| Chain sequence(s) |
A: EIVLTKSPATLSLSPGERATLSCSASQSVSYMNWYKQKPGLAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSNNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQLLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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 (00:16:22)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/5ac5f40528ff2b4/tmp/folded.pdb (00:16:22)
[INFO] Main: Simulation completed successfully. (00:26:11)
|
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 | -1.8530 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.8962 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2795 | |
| 6 | K | A | -0.5490 | |
| 7 | S | A | -0.5062 | |
| 8 | P | A | -0.4084 | |
| 9 | A | A | -0.5775 | |
| 10 | T | A | -0.5011 | |
| 11 | L | A | -0.4186 | |
| 12 | S | A | -0.8245 | |
| 13 | L | A | -1.1149 | |
| 14 | S | A | -1.6891 | |
| 15 | P | A | -2.0832 | |
| 16 | G | A | -2.4536 | |
| 17 | E | A | -3.0112 | |
| 18 | R | A | -3.3046 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5226 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.7020 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.9606 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.7141 | |
| 27 | Q | A | -1.6602 | |
| 28 | S | A | -1.3458 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.7281 | |
| 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 | -0.3382 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.7792 | |
| 39 | P | A | -0.3532 | |
| 40 | G | A | -0.3044 | |
| 41 | L | A | 0.1380 | |
| 42 | A | A | -0.1973 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.5108 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.1510 | |
| 49 | D | A | -0.7816 | |
| 50 | T | A | -0.5159 | |
| 51 | S | A | -0.5720 | |
| 52 | N | A | -0.4837 | |
| 53 | L | A | -0.1218 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.1433 | |
| 56 | G | A | -0.5827 | |
| 57 | I | A | -0.4467 | |
| 58 | P | A | -0.9475 | |
| 59 | D | A | -1.8688 | |
| 60 | R | A | -1.8952 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7026 | |
| 63 | G | A | -0.4393 | |
| 64 | S | A | -0.9084 | |
| 65 | G | A | -1.1607 | |
| 66 | S | A | -1.0675 | |
| 67 | G | A | -1.1825 | |
| 68 | T | A | -1.5588 | |
| 69 | D | A | -2.2682 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7499 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8062 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4523 | |
| 76 | R | A | -3.4341 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.6584 | |
| 79 | P | A | -1.8365 | |
| 80 | E | A | -2.4918 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.9855 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5582 | |
| 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 | -0.8685 | |
| 92 | N | A | -1.7521 | |
| 93 | N | A | -1.6593 | |
| 94 | P | A | -1.4082 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2039 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.2639 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2588 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.1856 | |
| 105 | I | A | -1.1489 | |
| 106 | K | A | -2.0265 | |
| 107 | G | A | -1.5497 | |
| 108 | G | A | -1.3879 | |
| 109 | G | A | -1.2676 | |
| 110 | G | A | -1.5060 | |
| 111 | S | A | -1.1836 | |
| 112 | G | A | -1.5539 | |
| 113 | G | A | -1.6223 | |
| 114 | G | A | -1.3598 | |
| 115 | G | A | -1.4251 | |
| 116 | S | A | -1.0006 | |
| 117 | G | A | -1.2746 | |
| 118 | G | A | -1.3124 | |
| 119 | G | A | -1.3186 | |
| 120 | G | A | -1.3484 | |
| 121 | S | A | -1.3011 | |
| 122 | Q | A | -1.8101 | |
| 123 | V | A | -0.9762 | |
| 124 | Q | A | -1.3780 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | -0.1449 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5859 | |
| 129 | G | A | -0.6169 | |
| 130 | A | A | 0.0136 | |
| 131 | E | A | 0.0996 | |
| 132 | V | A | 0.9932 | |
| 133 | Q | A | -0.7796 | |
| 134 | K | A | -2.0812 | |
| 135 | P | A | -2.1385 | |
| 136 | G | A | -1.4954 | |
| 137 | A | A | -1.1790 | |
