| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGNTYLEWYLQKPGQPPQLLIYKLSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSQVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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] (00:00:02)
[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 all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:19)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/9dcb0bac307772e/tmp/folded.pdb (00:06:19)
[INFO] Main: Simulation completed successfully. (00:13:07)
|
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 | -1.3649 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7245 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2767 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | 0.0516 | |
| 8 | P | A | 0.4618 | |
| 9 | L | A | 1.2668 | |
| 10 | S | A | 0.1633 | |
| 11 | L | A | -0.2202 | |
| 12 | S | A | -1.0877 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.5439 | |
| 15 | P | A | -1.6658 | |
| 16 | G | A | -1.5531 | |
| 17 | Q | A | -1.7890 | |
| 18 | P | A | -1.9325 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8682 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8992 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2559 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -1.0218 | |
| 27 | Q | A | -1.5627 | |
| 28 | S | A | -0.8726 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.5396 | |
| 31 | H | A | -0.2956 | |
| 32 | S | A | -0.5976 | |
| 33 | N | A | -1.1895 | |
| 34 | G | A | -0.7746 | |
| 35 | N | A | -0.4548 | |
| 36 | T | A | -0.0320 | |
| 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 | -0.9054 | |
| 44 | K | A | -1.6404 | |
| 45 | P | A | -1.0990 | |
| 46 | G | A | -1.4324 | |
| 47 | Q | A | -1.8402 | |
| 48 | P | A | -1.1659 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -0.9501 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.4151 | |
| 55 | K | A | 0.0787 | |
| 56 | L | A | -0.0063 | |
| 57 | S | A | 0.1059 | |
| 58 | Y | A | 0.7959 | |
| 59 | R | A | -0.6301 | |
| 60 | F | A | -0.0744 | |
| 61 | S | A | -0.3508 | |
| 62 | G | A | -0.9591 | |
| 63 | V | A | -0.9031 | |
| 64 | P | A | -1.2653 | |
| 65 | D | A | -2.4034 | |
| 66 | R | A | -2.1507 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.2210 | |
| 69 | G | A | -0.6214 | |
| 70 | S | A | -0.7646 | |
| 71 | G | A | -1.1105 | |
| 72 | S | A | -0.7603 | |
| 73 | G | A | -0.7180 | |
| 74 | T | A | -1.5324 | |
| 75 | D | A | -2.2674 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1887 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1387 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.2913 | |
| 82 | R | A | -3.0599 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.0450 | |
| 85 | A | A | -1.8751 | |
| 86 | E | A | -2.4001 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.0193 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0718 | |
| 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 | Q | A | -0.9911 | |
| 99 | V | A | -0.5328 | |
| 100 | P | A | -0.5308 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | 0.0128 | |
| 103 | F | A | 0.3062 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0125 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4472 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.6461 | |
| 111 | I | A | -1.8771 | |
| 112 | K | A | -2.3721 | |
| 113 | G | A | -1.8354 | |
| 114 | G | A | -1.6994 | |
| 115 | G | A | -1.3497 | |
| 116 | G | A | -1.4236 | |
| 117 | S | A | -1.2574 | |
| 118 | G | A | -1.6856 | |
| 119 | G | A | -1.5582 | |
| 120 | G | A | -1.7525 | |
| 121 | G | A | -1.4780 | |
| 122 | S | A | -1.0998 | |
| 123 | G | A | -1.3663 | |
| 124 | G | A | -1.1806 | |
| 125 | G | A | -1.3055 | |
| 126 | G | A | -1.1058 | |
| 127 | S | A | -0.9563 | |
| 128 | V | A | -0.8582 | |
| 129 | Q | A | -1.2658 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | 0.2877 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.5259 | |
| 134 | G | A | -0.6206 | |
| 135 | A | A | -0.0714 | |
| 136 | E | A | -0.1662 | |
| 137 | V | A | 0.8273 | |
| 138 | K | A | -0.9729 | |
| 139 | K | A | -2.1380 | |
| 140 | P | A | -2.1409 | |
| 141 | G | A | -1.4750 | |
| 142 | A | A | -1.1842 | |
| 143 | S | A | -1.2245 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.6278 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.5159 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -0.8325 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.6650 | |
| 152 | G | A | -0.7902 | |
| 153 | Y | A | -0.2754 | |
| 154 | T | A | -0.0644 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0611 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.0000 | |
| 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 | -0.4087 | |
| 165 | Q | A | -0.6642 | |
| 166 | A | A | -1.0537 | |
| 167 | P | A | -1.0395 | |
| 168 | G | A | -1.2139 | |
| 169 | Q | A | -1.7042 | |
| 170 | G | A | -0.9839 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.6374 | |
| 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 | 0.2816 | |
| 181 | Y | A | 0.4492 | |
| 182 | G | A | -0.0527 | |
| 183 | S | A | 0.0135 | |
| 184 | T | A | -0.0447 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | 0.0571 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | 0.0219 | |
| 189 | K | A | -1.5554 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -2.0265 | |
| 192 | G | A | -1.3651 | |
| 193 | R | A | -1.2954 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.5375 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5662 | |
