| Chain sequence(s) |
A: YNSGKLEEFIPGNLERECMEEKCSFEEAREVFENTERTTEFWKQYVDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTRAETVFPDVDYVNSTEAETILDNITQSTQSFNDFTRVVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
input PDB |
| Selected Chain(s) | A |
| 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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:08:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f87416428e7d9d0/tmp/folded.pdb (00:08:57)
[INFO] Main: Simulation completed successfully. (00:15:35)
|
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 | Y | A | -0.2410 | |
| 2 | N | A | -2.0347 | |
| 3 | S | A | -1.4596 | |
| 4 | G | A | -1.4805 | |
| 5 | K | A | -1.8734 | |
| 6 | L | A | -0.2899 | |
| 7 | E | A | -1.7294 | |
| 8 | E | A | -1.3594 | |
| 9 | F | A | 1.1191 | |
| 10 | I | A | 0.6602 | |
| 11 | P | A | -0.2094 | |
| 12 | G | A | -1.3008 | |
| 13 | N | A | -1.4837 | |
| 14 | L | A | -1.5194 | |
| 15 | E | A | -2.3229 | |
| 16 | R | A | -2.7200 | |
| 17 | E | A | -3.1529 | |
| 18 | C | A | 0.0000 | |
| 19 | M | A | -1.7626 | |
| 20 | E | A | -3.3131 | |
| 21 | E | A | -3.4130 | |
| 22 | K | A | -2.8713 | |
| 23 | C | A | -2.0792 | |
| 24 | S | A | -1.1428 | |
| 25 | F | A | -0.5383 | |
| 26 | E | A | -2.4469 | |
| 27 | E | A | -2.6082 | |
| 28 | A | A | 0.0000 | |
| 29 | R | A | -3.0224 | |
| 30 | E | A | -2.8147 | |
| 31 | V | A | -0.7024 | |
| 32 | F | A | -1.5082 | |
| 33 | E | A | -2.6451 | |
| 34 | N | A | -2.4370 | |
| 35 | T | A | -2.6337 | |
| 36 | E | A | -3.4412 | |
| 37 | R | A | -3.3045 | |
| 38 | T | A | 0.0000 | |
| 39 | T | A | -2.0772 | |
| 40 | E | A | -3.0463 | |
| 41 | F | A | -1.6135 | |
| 42 | W | A | -0.7588 | |
| 43 | K | A | -1.2665 | |
| 44 | Q | A | -1.7252 | |
| 45 | Y | A | -0.2629 | |
| 46 | V | A | 0.7742 | |
| 47 | D | A | -0.7685 | |
| 48 | G | A | -1.5773 | |
| 49 | D | A | -2.7281 | |
| 50 | Q | A | -2.7325 | |
| 51 | C | A | -2.6093 | |
| 52 | E | A | -2.8231 | |
| 53 | S | A | -1.9255 | |
| 54 | N | A | -1.8408 | |
| 55 | P | A | -1.4396 | |
| 56 | C | A | -1.1123 | |
| 57 | L | A | -0.7560 | |
| 58 | N | A | -1.2409 | |
| 59 | G | A | -0.4826 | |
| 60 | G | A | -0.5276 | |
| 61 | S | A | -0.4469 | |
| 62 | C | A | -1.2305 | |
| 63 | K | A | -2.0022 | |
| 64 | D | A | -2.7735 | |
| 65 | D | A | -2.3156 | |
| 66 | I | A | -0.5174 | |
| 67 | N | A | -1.3879 | |
| 68 | S | A | -1.5489 | |
| 69 | Y | A | -1.8679 | |
| 70 | E | A | -2.4070 | |
| 71 | C | A | -1.2304 | |
| 72 | W | A | 0.4384 | |
