| Chain sequence(s) |
A: ATLDSWLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVLKTLVDLFRNGDTSLLSTIENYISAQAIVQGISNPSGDLSSGAGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSTATDIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPEILCYLQSFWTGSFILANFDSSRSGKDANTLLGSIHTFDPEAACDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDTYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEVTDVSLDFFKALYSDAATGTYSSSSSTYSSIVDAVKTFADGFVSIVETHAASNGSMSEQYDKSDGEQLSARDLTWSYAALLTANNRRNSVVPASWGETSASSVPGTCAATSAIGTYSSVTVTSWP
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 (00:04:12)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/452c793f70eae72/tmp/folded.pdb (00:04:12)
[INFO] Main: Simulation completed successfully. (00:09:06)
|
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 |
|---|---|---|---|---|
| 25 | A | A | -0.3682 | |
| 26 | T | A | -0.4140 | |
| 27 | L | A | 0.0000 | |
| 28 | D | A | -1.6223 | |
| 29 | S | A | -1.0280 | |
| 30 | W | A | -0.8952 | |
| 31 | L | A | 0.0000 | |
| 32 | S | A | -1.1181 | |
| 33 | N | A | -1.4243 | |
| 34 | E | A | 0.0000 | |
| 35 | A | A | -0.4914 | |
| 36 | T | A | -0.4451 | |
| 37 | V | A | -0.1486 | |
| 38 | A | A | 0.0000 | |
| 39 | R | A | -0.3416 | |
| 40 | T | A | -0.0767 | |
| 41 | A | A | 0.0000 | |
| 42 | I | A | 0.0000 | |
| 43 | L | A | -0.1269 | |
| 44 | N | A | -0.3284 | |
| 45 | N | A | 0.0000 | |
| 46 | I | A | 0.0000 | |
| 47 | G | A | 0.0000 | |
| 48 | A | A | -1.5853 | |
| 49 | D | A | -1.9271 | |
| 50 | G | A | 0.0000 | |
| 51 | A | A | -0.2323 | |
| 52 | W | A | 0.1290 | |
| 53 | V | A | 0.0000 | |
| 54 | S | A | -0.8151 | |
| 55 | G | A | -1.2921 | |
| 56 | A | A | 0.0000 | |
| 57 | D | A | -2.0342 | |
| 58 | S | A | -1.3553 | |
| 59 | G | A | 0.0000 | |
| 60 | I | A | 0.0000 | |
| 61 | V | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | A | A | 0.0000 | |
| 64 | S | A | 0.0000 | |
| 65 | P | A | -0.5608 | |
| 66 | S | A | -1.4440 | |
| 67 | T | A | -1.7177 | |
| 68 | D | A | -2.9072 | |
| 69 | N | A | -2.6370 | |
| 70 | P | A | -2.2608 | |
| 71 | D | A | -2.1750 | |
| 72 | Y | A | -0.9693 | |
| 73 | F | A | -0.2575 | |
| 74 | Y | A | -0.1404 | |
| 75 | T | A | 0.0000 | |
| 76 | W | A | 0.0000 | |
| 77 | T | A | 0.0000 | |
| 78 | R | A | 0.0000 | |
| 79 | D | A | 0.0000 | |
| 80 | S | A | 0.0000 | |
| 81 | G | A | 0.0000 | |
| 82 | L | A | 0.0000 | |
| 83 | V | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | K | A | -0.2305 | |
| 86 | T | A | 0.0000 | |
| 87 | L | A | 0.0000 | |
| 88 | V | A | 0.0000 | |
| 89 | D | A | 0.0000 | |
| 90 | L | A | -0.7480 | |
| 91 | F | A | 0.0000 | |
| 92 | R | A | -1.3677 | |
| 93 | N | A | -1.7193 | |
| 94 | G | A | -1.4752 | |
