| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCSASSSVSYMNWYKQKPGLAPRLLIYDTSKLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:06)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:15:04)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d0247e713b70fe9/tmp/folded.pdb (00:15:04)
[INFO] Main: Simulation completed successfully. (00:25:29)
|
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 | -1.5746 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 1.0617 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2024 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.5243 | |
| 8 | P | A | -0.3341 | |
| 9 | A | A | -0.4533 | |
| 10 | T | A | -0.4561 | |
| 11 | L | A | -0.3266 | |
| 12 | S | A | -0.7748 | |
| 13 | L | A | -0.9886 | |
| 14 | S | A | -1.4964 | |
| 15 | P | A | -1.7756 | |
| 16 | G | A | -2.2742 | |
| 17 | E | A | -2.6599 | |
| 18 | R | A | -3.0464 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5567 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6414 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.7598 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.2681 | |
| 27 | S | A | -0.5565 | |
| 28 | S | A | -0.7578 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.6340 | |
| 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 | K | A | -0.6409 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.8603 | |
| 39 | P | A | -0.4082 | |
| 40 | G | A | -0.3659 | |
| 41 | L | A | -0.1311 | |
| 42 | A | A | -0.4808 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -1.4750 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.4193 | |
| 49 | D | A | -0.8541 | |
| 50 | T | A | -0.6614 | |
| 51 | S | A | -0.9208 | |
| 52 | K | A | -1.2707 | |
| 53 | L | A | -0.5196 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.3293 | |
| 56 | G | A | -0.6362 | |
| 57 | I | A | -0.5865 | |
| 58 | P | A | -0.9227 | |
| 59 | D | A | -1.8699 | |
| 60 | R | A | -1.8496 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.8573 | |
| 63 | G | A | -0.5898 | |
| 64 | S | A | -0.9790 | |
| 65 | G | A | -1.1622 | |
| 66 | S | A | -1.0648 | |
| 67 | G | A | -0.9982 | |
| 68 | T | A | -1.2887 | |
| 69 | D | A | -2.1671 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7339 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8120 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3437 | |
| 76 | R | A | -3.2415 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.0741 | |
| 79 | P | A | -1.4860 | |
| 80 | E | A | -2.2676 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.7100 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.3616 | |
| 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 | -0.4729 | |
| 92 | S | A | -0.8244 | |
| 93 | N | A | -1.1763 | |
| 94 | P | A | -1.1622 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | -0.0447 | |
| 97 | F | A | 0.0673 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.4630 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.0767 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.0399 | |
| 105 | I | A | -0.8282 | |
| 106 | K | A | -1.8576 | |
| 107 | G | A | -1.4991 | |
| 108 | G | A | -1.3320 | |
| 109 | G | A | -1.2456 | |
| 110 | G | A | -1.1040 | |
| 111 | S | A | -1.0016 | |
| 112 | G | A | -1.3872 | |
| 113 | G | A | -1.5956 | |
| 114 | G | A | -1.3688 | |
| 115 | G | A | -1.2885 | |
| 116 | S | A | -0.9261 | |
| 117 | G | A | -1.0996 | |
| 118 | G | A | -1.1128 | |
| 119 | G | A | -1.3286 | |
| 120 | G | A | -1.4102 | |
| 121 | S | A | -1.3589 | |
| 122 | Q | A | -1.7771 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.6440 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.2231 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.7663 | |
| 129 | G | A | -0.7401 | |
| 130 | A | A | -0.2245 | |
| 131 | E | A | -0.4621 | |
| 132 | V | A | 0.7891 | |
| 133 | Q | A | -0.8682 | |
| 134 | K | A | -2.0549 | |
| 135 | P | A | -2.1243 | |
| 136 | G | A | -1.4777 | |
| 137 | A | A | -1.1632 | |
