| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGKTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:32)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/887dec2b360bfd0/tmp/folded.pdb (00:03:32)
[INFO] Main: Simulation completed successfully. (00:05:30)
|
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 | D | A | -1.3242 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7600 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2572 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | 0.0483 | |
| 8 | P | A | 0.4864 | |
| 9 | L | A | 1.2666 | |
| 10 | S | A | 0.1552 | |
| 11 | L | A | -0.2432 | |
| 12 | S | A | -1.1282 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6574 | |
| 15 | P | A | -1.7836 | |
| 16 | G | A | -1.6928 | |
| 17 | Q | A | -1.9096 | |
| 18 | P | A | -1.9959 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.9009 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.9406 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2217 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9956 | |
| 27 | Q | A | -1.5605 | |
| 28 | S | A | -0.9282 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.1133 | |
| 31 | H | A | -0.4544 | |
| 32 | S | A | -0.6561 | |
| 33 | N | A | -1.0052 | |
| 34 | G | A | -0.9237 | |
| 35 | K | A | -1.0353 | |
| 36 | T | A | -0.4099 | |
| 37 | Y | A | 0.0000 | |
| 38 | L | A | 0.0000 | |
| 39 | E | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -0.9319 | |
| 44 | K | A | -1.6902 | |
| 45 | P | A | -1.1258 | |
| 46 | G | A | -1.5537 | |
| 47 | Q | A | -2.1623 | |
| 48 | S | A | -1.3011 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -1.0876 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.0000 | |
| 55 | K | A | -0.3259 | |
| 56 | L | A | -0.2263 | |
| 57 | S | A | -0.0509 | |
| 58 | Y | A | 0.5252 | |
| 59 | R | A | -0.9574 | |
| 60 | A | A | 0.0000 | |
| 61 | S | A | -0.5756 | |
| 62 | G | A | -1.0212 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.3727 | |
| 65 | D | A | -2.4456 | |
| 66 | R | A | -2.2171 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.3292 | |
| 69 | G | A | -0.7378 | |
| 70 | S | A | -0.8444 | |
| 71 | G | A | -1.1692 | |
| 72 | S | A | -0.8649 | |
| 73 | G | A | -0.8854 | |
| 74 | T | A | -1.5947 | |
| 75 | D | A | -2.3738 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.2503 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.2479 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3543 | |
| 82 | R | A | -3.1596 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2785 | |
| 85 | A | A | -1.7401 | |
| 86 | E | A | -2.3056 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.0537 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0652 | |
| 91 | Y | A | 0.0000 | |
| 92 | Y | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | G | A | 0.0000 | |
| 97 | S | A | 0.0000 | |
| 98 | H | A | -0.8028 | |
| 99 | V | A | -0.3271 | |
| 100 | P | A | -0.4271 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | 0.0373 | |
| 103 | F | A | 0.3039 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0153 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4736 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.7727 | |
| 111 | I | A | -1.9220 | |
| 112 | K | A | -2.3905 | |
| 113 | G | A | -1.8384 | |
| 114 | G | A | -1.7011 | |
| 115 | G | A | -1.3561 | |
| 116 | G | A | -1.2475 | |
| 117 | S | A | -1.3089 | |
| 118 | G | A | -1.5550 | |
| 119 | G | A | -1.6497 | |
| 120 | G | A | -1.6945 | |
| 121 | G | A | -1.7258 | |
| 122 | S | A | -1.0931 | |
| 123 | G | A | -1.3134 | |
| 124 | G | A | -1.2513 | |
| 125 | G | A | -1.2862 | |
| 126 | G | A | -1.1592 | |
| 127 | S | A | -0.9608 | |
| 128 | V | A | -0.8854 | |
| 129 | Q | A | -1.4230 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | -0.0928 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.7333 | |