| 95 | D | A | -1.0781 | |
| 96 | T | A | -0.7014 | |
| 97 | S | A | -0.3296 | |
| 98 | L | A | 0.0000 | |
| 99 | L | A | -0.1116 | |
| 100 | S | A | -0.3999 | |
| 101 | T | A | -0.4825 | |
| 102 | I | A | 0.0000 | |
| 103 | E | A | -0.6844 | |
| 104 | N | A | -0.9042 | |
| 105 | Y | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | S | A | 0.3401 | |
| 108 | A | A | 0.0000 | |
| 109 | Q | A | 0.0000 | |
| 110 | A | A | 0.0000 | |
| 111 | I | A | 1.4540 | |
| 112 | V | A | 0.0000 | |
| 113 | Q | A | 0.0000 | |
| 114 | G | A | -0.1893 | |
| 115 | I | A | -0.0227 | |
| 116 | S | A | -0.8117 | |
| 117 | N | A | -0.6091 | |
| 118 | P | A | -0.5601 | |
| 119 | S | A | -0.5344 | |
| 120 | G | A | -0.8925 | |
| 121 | D | A | -1.4805 | |
| 122 | L | A | 0.0000 | |
| 123 | S | A | -0.7294 | |
| 124 | S | A | -0.6430 | |
| 125 | G | A | 0.0000 | |
| 126 | A | A | -0.4682 | |
| 127 | G | A | 0.0000 | |
| 128 | L | A | 0.0000 | |
| 129 | G | A | 0.0000 | |
| 130 | E | A | 0.0000 | |
| 131 | P | A | 0.0000 | |
| 132 | K | A | 0.0000 | |
| 133 | F | A | 0.0000 | |
| 134 | N | A | -0.8532 | |
| 135 | V | A | 0.0000 | |
| 136 | D | A | -2.3658 | |
| 137 | E | A | -1.0593 | |
| 138 | T | A | -0.5794 | |
| 139 | A | A | -0.3661 | |
| 140 | Y | A | 0.0172 | |
| 141 | T | A | -0.1662 | |
| 142 | G | A | -0.2001 | |
| 143 | S | A | -0.1984 | |
| 144 | W | A | -0.0796 | |
| 145 | G | A | -0.4845 | |
| 146 | R | A | -0.5025 | |
| 147 | P | A | -0.2928 | |
| 148 | Q | A | 0.0000 | |
| 149 | R | A | 0.0000 | |
| 150 | D | A | 0.0000 | |
| 151 | G | A | 0.0000 | |
| 152 | P | A | 0.0000 | |
| 153 | A | A | 0.0000 | |
| 154 | L | A | 0.0000 | |
| 155 | R | A | 0.0000 | |
| 156 | A | A | 0.0000 | |
| 157 | T | A | 0.0000 | |
| 158 | A | A | 0.0000 | |
| 159 | M | A | 0.0000 | |
| 160 | I | A | 0.0000 | |
| 161 | G | A | 0.0000 | |
| 162 | F | A | 0.0000 | |
| 163 | G | A | 0.0000 | |
| 164 | Q | A | -0.7020 | |
| 165 | W | A | -0.8846 | |
| 166 | L | A | 0.0000 | |
| 167 | L | A | -0.8973 | |
| 168 | D | A | -2.2268 | |
| 169 | N | A | -1.9218 | |
| 170 | G | A | -1.0519 | |
| 171 | Y | A | 0.0665 | |
| 172 | T | A | -0.4271 | |
| 173 | S | A | -0.3508 | |
| 174 | T | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | T | A | -0.7419 | |
| 177 | D | A | -1.7328 | |
| 178 | I | A | -0.4072 | |
| 179 | V | A | 0.0000 | |
| 180 | W | A | 0.0000 | |
| 181 | P | A | -0.5999 | |
| 182 | L | A | 0.0000 | |
| 183 | V | A | 0.0000 | |
| 184 | R | A | -0.5562 | |
| 185 | N | A | 0.0000 | |
| 186 | D | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | S | A | 0.0000 | |
| 189 | Y | A | 0.0000 | |
| 190 | V | A | 0.0000 | |
| 191 | A | A | 0.0000 | |
| 192 | Q | A | 0.1065 | |