| 73 | C | A | 0.0273 | |
| 74 | P | A | 0.7311 | |
| 75 | F | A | 0.9454 | |
| 76 | G | A | -0.3578 | |
| 77 | F | A | -0.5512 | |
| 78 | E | A | -2.1267 | |
| 79 | G | A | -2.2561 | |
| 80 | K | A | -2.6660 | |
| 81 | N | A | -2.0654 | |
| 82 | C | A | 0.0000 | |
| 83 | E | A | -2.6474 | |
| 84 | L | A | -1.6335 | |
| 85 | D | A | -1.3774 | |
| 86 | V | A | 0.0000 | |
| 87 | T | A | -1.4717 | |
| 88 | C | A | -2.1254 | |
| 89 | N | A | -2.0900 | |
| 90 | I | A | -1.3767 | |
| 91 | K | A | -2.5638 | |
| 92 | N | A | -2.2626 | |
| 93 | G | A | 0.0000 | |
| 94 | R | A | -2.6124 | |
| 95 | C | A | 0.0000 | |
| 96 | E | A | -2.0413 | |
| 97 | Q | A | 0.0000 | |
| 98 | F | A | -0.5968 | |
| 99 | C | A | 0.0000 | |
| 100 | K | A | -2.5369 | |
| 101 | N | A | -3.0787 | |
| 102 | S | A | -2.2388 | |
| 103 | A | A | -1.8735 | |
| 104 | D | A | -2.5939 | |
| 105 | N | A | -2.7560 | |
| 106 | K | A | -2.0042 | |
| 107 | V | A | -1.6876 | |
| 108 | V | A | -1.1060 | |
| 109 | C | A | 0.0000 | |
| 110 | S | A | -0.8268 | |
| 111 | C | A | -1.0714 | |
| 112 | T | A | 0.0000 | |
| 113 | E | A | -1.9091 | |
| 114 | G | A | -1.1252 | |
| 115 | Y | A | -1.6454 | |
| 116 | R | A | -2.7359 | |
| 117 | L | A | -2.0881 | |
| 118 | A | A | -2.5682 | |
| 119 | E | A | -3.2360 | |
| 120 | N | A | -2.8232 | |
| 121 | Q | A | -2.8690 | |
| 122 | K | A | -2.3387 | |
| 123 | S | A | -2.3483 | |
| 124 | C | A | 0.0000 | |
| 125 | E | A | -2.5272 | |
| 126 | P | A | -1.2930 | |
| 127 | A | A | -0.7622 | |
| 128 | V | A | 0.3383 | |
| 129 | P | A | 0.3981 | |
| 130 | F | A | 0.6925 | |
| 131 | P | A | 0.0000 | |
| 132 | C | A | -0.1689 | |
| 133 | G | A | 0.0000 | |
| 134 | R | A | -0.4921 | |
| 135 | V | A | -0.1197 | |
| 136 | S | A | -0.1473 | |
| 137 | V | A | -0.4608 | |
| 138 | S | A | -0.7519 | |
| 139 | Q | A | -1.6458 | |
| 140 | T | A | -1.0141 | |
| 141 | S | A | -0.9746 | |
| 142 | K | A | -1.5010 | |
| 143 | L | A | -0.0791 | |
| 144 | T | A | -0.9940 | |
| 145 | R | A | -2.1775 | |
| 146 | A | A | -1.1899 | |
| 147 | E | A | -1.6685 | |
| 148 | T | A | 0.2413 | |
| 149 | V | A | 1.9038 | |
| 150 | F | A | 2.2137 | |
| 151 | P | A | 0.6602 | |
| 152 | D | A | -0.6642 | |
| 153 | V | A | 0.8756 | |
| 154 | D | A | -0.5387 | |
| 155 | Y | A | 1.2347 | |
| 156 | V | A | 1.4910 | |
| 157 | N | A | -0.5896 | |
| 158 | S | A | -0.7154 | |
| 159 | T | A | -1.1655 | |
| 160 | E | A | -2.4594 | |
| 161 | A | A | -1.5560 | |
| 162 | E | A | -1.5991 | |
| 163 | T | A | 0.0466 | |
| 164 | I | A | 1.7015 | |