| 138 | S | A | -1.3160 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.0978 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.7646 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.2969 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.9369 | |
| 147 | G | A | -0.9377 | |
| 148 | Y | A | -0.5591 | |
| 149 | T | A | -0.5455 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.3179 | |
| 152 | R | A | -1.7652 | |
| 153 | Y | A | -0.5207 | |
| 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 | -0.2910 | |
| 160 | Q | A | -0.5590 | |
| 161 | A | A | -0.8944 | |
| 162 | P | A | -0.8363 | |
| 163 | G | A | -1.5070 | |
| 164 | Q | A | -1.8341 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.4566 | |
| 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 | -0.9881 | |
| 175 | R | A | -0.9487 | |
| 176 | G | A | -0.0713 | |
| 177 | Y | A | 0.2217 | |
| 178 | Y | A | 1.2025 | |
| 179 | N | A | 0.0027 | |
| 180 | Y | A | -1.1392 | |
| 181 | A | A | 0.0000 | |
| 182 | Q | A | -2.9315 | |
| 183 | K | A | -3.0396 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5449 | |
| 186 | D | A | -3.2538 | |
| 187 | R | A | -2.2282 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.9344 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3222 | |
| 192 | R | A | -1.1082 | |
| 193 | D | A | -1.1432 | |
| 194 | T | A | -0.7727 | |
| 195 | S | A | -0.5547 | |
| 196 | T | A | -0.7229 | |
| 197 | S | A | -0.8913 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.8214 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.4931 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2555 | |
| 205 | S | A | -1.2194 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8076 | |
| 208 | S | A | -2.2687 | |
| 209 | E | A | -2.4567 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.9023 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.0697 | |
| 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 | -0.5361 | |
| 221 | D | A | -1.2780 | |
| 222 | D | A | -2.1281 | |
| 223 | H | A | -1.3373 | |
| 224 | Y | A | -0.6141 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | -0.3762 | |
| 228 | Y | A | -0.4215 | |
| 229 | W | A | -0.4074 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.9821 | |
| 232 | G | A | -0.4025 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | -0.0905 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.3669 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8077 | |
| 239 | S | A | -1.1239 | |
| 1 | M | B | 0.7957 | |
| 2 | Q | B | 0.0000 | |
| 3 | S | B | -0.7009 | |
| 4 | I | B | -1.0279 | |
| 5 | K | B | -2.2603 | |
| 6 | G | B | -1.8012 | |
| 7 | N | B | -1.8244 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.1957 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.4432 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.5887 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.6238 | |
| 16 | Q | B | -1.1093 | |
| 17 | E | B | -2.5548 | |
| 18 | D | B | -2.7075 | |
| 19 | G | B | -1.4827 | |
| 20 | S | B | -1.3053 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4903 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3664 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.4280 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.3076 | |
| 29 | A | B | -3.0096 | |
| 30 | K | B | -3.7477 | |
| 31 | N | B | -2.6033 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.6081 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.3356 | |
| 36 | K | B | -1.4332 | |
| 37 | D | B | -2.0103 | |
| 38 | G | B | -1.2513 | |
| 39 | K | B | -1.6436 | |
| 40 | M | B | 0.4975 | |
| 41 | I | B | 0.8689 | |
| 42 | G | B | 1.3942 | |
| 43 | F | B | 1.6464 | |
| 44 | L | B | -0.9508 | |
| 45 | T | B | -2.6046 | |
| 46 | E | B | -4.5952 | |
| 47 | D | B | -4.2350 | |
| 48 | K | B | -4.0753 | |
| 49 | K | B | -3.9288 | |
| 50 | K | B | -2.8068 | |
| 51 | W | B | -1.0907 | |
| 52 | N | B | -1.6863 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.2054 | |
| 55 | S | B | -1.4373 | |
| 56 | N | B | -1.4699 | |
| 57 | A | B | -1.1985 | |
| 58 | K | B | -2.2145 | |
| 59 | D | B | -1.7220 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.4185 | |
| 62 | G | B | -0.9663 | |