| 134 | G | A | -0.7295 | |
| 135 | A | A | -0.2291 | |
| 136 | E | A | -0.5198 | |
| 137 | V | A | 0.6696 | |
| 138 | K | A | -1.0562 | |
| 139 | K | A | -2.1348 | |
| 140 | P | A | -2.1086 | |
| 141 | G | A | -1.4833 | |
| 142 | A | A | -1.1901 | |
| 143 | S | A | -1.3190 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -2.1002 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.7218 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -1.2094 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.7886 | |
| 152 | G | A | -0.7941 | |
| 153 | Y | A | -0.2418 | |
| 154 | T | A | -0.1122 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0209 | |
| 157 | D | A | -0.0843 | |
| 158 | Y | A | 0.0586 | |
| 159 | I | A | 0.0000 | |
| 160 | M | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | W | A | 0.0000 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | 0.0000 | |
| 165 | Q | A | -0.5845 | |
| 166 | A | A | -1.0034 | |
| 167 | P | A | -1.0129 | |
| 168 | G | A | -1.2121 | |
| 169 | Q | A | -1.6819 | |
| 170 | G | A | -0.9588 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5654 | |
| 173 | W | A | 0.0000 | |
| 174 | M | A | 0.0000 | |
| 175 | G | A | 0.0000 | |
| 176 | N | A | 0.0000 | |
| 177 | I | A | 0.0000 | |
| 178 | D | A | 0.0000 | |
| 179 | P | A | 0.0000 | |
| 180 | Y | A | 0.2627 | |
| 181 | Y | A | 0.4344 | |
| 182 | G | A | -0.0718 | |
| 183 | S | A | -0.2275 | |
| 184 | T | A | 0.0000 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.3996 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | 0.0767 | |
| 189 | K | A | -1.3962 | |
| 190 | F | A | 0.0000 | |
| 191 | Q | A | -1.4543 | |
| 192 | G | A | -1.2619 | |
| 193 | R | A | -1.2463 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.7981 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5359 | |
| 198 | R | A | -0.9942 | |
| 199 | D | A | -1.2096 | |
| 200 | T | A | -0.6652 | |
| 201 | S | A | -0.5551 | |
| 202 | T | A | -0.6980 | |
| 203 | S | A | -0.7993 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8006 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.4781 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.0772 | |
| 211 | S | A | -1.1122 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.6844 | |
| 214 | S | A | -2.1941 | |
| 215 | E | A | -2.4252 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.7748 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.1936 | |
| 220 | Y | A | 0.0000 | |
| 221 | Y | A | 0.0000 | |
| 222 | C | A | 0.0000 | |
| 223 | A | A | 0.0000 | |
| 224 | R | A | 0.0000 | |
| 225 | D | A | 0.0000 | |
| 226 | G | A | 0.0000 | |
| 227 | N | A | -0.5318 | |
| 228 | Y | A | -0.1155 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.3541 | |
| 232 | Y | A | -0.3735 | |
| 233 | W | A | -0.4029 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.3564 | |
| 236 | G | A | -0.5996 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0731 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3823 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -0.8728 | |
| 243 | S | A | -0.9923 | |
| 1 | A | B | -1.5892 | |
| 2 | Q | B | -1.6772 | |
| 3 | E | B | -1.8754 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.6378 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4840 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | 0.0000 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.9556 | |
| 15 | V | B | -0.4387 | |
| 16 | G | B | -0.8865 | |
| 17 | A | B | -0.5551 | |
| 18 | S | B | -0.8103 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8769 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8743 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.6513 | |
| 25 | T | B | -1.8263 | |
| 26 | S | B | -1.7067 | |
| 27 | G | B | -1.3794 | |
| 28 | G | B | -1.5817 | |
| 29 | L | B | -1.8262 | |