| 198 | R | A | -0.9906 | |
| 199 | D | A | -1.1841 | |
| 200 | T | A | -0.6695 | |
| 201 | S | A | -0.5608 | |
| 202 | T | A | -0.6494 | |
| 203 | S | A | -0.7229 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.6932 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.3020 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.0118 | |
| 211 | S | A | -1.0569 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.8153 | |
| 214 | S | A | -2.2620 | |
| 215 | E | A | -2.4786 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8797 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.1933 | |
| 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 | -0.2204 | |
| 228 | Y | A | 0.5336 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | 0.0000 | |
| 232 | Y | A | -0.1532 | |
| 233 | W | A | -0.2649 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.1975 | |
| 236 | G | A | -0.5166 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | 0.0078 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3164 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -0.8916 | |
| 243 | S | A | -0.9907 | |
| 1 | A | B | -0.6102 | |
| 2 | Q | B | -1.1402 | |
| 3 | E | B | -2.1378 | |
| 4 | V | B | -1.6230 | |
| 5 | Q | B | -1.8035 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4978 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | -0.3035 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -1.2285 | |
| 15 | V | B | -0.8830 | |
| 16 | G | B | -1.3459 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.8085 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8978 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8613 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7513 | |
| 25 | T | B | -1.7851 | |
| 26 | S | B | -1.5644 | |
| 27 | G | B | -1.2242 | |
| 28 | G | B | -1.4000 | |
| 29 | L | B | -1.4509 | |
| 30 | R | B | -2.4636 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0886 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.6701 | |
| 36 | Q | B | 0.0000 | |
| 37 | L | B | -0.6484 | |
| 38 | G | B | -1.1704 | |
| 39 | P | B | -1.3025 | |
| 40 | Q | B | -1.7633 | |
| 41 | P | B | -1.4467 | |
| 42 | Q | B | -1.5939 | |
| 43 | D | B | -1.3616 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.4411 | |
| 47 | Y | B | 0.0824 | |
| 48 | E | B | -0.9588 | |
| 49 | D | B | -1.5686 | |
| 50 | G | B | -0.1689 | |
| 51 | V | B | 1.5172 | |
| 52 | V | B | 2.0458 | |
| 53 | P | B | 0.8227 | |
| 54 | T | B | 0.2138 | |
| 55 | T | B | -1.2668 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -3.0339 | |
| 58 | R | B | -2.4907 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.1970 | |
| 61 | G | B | -2.2830 | |
| 62 | R | B | -2.1835 | |
| 63 | I | B | -1.5977 | |
| 64 | D | B | -1.9691 | |
| 65 | F | B | -0.6897 | |
| 66 | S | B | -0.9197 | |
| 67 | G | B | -1.2501 | |
| 68 | S | B | -1.5919 | |
| 69 | Q | B | -2.0002 | |
| 70 | D | B | -2.4806 | |
| 71 | N | B | -2.2248 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0244 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9275 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7612 | |
| 78 | R | B | -2.2974 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.1019 | |
| 81 | L | B | -0.0485 | |
| 82 | S | B | -0.1898 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.1051 | |
| 85 | G | B | -0.2321 | |
| 86 | T | B | -0.1512 | |
| 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 | -0.4479 | |
| 93 | T | B | -0.9038 | |
| 94 | E | B | -1.2729 | |
| 95 | V | B | 0.7288 | |
| 96 | N | B | 0.1190 | |
| 97 | V | B | 0.0331 | |
| 98 | Y | B | -0.2700 | |
| 99 | G | B | -0.8625 | |
| 100 | S | B | -0.8541 | |
| 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 | -3.0993 | |
| 109 | E | B | -3.3658 | |
| 110 | Q | B | -2.9734 | |
| 111 | S | B | -2.0847 | |
| 112 | Q | B | -2.3173 | |
| 113 | G | B | -1.5718 | |
| 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 | -0.5241 | |
| 120 | A | B | 0.0000 | |
| 121 | P | B | -0.8121 | |
| 122 | P | B | -1.2200 | |
| 123 | R | B | -1.9945 | |
| 124 | A | B | -0.9002 | |
| 125 | S | B | -0.6218 | |
| 126 | A | B | -0.1345 | |
| 127 | L | B | 0.1476 | |
| 128 | P | B | -0.1227 | |
| 129 | A | B | 0.1028 | |
| 130 | P | B | -0.4518 | |
| 131 | P | B | -0.5111 | |
| 132 | T | B | -0.4676 | |
| 133 | G | B | -0.4764 | |
| 134 | S | B | -0.0629 | |
| 135 | A | B | 0.1613 | |
| 136 | L | B | 0.8149 | |
| 137 | P | B | -0.6802 | |
| 138 | D | B | -1.9938 | |
| 139 | P | B | -1.3377 | |
| 140 | Q | B | -1.9595 | |
| 141 | T | B | -1.0100 | |
| 142 | A | B | -0.2044 | |
| 143 | S | B | 0.0202 | |
| 144 | A | B | 0.3507 | |
| 145 | L | B | 0.8951 | |
| 146 | P | B | -0.5009 | |
| 147 | D | B | -1.6838 | |
| 148 | P | B | -1.0441 | |
| 149 | P | B | -0.8846 | |
| 150 | A | B | -0.4454 | |
| 151 | A | B | 0.1150 | |
| 152 | S | B | 0.2224 | |
| 153 | A | B | 0.6661 | |
| 154 | L | B | 1.4023 | |
| 155 | P | B | 0.4782 |
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 | -0.3597 | 3.5836 | View | CSV | PDB |
| 4.5 | -0.4 | 3.3899 | View | CSV | PDB |
| 5.0 | -0.4481 | 3.184 | View | CSV | PDB |
| 5.5 | -0.4962 | 2.9739 | View | CSV | PDB |
| 6.0 | -0.5372 | 2.866 | View | CSV | PDB |
| 6.5 | -0.5657 | 2.866 | View | CSV | PDB |
| 7.0 | -0.581 | 2.866 | View | CSV | PDB |
| 7.5 | -0.5866 | 2.866 | View | CSV | PDB |
| 8.0 | -0.5862 | 2.866 | View | CSV | PDB |
| 8.5 | -0.5803 | 2.866 | View | CSV | PDB |
| 9.0 | -0.5682 | 2.866 | 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