| 138 | S | A | -1.1980 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.4571 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5782 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -1.0922 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8692 | |
| 147 | G | A | -1.0476 | |
| 148 | Y | A | -0.5607 | |
| 149 | T | A | -0.5562 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.4059 | |
| 152 | R | A | -1.6751 | |
| 153 | Y | A | -0.5114 | |
| 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 | -0.2306 | |
| 161 | A | A | -0.6778 | |
| 162 | P | A | -0.7317 | |
| 163 | G | A | -1.1080 | |
| 164 | Q | A | -1.0013 | |
| 165 | L | A | 0.0000 | |
| 166 | L | A | -0.1112 | |
| 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 | -1.0277 | |
| 175 | R | A | -0.9988 | |
| 176 | G | A | -0.0294 | |
| 177 | Y | A | 0.4545 | |
| 178 | Y | A | 1.2136 | |
| 179 | N | A | -0.0179 | |
| 180 | Y | A | -1.1923 | |
| 181 | A | A | -1.8458 | |
| 182 | Q | A | -2.8784 | |
| 183 | K | A | -3.0219 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5277 | |
| 186 | D | A | -3.2570 | |
| 187 | R | A | -2.1222 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8942 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3210 | |
| 192 | R | A | -1.1391 | |
| 193 | D | A | -1.1308 | |
| 194 | T | A | -0.8121 | |
| 195 | S | A | -0.5536 | |
| 196 | T | A | -0.6780 | |
| 197 | S | A | -0.8587 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.6532 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.2644 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.1857 | |
| 205 | S | A | -1.2254 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8226 | |
| 208 | S | A | -2.2643 | |
| 209 | E | A | -2.4670 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8253 | |
| 212 | A | A | -0.2799 | |
| 213 | V | A | 0.1144 | |
| 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 | -0.4462 | |
| 221 | D | A | -1.2131 | |
| 222 | D | A | -2.1123 | |
| 223 | H | A | -1.2341 | |
| 224 | Y | A | -0.6234 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1038 | |
| 229 | W | A | -0.1051 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.9484 | |
| 232 | G | A | -0.3731 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0411 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2526 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8336 | |
| 239 | S | A | -0.9596 | |
| 1 | M | B | 0.6510 | |
| 2 | Q | B | -0.9021 | |
| 3 | S | B | -1.1326 | |
| 4 | I | B | -1.4009 | |
| 5 | K | B | -2.5463 | |
| 6 | G | B | -2.0818 | |
| 7 | N | B | -2.4355 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.3402 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.5108 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.4600 | |
| 14 | D | B | -0.0222 | |
| 15 | Y | B | 0.4424 | |
| 16 | Q | B | -1.3316 | |
| 17 | E | B | -2.6624 | |
| 18 | D | B | -2.7638 | |
| 19 | G | B | -1.5409 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.6628 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3088 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.1137 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.1219 | |
| 29 | A | B | -2.8371 | |
| 30 | K | B | -3.5653 | |
| 31 | N | B | -2.3761 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.5960 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | -0.1948 | |
| 36 | K | B | -1.1592 | |
| 37 | D | B | -1.6577 | |
| 38 | G | B | -1.0689 | |
| 39 | K | B | -1.3462 | |
| 40 | M | B | 0.6295 | |
| 41 | I | B | 0.9558 | |
| 42 | G | B | 1.3688 | |
| 43 | F | B | 1.6438 | |
| 44 | L | B | -0.9484 | |
| 45 | T | B | -2.4083 | |
| 46 | E | B | -4.2395 | |
| 47 | D | B | -4.0539 | |
| 48 | K | B | -3.8662 | |
| 49 | K | B | -3.8028 | |
| 50 | K | B | -2.8091 | |
| 51 | W | B | -1.1126 | |
| 52 | N | B | -1.7021 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1481 | |
| 55 | S | B | -1.4234 | |
| 56 | N | B | -1.4088 | |
| 57 | A | B | -1.1382 | |
| 58 | K | B | -2.1637 | |
| 59 | D | B | -1.6247 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.4202 | |
| 62 | G | B | -0.8796 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.7683 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.8298 | |
