| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASQSVSYMNWYQQKPGQAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVKKPGASVKVSCKASGYTFTRYTMHWVRQAPGQGLWMGYINPSRGYTNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTLVTVSS
B: MQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMGSADDAKKDAAKKDDAKKDDAKKDGSDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARV 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 (00:15:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/cb9cf924be374ba/tmp/folded.pdb (00:15:57)
[INFO] Main: Simulation completed successfully. (00:26:49)
|
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 | -1.7176 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.8778 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2725 | |
| 6 | K | A | -0.5096 | |
| 7 | S | A | -0.4848 | |
| 8 | P | A | -0.4014 | |
| 9 | A | A | -0.5148 | |
| 10 | T | A | -0.4918 | |
| 11 | L | A | -0.3432 | |
| 12 | S | A | -0.8116 | |
| 13 | L | A | -1.0778 | |
| 14 | S | A | -1.6195 | |
| 15 | P | A | -1.9559 | |
| 16 | G | A | -2.2610 | |
| 17 | E | A | -2.8748 | |
| 18 | R | A | -3.2350 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6337 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6929 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.9475 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7178 | |
| 27 | Q | A | -1.5673 | |
| 28 | S | A | -1.2568 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.7780 | |
| 31 | Y | A | 0.0000 | |
| 32 | M | A | 0.0000 | |
| 33 | N | A | 0.0000 | |
| 34 | W | A | 0.0000 | |
| 35 | Y | A | 0.0000 | |
| 36 | Q | A | -0.4833 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.4869 | |
| 39 | P | A | -1.0675 | |
| 40 | G | A | -1.3195 | |
| 41 | Q | A | -1.8284 | |
| 42 | A | A | -1.1281 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.7855 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.3809 | |
| 49 | D | A | -0.8096 | |
| 50 | T | A | -0.5319 | |
| 51 | S | A | -0.5785 | |
| 52 | N | A | -0.4931 | |
| 53 | L | A | -0.0891 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.2223 | |
| 56 | G | A | -0.6611 | |
| 57 | I | A | -0.4065 | |
| 58 | P | A | -0.9447 | |
| 59 | D | A | -1.8786 | |
| 60 | R | A | -1.8961 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7002 | |
| 63 | G | A | -0.4368 | |
| 64 | S | A | -0.9053 | |
| 65 | G | A | -1.1539 | |
| 66 | S | A | -1.0634 | |
| 67 | G | A | -1.1823 | |
| 68 | T | A | -1.5638 | |
| 69 | D | A | -2.2682 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7428 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8162 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4275 | |
| 76 | R | A | -3.3279 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.4947 | |
| 79 | P | A | -1.7345 | |
| 80 | E | A | -2.5268 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.9300 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.4086 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | W | A | 0.0000 | |
| 91 | S | A | -0.5781 | |
| 92 | S | A | -1.1681 | |
| 93 | N | A | -1.2822 | |
| 94 | P | A | -1.2187 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.0929 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.5349 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2302 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.1208 | |
| 105 | I | A | -1.0373 | |
| 106 | K | A | -1.9875 | |
| 107 | G | A | -1.5451 | |
| 108 | G | A | -1.3999 | |
| 109 | G | A | -1.2812 | |
| 110 | G | A | -1.3594 | |
| 111 | S | A | -1.0258 | |
| 112 | G | A | -1.5920 | |
| 113 | G | A | -1.6266 | |
| 114 | G | A | -1.7873 | |
| 115 | G | A | -1.6010 | |
| 116 | S | A | -1.1977 | |
| 117 | G | A | -1.2596 | |
| 118 | G | A | -1.2226 | |
| 119 | G | A | -1.3786 | |
| 120 | G | A | -1.4193 | |
| 121 | S | A | -1.3995 | |
| 122 | Q | A | -1.7543 | |
| 123 | V | A | -1.1526 | |
| 124 | Q | A | -1.7160 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.5726 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.6697 | |
| 129 | G | A | -0.5853 | |
| 130 | A | A | 0.1696 | |
| 131 | E | A | -0.2325 | |
| 132 | V | A | 0.8836 | |
| 133 | K | A | -0.9810 | |
| 134 | K | A | -2.0958 | |
| 135 | P | A | -2.1252 | |
| 136 | G | A | -1.4839 | |
| 137 | A | A | -1.1709 | |