| 165 | L | A | 1.3676 | |
| 166 | D | A | -0.5625 | |
| 167 | N | A | -0.6947 | |
| 168 | I | A | 0.6161 | |
| 169 | T | A | -0.3403 | |
| 170 | Q | A | -1.1084 | |
| 171 | S | A | -0.9594 | |
| 172 | T | A | -0.9106 | |
| 173 | Q | A | -1.2444 | |
| 174 | S | A | -0.5166 | |
| 175 | F | A | 0.8533 | |
| 176 | N | A | -0.9333 | |
| 177 | D | A | -1.2512 | |
| 178 | F | A | 0.5886 | |
| 179 | T | A | -0.2964 | |
| 180 | R | A | -1.2985 | |
| 181 | V | A | -0.6019 | |
| 182 | V | A | -0.1270 | |
| 183 | G | A | -1.0222 | |
| 184 | G | A | -1.7820 | |
| 185 | E | A | -2.6483 | |
| 186 | D | A | -2.2128 | |
| 187 | A | A | 0.0000 | |
| 188 | K | A | -2.3249 | |
| 189 | P | A | -1.1031 | |
| 190 | G | A | -0.4847 | |
| 191 | Q | A | -0.9221 | |
| 192 | F | A | 0.0000 | |
| 193 | P | A | 0.0000 | |
| 194 | W | A | 0.0000 | |
| 195 | Q | A | 0.0000 | |
| 196 | V | A | 0.0000 | |
| 197 | V | A | 0.0000 | |
| 198 | L | A | 0.0000 | |
| 199 | N | A | -1.2600 | |
| 200 | G | A | -1.4619 | |
| 201 | K | A | -1.5472 | |
| 202 | V | A | 0.1087 | |
| 203 | D | A | -1.2363 | |
| 204 | A | A | -0.3998 | |
| 205 | F | A | -0.1327 | |
| 206 | C | A | 0.0000 | |
| 207 | G | A | 0.0000 | |
| 208 | G | A | 0.0000 | |
| 209 | S | A | 0.0000 | |
| 210 | I | A | 0.0000 | |
| 211 | V | A | 0.0000 | |
| 212 | N | A | -0.9552 | |
| 213 | E | A | -1.2446 | |
| 214 | K | A | -1.5822 | |
| 215 | W | A | 0.0000 | |
| 216 | I | A | 0.0000 | |
| 217 | V | A | 0.0000 | |
| 218 | T | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | A | A | 0.0000 | |
| 221 | H | A | -0.8946 | |
| 222 | C | A | 0.0000 | |
| 223 | V | A | -0.8811 | |
| 224 | E | A | -2.0242 | |
| 225 | T | A | -1.2043 | |
| 226 | G | A | -1.2500 | |
| 227 | V | A | -1.6693 | |
| 228 | K | A | -2.0807 | |
| 229 | I | A | 0.0000 | |
| 230 | T | A | -1.3604 | |
| 231 | V | A | 0.0000 | |
| 232 | V | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | G | A | 0.0000 | |
| 235 | E | A | -1.0768 | |
| 236 | H | A | -1.0439 | |
| 237 | N | A | -1.0495 | |
| 238 | I | A | -1.1795 | |
| 239 | E | A | -2.4661 | |
| 240 | E | A | -2.8962 | |
| 241 | T | A | -2.0342 | |
| 242 | E | A | -2.0530 | |
| 243 | H | A | -1.7389 | |
| 244 | T | A | -1.0912 | |
| 245 | E | A | -1.2345 | |
| 246 | Q | A | -0.9680 | |
| 247 | K | A | -2.3919 | |
| 248 | R | A | -1.8777 | |
| 249 | N | A | -1.5834 | |
| 250 | V | A | -0.4998 | |
| 251 | I | A | 0.6404 | |
| 252 | R | A | -0.1839 | |
| 253 | I | A | 0.3021 | |
| 254 | I | A | -0.0794 | |