| 63 | M | B | -1.1123 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8443 | |
| 68 | G | B | -2.6900 | |
| 69 | S | B | -2.0676 | |
| 70 | Q | B | -2.4813 | |
| 71 | N | B | -2.5604 | |
| 72 | K | B | -2.1275 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.0153 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5801 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0751 | |
| 82 | M | B | -1.0916 | |
| 83 | G | B | -1.4876 | |
| 84 | S | B | -1.2838 | |
| 85 | A | B | -1.7871 | |
| 86 | D | B | -3.3834 | |
| 87 | D | B | -4.0611 | |
| 88 | A | B | -3.2342 | |
| 89 | K | B | -4.1809 | |
| 90 | K | B | -4.6839 | |
| 91 | D | B | -4.2372 | |
| 92 | A | B | -3.1880 | |
| 93 | A | B | -3.3775 | |
| 94 | K | B | -4.5652 | |
| 95 | K | B | -4.6094 | |
| 96 | D | B | -4.3207 | |
| 97 | D | B | -4.3662 | |
| 98 | A | B | -3.6647 | |
| 99 | K | B | -4.3232 | |
| 100 | K | B | -4.1410 | |
| 101 | D | B | -4.1106 | |
| 102 | D | B | -3.9465 | |
| 103 | A | B | -2.9246 | |
| 104 | K | B | -3.8335 | |
| 105 | K | B | -3.7683 | |
| 106 | D | B | -3.6190 | |
| 107 | G | B | -2.9183 | |
| 108 | S | B | -2.4219 | |
| 109 | D | B | -3.2053 | |
| 110 | G | B | -2.9102 | |
| 111 | N | B | -3.5304 | |
| 112 | E | B | -3.5008 | |
| 113 | E | B | -2.9114 | |
| 114 | M | B | -0.9973 | |
| 115 | G | B | -0.4855 | |
| 116 | G | B | -0.3502 | |
| 117 | I | B | 1.2782 | |
| 118 | T | B | 0.2637 | |
| 119 | Q | B | -0.0949 | |
| 120 | T | B | -0.5391 | |
| 121 | P | B | -0.9217 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6309 | |
| 124 | V | B | -0.5161 | |
| 125 | S | B | -0.1157 | |
| 126 | I | B | 0.2308 | |
| 127 | S | B | -0.1356 | |
| 128 | G | B | -0.5872 | |
| 129 | T | B | -1.0592 | |
| 130 | T | B | -0.9298 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1225 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | 0.0000 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.5119 | |
| 138 | Y | B | -0.5542 | |
| 139 | P | B | -0.7133 | |
| 140 | G | B | -0.6534 | |
| 141 | S | B | -0.6413 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6352 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.6114 | |
| 147 | H | B | -1.4752 | |
| 148 | N | B | -1.3804 | |
| 149 | D | B | -2.1319 | |
| 150 | K | B | -2.8918 | |
| 151 | N | B | -2.9260 | |
| 152 | I | B | -1.6829 | |
| 153 | G | B | -1.8429 | |
| 154 | G | B | -2.4437 | |
| 155 | D | B | -3.1517 | |
| 156 | E | B | -4.0144 | |
| 157 | D | B | -3.8319 | |
| 158 | D | B | -3.4776 | |
| 159 | K | B | -3.2590 | |
| 160 | N | B | -2.6197 | |
| 161 | I | B | -1.9186 | |
| 162 | G | B | -1.8805 | |
| 163 | S | B | -1.6702 | |
| 164 | D | B | -3.0195 | |
| 165 | E | B | -3.0712 | |
| 166 | D | B | -2.0468 | |
| 167 | H | B | -1.7832 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8357 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.6360 | |
| 172 | E | B | -2.4278 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.0155 | |
| 175 | E | B | -0.6366 | |
| 176 | L | B | 0.2255 | |
| 177 | E | B | -1.2143 | |
| 178 | Q | B | -0.9838 | |
| 179 | S | B | -0.6970 | |
| 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 | -0.3014 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.5789 | |
| 190 | K | B | -1.1020 | |
| 191 | P | B | -1.3029 | |
| 192 | E | B | -2.0335 | |
| 193 | D | B | -2.2027 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.0941 | |
| 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 | -0.7097 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1308 | |
| 204 | V | B | 0.0522 |
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 | -0.9096 | 3.9349 | View | CSV | PDB |
| 4.5 | -0.9893 | 3.9081 | View | CSV | PDB |
| 5.0 | -1.0815 | 3.8746 | View | CSV | PDB |
| 5.5 | -1.17 | 3.8488 | View | CSV | PDB |
| 6.0 | -1.237 | 3.8492 | View | CSV | PDB |
| 6.5 | -1.2699 | 3.887 | View | CSV | PDB |
| 7.0 | -1.2692 | 3.9584 | View | CSV | PDB |
| 7.5 | -1.2464 | 4.0502 | View | CSV | PDB |
| 8.0 | -1.2103 | 4.151 | View | CSV | PDB |
| 8.5 | -1.1622 | 4.2546 | View | CSV | PDB |
| 9.0 | -1.0996 | 4.358 | 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