| 138 | S | A | -1.2769 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.8673 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.7642 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.4263 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.9928 | |
| 147 | G | A | -0.9162 | |
| 148 | Y | A | -0.5072 | |
| 149 | T | A | -0.3990 | |
| 150 | F | A | 0.0000 | |
| 151 | T | A | -0.9622 | |
| 152 | R | A | -1.6931 | |
| 153 | Y | A | -0.5021 | |
| 154 | T | A | 0.0000 | |
| 155 | M | A | 0.0000 | |
| 156 | H | A | 0.0000 | |
| 157 | W | A | 0.0000 | |
| 158 | V | A | 0.0000 | |
| 159 | R | A | 0.0000 | |
| 160 | Q | A | -0.2356 | |
| 161 | A | A | -0.6350 | |
| 162 | P | A | -0.8536 | |
| 163 | G | A | -1.4309 | |
| 164 | Q | A | -1.5548 | |
| 165 | G | A | 0.0000 | |
| 166 | L | A | -0.3635 | |
| 167 | W | A | 0.0000 | |
| 168 | M | A | 0.0000 | |
| 169 | G | A | 0.0000 | |
| 170 | Y | A | 0.0000 | |
| 171 | I | A | 0.0000 | |
| 172 | N | A | 0.0000 | |
| 173 | P | A | 0.0000 | |
| 174 | S | A | -0.9978 | |
| 175 | R | A | -1.0452 | |
| 176 | G | A | -0.5872 | |
| 177 | Y | A | -0.2232 | |
| 178 | T | A | -0.0719 | |
| 179 | N | A | -0.6100 | |
| 180 | Y | A | -1.3861 | |
| 181 | A | A | -1.8030 | |
| 182 | Q | A | -2.9146 | |
| 183 | K | A | -3.0220 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5116 | |
| 186 | D | A | -3.2351 | |
| 187 | R | A | -2.2483 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -1.1363 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.5795 | |
| 192 | R | A | -1.2747 | |
| 193 | D | A | -1.2772 | |
| 194 | T | A | -0.7401 | |
| 195 | S | A | -0.5713 | |
| 196 | T | A | -0.7231 | |
| 197 | S | A | -0.8352 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.8126 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.5428 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2602 | |
| 205 | S | A | -1.2145 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8051 | |
| 208 | S | A | -2.2578 | |
| 209 | E | A | -2.4527 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.6851 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.6029 | |
| 214 | Y | A | 0.0000 | |
| 215 | Y | A | 0.0000 | |
| 216 | C | A | 0.0000 | |
| 217 | A | A | 0.0000 | |
| 218 | R | A | 0.0000 | |
| 219 | Y | A | 0.0000 | |
| 220 | Y | A | -0.5401 | |
| 221 | D | A | -1.2601 | |
| 222 | D | A | -2.0904 | |
| 223 | H | A | -1.2627 | |
| 224 | Y | A | -0.6798 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.0745 | |
| 228 | Y | A | -0.1631 | |
| 229 | W | A | -0.4079 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -1.3438 | |
| 232 | G | A | -0.4525 | |
| 233 | T | A | 0.0000 | |
| 234 | L | A | 1.0543 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.1222 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8667 | |
| 239 | S | A | -1.1703 | |
| 1 | M | B | 0.5577 | |
| 2 | Q | B | -1.1422 | |
| 3 | S | B | -1.1260 | |
| 4 | I | B | -1.6189 | |
| 5 | K | B | -2.8849 | |
| 6 | G | B | -2.4235 | |
| 7 | N | B | -2.7116 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.2726 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.4737 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.4120 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.4805 | |
| 16 | Q | B | -1.2875 | |
| 17 | E | B | -2.6254 | |
| 18 | D | B | -2.7453 | |
| 19 | G | B | -1.5336 | |
| 20 | S | B | -1.3640 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | 0.0000 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3847 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.5836 | |
| 27 | A | B | -2.7729 | |
| 28 | E | B | -3.1208 | |
| 29 | A | B | -3.2502 | |
| 30 | K | B | -3.8892 | |
| 31 | N | B | -2.9541 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.5430 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.4663 | |
| 36 | K | B | -1.6253 | |
| 37 | D | B | -2.5774 | |
| 38 | G | B | -1.7109 | |
| 39 | K | B | -1.9910 | |
| 40 | M | B | 0.2510 | |
| 41 | I | B | 0.7409 | |
| 42 | G | B | 1.3488 | |
| 43 | F | B | 1.9077 | |
| 44 | L | B | -0.8710 | |
| 45 | T | B | -2.2240 | |
| 46 | E | B | -4.1545 | |
| 47 | D | B | -4.3052 | |
| 48 | K | B | -4.0793 | |
| 49 | K | B | -3.4917 | |
| 50 | K | B | -2.6501 | |
| 51 | W | B | -0.9900 | |
| 52 | N | B | -1.4229 | |
| 53 | L | B | -1.0007 | |
| 54 | G | B | -1.1374 | |
| 55 | S | B | -1.3950 | |
| 56 | N | B | -1.3867 | |
| 57 | A | B | -1.1691 | |
| 58 | K | B | -2.1417 | |
| 59 | D | B | -1.6021 | |
