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.1458 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.3955 | |
| 93 | T | B | -1.0694 | |
| 94 | E | B | -1.4321 | |
| 95 | V | B | 0.5032 | |
| 96 | N | B | -0.3798 | |
| 97 | V | B | 0.0008 | |
| 98 | Y | B | 0.4274 | |
| 99 | G | B | -0.3816 | |
| 100 | S | B | -0.3734 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.5160 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.7165 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.1293 | |
| 108 | E | B | -2.6681 | |
| 109 | E | B | -3.3476 | |
| 110 | Q | B | -2.6946 | |
| 111 | S | B | -2.1857 | |
| 112 | Q | B | -1.9979 | |
| 113 | G | B | -1.8247 | |
| 114 | W | B | -1.5317 | |
| 115 | H | B | -1.9137 | |
| 116 | R | B | -2.5346 | |
| 117 | C | B | -1.4937 | |
| 118 | S | B | -1.8036 | |
| 119 | D | B | -2.3049 | |
| 120 | A | B | -1.4312 | |
| 121 | P | B | -1.4572 | |
| 122 | P | B | -1.6350 | |
| 123 | R | B | -2.0524 | |
| 124 | A | B | -0.7693 | |
| 125 | S | B | -0.3987 | |
| 126 | A | B | 0.3846 | |
| 127 | L | B | 1.3718 | |
| 128 | P | B | 0.3859 | |
| 129 | A | B | 0.1789 | |
| 130 | P | B | -0.2459 | |
| 131 | P | B | -0.6266 | |
| 132 | T | B | -0.5365 | |
| 133 | G | B | -0.4453 | |
| 134 | S | B | -0.0704 | |
| 135 | A | B | 0.1791 | |
| 136 | L | B | 0.7887 | |
| 137 | P | B | -0.6652 | |
| 138 | D | B | -1.9701 | |
| 139 | P | B | -1.5243 | |
| 140 | Q | B | -1.9297 | |
| 141 | T | B | -1.0291 | |
| 142 | A | B | -0.2103 | |
| 143 | S | B | 0.0329 | |
| 144 | A | B | 0.3524 | |
| 145 | L | B | 0.9036 | |
| 146 | P | B | -0.4992 | |
| 147 | D | B | -1.6900 | |
| 148 | P | B | -1.0524 | |
| 149 | P | B | -0.8808 | |
| 150 | A | B | -0.4473 | |
| 151 | A | B | 0.1216 | |
| 152 | S | B | 0.2174 | |
| 153 | A | B | 0.6664 | |
| 154 | L | B | 1.4033 | |
| 155 | P | B | 0.4796 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -0.4098 | 3.8938 | View | CSV | PDB |
| 4.5 | -0.4572 | 3.8938 | View | CSV | PDB |
| 5.0 | -0.5138 | 3.8938 | View | CSV | PDB |
| 5.5 | -0.5716 | 3.8938 | View | CSV | PDB |
| 6.0 | -0.623 | 3.8938 | View | CSV | PDB |
| 6.5 | -0.6621 | 3.8938 | View | CSV | PDB |
| 7.0 | -0.6878 | 3.8938 | View | CSV | PDB |
| 7.5 | -0.7035 | 3.8938 | View | CSV | PDB |
| 8.0 | -0.7124 | 3.8938 | View | CSV | PDB |
| 8.5 | -0.7147 | 3.8938 | View | CSV | PDB |
| 9.0 | -0.7094 | 3.8938 | 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