| 255 | P | A | -0.7796 | |
| 256 | H | A | -1.0599 | |
| 257 | H | A | -1.7959 | |
| 258 | N | A | -2.0971 | |
| 259 | Y | A | -1.4265 | |
| 260 | N | A | -1.3311 | |
| 261 | A | A | -0.6109 | |
| 262 | A | A | 0.3369 | |
| 263 | I | A | 1.3136 | |
| 264 | N | A | -0.1566 | |
| 265 | K | A | -1.0089 | |
| 266 | Y | A | -0.2309 | |
| 267 | N | A | -0.6998 | |
| 268 | H | A | -1.4057 | |
| 269 | D | A | 0.0000 | |
| 270 | I | A | 0.0000 | |
| 271 | A | A | 0.0000 | |
| 272 | L | A | 0.0000 | |
| 273 | L | A | 0.0000 | |
| 274 | E | A | 0.0000 | |
| 275 | L | A | 0.0000 | |
| 276 | D | A | -1.8801 | |
| 277 | E | A | -2.5080 | |
| 278 | P | A | -1.4552 | |
| 279 | L | A | 0.0000 | |
| 280 | V | A | 1.2880 | |
| 281 | L | A | 0.8366 | |
| 282 | N | A | 0.3794 | |
| 283 | S | A | 0.0985 | |
| 284 | Y | A | 0.4986 | |
| 285 | V | A | 0.0000 | |
| 286 | T | A | 0.0000 | |
| 287 | P | A | 0.0000 | |
| 288 | I | A | 0.0000 | |
| 289 | C | A | 0.0000 | |
| 290 | I | A | -0.5713 | |
| 291 | A | A | 0.0000 | |
| 292 | D | A | -2.5465 | |
| 293 | K | A | -3.4543 | |
| 294 | E | A | -2.8819 | |
| 295 | Y | A | -1.4453 | |
| 296 | T | A | 0.0000 | |
| 297 | N | A | -1.5553 | |
| 298 | I | A | -0.3309 | |
| 299 | F | A | 0.0000 | |
| 300 | L | A | 0.0000 | |
| 301 | K | A | -0.7696 | |
| 302 | F | A | 0.9915 | |
| 303 | G | A | 0.1658 | |
| 304 | S | A | -0.3355 | |
| 305 | G | A | 0.0000 | |
| 306 | Y | A | -0.7040 | |
| 307 | V | A | 0.0000 | |
| 308 | S | A | 0.0000 | |
| 309 | G | A | 0.0000 | |
| 310 | W | A | 0.0000 | |
| 311 | G | A | 0.0000 | |
| 312 | R | A | -1.7736 | |
| 313 | V | A | 0.0000 | |
| 314 | F | A | -0.0293 | |
| 315 | H | A | -1.1314 | |
| 316 | K | A | -2.3221 | |
| 317 | G | A | -1.6642 | |
| 318 | R | A | -2.3122 | |
| 319 | S | A | -1.4890 | |
| 320 | A | A | 0.0000 | |
| 321 | L | A | -0.6254 | |
| 322 | V | A | -0.7678 | |
| 323 | L | A | 0.0000 | |
| 324 | Q | A | 0.0000 | |
| 325 | Y | A | -1.2011 | |
| 326 | L | A | 0.0000 | |
| 327 | R | A | -2.0340 | |
| 328 | V | A | 0.0000 | |
| 329 | P | A | -0.4248 | |
| 330 | L | A | -0.3390 | |
| 331 | V | A | -1.0268 | |
| 332 | D | A | -2.3051 | |
| 333 | R | A | -2.2172 | |
| 334 | A | A | -1.3362 | |
| 335 | T | A | -1.4998 | |
| 336 | C | A | 0.0000 | |
| 337 | L | A | -0.8845 | |
| 338 | R | A | -1.9212 | |
| 339 | S | A | -1.3027 | |
| 340 | T | A | -0.8855 | |
| 341 | K | A | -1.2163 | |
| 342 | F | A | 0.6302 | |
| 343 | T | A | 0.3582 | |
| 344 | I | A | 0.0000 | |
| 345 | Y | A | -0.0432 | |