| 30 | R | B | -2.3984 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1368 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.6602 | |
| 36 | Q | B | -0.7562 | |
| 37 | L | B | -0.3172 | |
| 38 | G | B | -1.0195 | |
| 39 | P | B | -1.0944 | |
| 40 | Q | B | -1.6168 | |
| 41 | P | B | -1.2933 | |
| 42 | Q | B | -1.5008 | |
| 43 | D | B | -1.3527 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3882 | |
| 47 | Y | B | 0.1631 | |
| 48 | E | B | -0.7210 | |
| 49 | D | B | -1.3220 | |
| 50 | G | B | -0.0522 | |
| 51 | V | B | 1.5978 | |
| 52 | V | B | 2.1015 | |
| 53 | P | B | 0.8167 | |
| 54 | T | B | -0.0140 | |
| 55 | T | B | -1.4164 | |
| 56 | D | B | -2.3286 | |
| 57 | R | B | -3.3331 | |
| 58 | R | B | -2.7615 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.3163 | |
| 61 | G | B | -2.3526 | |
| 62 | R | B | -2.2614 | |
| 63 | I | B | -1.6360 | |
| 64 | D | B | -1.9857 | |
| 65 | F | B | -0.6907 | |
| 66 | S | B | -0.9167 | |
| 67 | G | B | -1.2428 | |
| 68 | S | B | -1.5587 | |
| 69 | Q | B | -1.9230 | |
| 70 | D | B | -2.6122 | |
| 71 | N | B | -2.3195 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0271 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9336 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7424 | |
| 78 | R | B | -2.1405 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.8709 | |
| 81 | L | B | 0.2598 | |
| 82 | S | B | 0.0498 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0593 | |
| 85 | G | B | -0.1360 | |
| 86 | T | B | -0.1565 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.3656 | |
| 93 | T | B | -1.1075 | |
| 94 | E | B | -1.4749 | |
| 95 | V | B | 0.2560 | |
| 96 | N | B | 0.1764 | |
| 97 | V | B | 0.0063 | |
| 98 | Y | B | -0.2565 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.9367 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.0000 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | 0.0000 | |
| 108 | E | B | -2.9395 | |
| 109 | E | B | -3.5547 | |
| 110 | Q | B | -2.8472 | |
| 111 | S | B | -1.8253 | |
| 112 | Q | B | -2.6655 | |
| 113 | G | B | -1.7666 | |
| 114 | W | B | 0.0000 | |
| 115 | H | B | 0.0000 | |
| 116 | R | B | 0.0000 | |
| 117 | C | B | 0.0000 | |
| 118 | S | B | 0.0000 | |
| 119 | D | B | -0.5849 | |
| 120 | A | B | 0.0000 | |
| 121 | P | B | -0.8069 | |
| 122 | P | B | -1.2627 | |
| 123 | R | B | -2.0343 | |
| 124 | A | B | -0.8344 | |
| 125 | S | B | -0.4499 | |
| 126 | A | B | 0.2560 | |
| 127 | L | B | 0.7539 | |
| 128 | P | B | 0.1714 | |
| 129 | A | B | -0.0559 | |
| 130 | P | B | -0.4249 | |
| 131 | P | B | -0.6167 | |
| 132 | T | B | -0.5308 | |
| 133 | G | B | -0.4484 | |
| 134 | S | B | -0.0783 | |
| 135 | A | B | 0.1900 | |
| 136 | L | B | 0.8006 | |
| 137 | P | B | -0.6701 | |
| 138 | D | B | -1.9766 | |
| 139 | P | B | -1.5297 | |
| 140 | Q | B | -1.9329 | |
| 141 | T | B | -1.0348 | |
| 142 | A | B | -0.2114 | |
| 143 | S | B | 0.0251 | |
| 144 | A | B | 0.3636 | |
| 145 | L | B | 0.9047 | |
| 146 | P | B | -0.4977 | |
| 147 | D | B | -1.6899 | |
| 148 | P | B | -1.0521 | |
| 149 | P | B | -0.8764 | |
| 150 | A | B | -0.4327 | |
| 151 | A | B | 0.1228 | |
| 152 | S | B | 0.2264 | |
| 153 | A | B | 0.6664 | |
| 154 | L | B | 1.4028 | |
| 155 | P | B | 0.4735 |
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 | -0.3928 | 3.5657 | View | CSV | PDB |
| 4.5 | -0.4322 | 3.5484 | View | CSV | PDB |
| 5.0 | -0.4793 | 3.5484 | View | CSV | PDB |
| 5.5 | -0.527 | 3.5484 | View | CSV | PDB |
| 6.0 | -0.5679 | 3.5484 | View | CSV | PDB |
| 6.5 | -0.5971 | 3.5484 | View | CSV | PDB |
| 7.0 | -0.6132 | 3.5484 | View | CSV | PDB |
| 7.5 | -0.6196 | 3.5484 | View | CSV | PDB |
| 8.0 | -0.6194 | 3.5484 | View | CSV | PDB |
| 8.5 | -0.6133 | 3.5484 | View | CSV | PDB |
| 9.0 | -0.6006 | 3.5484 | 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