| 60 | P | B | -1.2277 | |
| 61 | R | B | -1.4213 | |
| 62 | G | B | -1.0511 | |
| 63 | M | B | -1.1840 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.8258 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8607 | |
| 68 | G | B | 0.0000 | |
| 69 | S | B | -2.1653 | |
| 70 | Q | B | -2.4356 | |
| 71 | N | B | -2.4889 | |
| 72 | K | B | -1.8896 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.4503 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5653 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0497 | |
| 82 | M | B | 0.0000 | |
| 83 | G | B | -1.4791 | |
| 84 | S | B | -1.4846 | |
| 85 | A | B | -1.9931 | |
| 86 | D | B | -3.5666 | |
| 87 | D | B | -3.8569 | |
| 88 | A | B | -3.2400 | |
| 89 | K | B | -4.2351 | |
| 90 | K | B | -4.7794 | |
| 91 | D | B | -4.7908 | |
| 92 | A | B | -3.6442 | |
| 93 | A | B | -3.6989 | |
| 94 | K | B | -5.0343 | |
| 95 | K | B | -5.0900 | |
| 96 | D | B | -4.9956 | |
| 97 | D | B | -4.9780 | |
| 98 | A | B | -4.3825 | |
| 99 | K | B | -5.0592 | |
| 100 | K | B | -5.0088 | |
| 101 | D | B | -4.5264 | |
| 102 | D | B | -4.3269 | |
| 103 | A | B | -3.4675 | |
| 104 | K | B | -4.0238 | |
| 105 | K | B | -4.0941 | |
| 106 | D | B | -3.6115 | |
| 107 | G | B | -2.7398 | |
| 108 | S | B | -2.3298 | |
| 109 | D | B | -3.3770 | |
| 110 | G | B | -2.9241 | |
| 111 | N | B | -3.4288 | |
| 112 | E | B | -3.4680 | |
| 113 | E | B | -2.6853 | |
| 114 | M | B | -0.8066 | |
| 115 | G | B | -0.4615 | |
| 116 | G | B | -0.2916 | |
| 117 | I | B | 1.4115 | |
| 118 | T | B | 0.2489 | |
| 119 | Q | B | -0.2058 | |
| 120 | T | B | -0.5391 | |
| 121 | P | B | -0.8425 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6567 | |
| 124 | V | B | -0.5407 | |
| 125 | S | B | -0.1703 | |
| 126 | I | B | 0.0938 | |
| 127 | S | B | -0.2246 | |
| 128 | G | B | -0.6690 | |
| 129 | T | B | -1.1726 | |
| 130 | T | B | -1.1000 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.2078 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | 0.0000 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.3635 | |
| 138 | Y | B | -0.6985 | |
| 139 | P | B | -0.7972 | |
| 140 | G | B | -0.8388 | |
| 141 | S | B | -0.8797 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.3480 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | 0.0000 | |
| 147 | H | B | -1.6270 | |
| 148 | N | B | -2.2025 | |
| 149 | D | B | -3.4669 | |
| 150 | K | B | -3.0768 | |
| 151 | N | B | -2.5991 | |
| 152 | I | B | -1.5267 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.1194 | |
| 155 | D | B | -2.6044 | |
| 156 | E | B | -3.5876 | |
| 157 | D | B | -3.6401 | |
| 158 | D | B | -3.4238 | |
| 159 | K | B | -3.2008 | |
| 160 | N | B | -2.7417 | |
| 161 | I | B | -2.0325 | |
| 162 | G | B | -1.8629 | |
| 163 | S | B | -1.6105 | |
| 164 | D | B | -3.0763 | |
| 165 | E | B | -2.8940 | |
| 166 | D | B | -2.0588 | |
| 167 | H | B | -1.8012 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.9228 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.9081 | |
| 172 | E | B | -2.5777 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1486 | |
| 175 | E | B | -0.7127 | |
| 176 | L | B | 0.2130 | |
| 177 | E | B | -1.2390 | |
| 178 | Q | B | -1.0021 | |
| 179 | S | B | -0.6814 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | 0.0000 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.5170 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7722 | |
| 190 | K | B | -1.3017 | |
| 191 | P | B | -1.7747 | |
| 192 | E | B | -2.8319 | |
| 193 | D | B | -2.9592 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.5736 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | 0.0000 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.6342 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1950 | |
| 204 | V | B | -0.0926 |
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 | -0.9405 | 4.3849 | View | CSV | PDB |
| 4.5 | -1.024 | 4.3856 | View | CSV | PDB |
| 5.0 | -1.1224 | 4.3876 | View | CSV | PDB |
| 5.5 | -1.219 | 4.3934 | View | CSV | PDB |
| 6.0 | -1.296 | 4.4072 | View | CSV | PDB |
| 6.5 | -1.3386 | 4.4326 | View | CSV | PDB |
| 7.0 | -1.3461 | 4.4674 | View | CSV | PDB |
| 7.5 | -1.3296 | 4.507 | View | CSV | PDB |
| 8.0 | -1.2992 | 4.5485 | View | CSV | PDB |
| 8.5 | -1.2565 | 4.5905 | View | CSV | PDB |
| 9.0 | -1.1985 | 4.6324 | 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