| 346 | N | A | -1.5810 | |
| 347 | N | A | 0.0000 | |
| 348 | M | A | 0.0000 | |
| 349 | F | A | 0.0000 | |
| 350 | C | A | 0.0000 | |
| 351 | A | A | 0.0000 | |
| 352 | G | A | 0.0000 | |
| 353 | F | A | -1.4040 | |
| 354 | H | A | -2.3362 | |
| 355 | E | A | -3.0075 | |
| 356 | G | A | 0.0000 | |
| 357 | G | A | -1.2811 | |
| 358 | R | A | -1.5090 | |
| 359 | D | A | 0.0000 | |
| 360 | S | A | -0.6680 | |
| 361 | C | A | 0.0000 | |
| 362 | Q | A | -1.7586 | |
| 363 | G | A | -0.8325 | |
| 364 | D | A | -0.6477 | |
| 365 | S | A | -0.3969 | |
| 366 | G | A | 0.0000 | |
| 367 | G | A | 0.0000 | |
| 368 | P | A | 0.0000 | |
| 369 | H | A | 0.0000 | |
| 370 | V | A | 0.0000 | |
| 371 | T | A | 0.0000 | |
| 372 | E | A | -1.9623 | |
| 373 | V | A | 0.0000 | |
| 374 | E | A | -2.5580 | |
| 375 | G | A | -1.8948 | |
| 376 | T | A | 0.0000 | |
| 377 | S | A | 0.0000 | |
| 378 | F | A | 0.0000 | |
| 379 | L | A | 0.0000 | |
| 380 | T | A | 0.0000 | |
| 381 | G | A | 0.0000 | |
| 382 | I | A | 0.0000 | |
| 383 | I | A | 0.0000 | |
| 384 | S | A | 0.0000 | |
| 385 | W | A | -0.4892 | |
| 386 | G | A | -0.8514 | |
| 387 | E | A | -0.8359 | |
| 388 | E | A | -1.6334 | |
| 389 | C | A | -1.0621 | |
| 390 | A | A | -1.0342 | |
| 391 | M | A | -1.4480 | |
| 392 | K | A | -2.7503 | |
| 393 | G | A | -1.9665 | |
| 394 | K | A | -1.6607 | |
| 395 | Y | A | 0.0000 | |
| 396 | G | A | 0.0000 | |
| 397 | I | A | 0.0000 | |
| 398 | Y | A | 0.0000 | |
| 399 | T | A | 0.0000 | |
| 400 | K | A | -1.0581 | |
| 401 | V | A | 0.0000 | |
| 402 | S | A | -2.3260 | |
| 403 | R | A | -3.0118 | |
| 404 | Y | A | 0.0000 | |
| 405 | V | A | 0.0000 | |
| 406 | N | A | -2.6523 | |
| 407 | W | A | -1.9975 | |
| 408 | I | A | 0.0000 | |
| 409 | K | A | -2.3733 | |
| 410 | E | A | -3.1581 | |
| 411 | K | A | -2.3079 | |
| 412 | T | A | 0.0000 | |
| 413 | K | A | -2.5214 | |
| 414 | L | A | -1.6758 | |
| 415 | T | A | -1.2209 |
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 | -0.62 | 5.9862 | View | CSV | PDB |
| 4.5 | -0.7216 | 5.841 | View | CSV | PDB |
| 5.0 | -0.8507 | 5.6704 | View | CSV | PDB |
| 5.5 | -0.983 | 5.4927 | View | CSV | PDB |
| 6.0 | -1.0927 | 5.3209 | View | CSV | PDB |
| 6.5 | -1.1595 | 5.1652 | View | CSV | PDB |
| 7.0 | -1.1786 | 5.0278 | View | CSV | PDB |
| 7.5 | -1.163 | 4.9033 | View | CSV | PDB |
| 8.0 | -1.1283 | 4.7884 | View | CSV | PDB |
| 8.5 | -1.0822 | 4.6884 | View | CSV | PDB |
| 9.0 | -1.0267 | 4.615 | 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