| 68 | G | B | -2.1029 | |
| 69 | S | B | -1.9729 | |
| 70 | Q | B | -2.2212 | |
| 71 | N | B | -2.5295 | |
| 72 | K | B | -2.1927 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.4896 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5544 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -1.0380 | |
| 82 | M | B | -1.0502 | |
| 83 | G | B | -1.5590 | |
| 84 | S | B | -1.4457 | |
| 85 | A | B | -1.8573 | |
| 86 | D | B | -3.6695 | |
| 87 | D | B | -4.2055 | |
| 88 | A | B | -3.3078 | |
| 89 | K | B | -4.2612 | |
| 90 | K | B | -4.8105 | |
| 91 | D | B | -4.7343 | |
| 92 | A | B | -3.3482 | |
| 93 | A | B | -3.4474 | |
| 94 | K | B | -4.6169 | |
| 95 | K | B | -4.7280 | |
| 96 | D | B | -4.7319 | |
| 97 | D | B | -4.3836 | |
| 98 | A | B | -3.6452 | |
| 99 | K | B | -4.4016 | |
| 100 | K | B | -4.3393 | |
| 101 | D | B | -4.1204 | |
| 102 | D | B | -4.0067 | |
| 103 | A | B | -3.0911 | |
| 104 | K | B | -3.9062 | |
| 105 | K | B | -3.7958 | |
| 106 | D | B | -3.6464 | |
| 107 | G | B | -2.7877 | |
| 108 | S | B | -2.3995 | |
| 109 | D | B | -3.1522 | |
| 110 | G | B | -2.8690 | |
| 111 | N | B | -3.3495 | |
| 112 | E | B | -3.5100 | |
| 113 | E | B | -2.8331 | |
| 114 | M | B | -1.2832 | |
| 115 | G | B | -1.2255 | |
| 116 | G | B | -0.9168 | |
| 117 | I | B | -0.5141 | |
| 118 | T | B | -0.3679 | |
| 119 | Q | B | -0.8484 | |
| 120 | T | B | -0.8043 | |
| 121 | P | B | -0.8387 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6163 | |
| 124 | V | B | -0.5554 | |
| 125 | S | B | -0.2293 | |
| 126 | I | B | -0.1050 | |
| 127 | S | B | -0.2341 | |
| 128 | G | B | -0.6843 | |
| 129 | T | B | -1.1583 | |
| 130 | T | B | -0.9966 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1930 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3906 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.5497 | |
| 138 | Y | B | -0.6312 | |
| 139 | P | B | -0.7873 | |
| 140 | G | B | -0.7064 | |
| 141 | S | B | -0.7429 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.5619 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.7062 | |
| 147 | H | B | -1.6303 | |
| 148 | N | B | -1.9888 | |
| 149 | D | B | -3.3352 | |
| 150 | K | B | -3.1023 | |
| 151 | N | B | -2.7183 | |
| 152 | I | B | -1.5962 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.2345 | |
| 155 | D | B | -2.9489 | |
| 156 | E | B | -3.8930 | |
| 157 | D | B | -3.7704 | |
| 158 | D | B | -3.2396 | |
| 159 | K | B | -3.1009 | |
| 160 | N | B | -2.5627 | |
| 161 | I | B | -1.9119 | |
| 162 | G | B | -1.8899 | |
| 163 | S | B | -1.6744 | |
| 164 | D | B | -3.0553 | |
| 165 | E | B | -3.0651 | |
| 166 | D | B | -2.0178 | |
| 167 | H | B | -1.8816 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8496 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.4765 | |
| 172 | E | B | -2.4554 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1010 | |
| 175 | E | B | -0.6863 | |
| 176 | L | B | 0.2337 | |
| 177 | E | B | -1.2331 | |
| 178 | Q | B | -0.9721 | |
| 179 | S | B | 0.0000 | |
| 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 | -0.5558 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7627 | |
| 190 | K | B | -1.1280 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.0190 | |
| 193 | D | B | -2.1756 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.3615 | |
| 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 | -0.5525 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1675 | |
| 204 | V | B | -0.2636 |
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 | -0.9136 | 3.9093 | View | CSV | PDB |
| 4.5 | -0.9927 | 3.8885 | View | CSV | PDB |
| 5.0 | -1.0833 | 3.8629 | View | CSV | PDB |
| 5.5 | -1.1689 | 3.8461 | View | CSV | PDB |
| 6.0 | -1.2328 | 3.8537 | View | CSV | PDB |
| 6.5 | -1.2641 | 3.8955 | View | CSV | PDB |
| 7.0 | -1.2643 | 3.9694 | View | CSV | PDB |
| 7.5 | -1.2436 | 4.0639 | View | CSV | PDB |
| 8.0 | -1.2099 | 4.1676 | View | CSV | PDB |
| 8.5 | -1.1641 | 4.2741 | View | CSV | PDB |
| 9.0 | -1.1038 | 4.3801 | 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