| 193 | Y | A | -0.3980 | |
| 194 | W | A | 0.0000 | |
| 195 | N | A | -1.3949 | |
| 196 | Q | A | -1.6174 | |
| 197 | T | A | -0.9119 | |
| 198 | G | A | 0.0000 | |
| 199 | Y | A | -0.4378 | |
| 200 | D | A | 0.0000 | |
| 201 | L | A | 0.0000 | |
| 202 | W | A | 0.0000 | |
| 203 | E | A | -0.8879 | |
| 204 | E | A | -1.2153 | |
| 205 | V | A | -0.9388 | |
| 206 | N | A | -1.2728 | |
| 207 | G | A | -1.0605 | |
| 208 | S | A | -0.6939 | |
| 209 | S | A | 0.0000 | |
| 210 | F | A | 0.0000 | |
| 211 | F | A | 0.0000 | |
| 212 | T | A | 0.0000 | |
| 213 | I | A | 0.0000 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.0000 | |
| 216 | Q | A | 0.0000 | |
| 217 | H | A | 0.0000 | |
| 218 | R | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | L | A | 0.0000 | |
| 221 | V | A | -0.2384 | |
| 222 | E | A | 0.0000 | |
| 223 | G | A | 0.0000 | |
| 224 | S | A | -0.5012 | |
| 225 | A | A | -0.1710 | |
| 226 | F | A | 0.0000 | |
| 227 | A | A | 0.0000 | |
| 228 | T | A | -0.2394 | |
| 229 | A | A | -0.0677 | |
| 230 | V | A | -0.3190 | |
| 231 | G | A | -0.4754 | |
| 232 | S | A | -0.4006 | |
| 233 | S | A | -0.6330 | |
| 234 | C | A | 0.0000 | |
| 235 | S | A | -0.5818 | |
| 236 | W | A | -0.2122 | |
| 237 | C | A | 0.0000 | |
| 238 | D | A | -1.9255 | |
| 239 | S | A | -1.1409 | |
| 240 | Q | A | 0.0000 | |
| 241 | A | A | 0.0000 | |
| 242 | P | A | -0.3240 | |
| 243 | E | A | -0.3364 | |
| 244 | I | A | 0.0000 | |
| 245 | L | A | 0.0000 | |
| 246 | C | A | 0.0000 | |
| 247 | Y | A | 0.2323 | |
| 248 | L | A | 0.0000 | |
| 249 | Q | A | 0.0182 | |
| 250 | S | A | -0.0159 | |
| 251 | F | A | 0.0000 | |
| 252 | W | A | -0.0470 | |
| 253 | T | A | -0.1465 | |
| 254 | G | A | -0.2298 | |
| 255 | S | A | -0.1239 | |
| 256 | F | A | 0.0362 | |
| 257 | I | A | 0.0000 | |
| 258 | L | A | 0.3309 | |
| 259 | A | A | 0.0000 | |
| 260 | N | A | 0.0000 | |
| 261 | F | A | -0.6666 | |
| 262 | D | A | -1.8863 | |
| 263 | S | A | -1.1242 | |
| 264 | S | A | -0.8215 | |
| 265 | R | A | -0.8057 | |
| 266 | S | A | -0.4585 | |
| 267 | G | A | 0.0000 | |
| 268 | K | A | -0.4098 | |
| 269 | D | A | 0.0000 | |
| 270 | A | A | 0.0000 | |
| 271 | N | A | 0.0000 | |
| 272 | T | A | 0.0000 | |
| 273 | L | A | 0.0000 | |
| 274 | L | A | 0.0000 | |
| 275 | G | A | 0.0000 | |
| 276 | S | A | 0.0000 | |
| 277 | I | A | 0.0000 | |
| 278 | H | A | -0.2146 | |
| 279 | T | A | 0.0000 | |
| 280 | F | A | 0.0000 | |
| 281 | D | A | 0.0000 | |
| 282 | P | A | -1.0695 | |
| 283 | E | A | -2.2402 | |
| 284 | A | A | -1.3118 | |
| 285 | A | A | -0.8595 | |
| 286 | C | A | -0.4945 | |
| 287 | D | A | -0.6264 | |
| 288 | D | A | -0.7691 | |
| 289 | S | A | -0.2647 | |
| 290 | T | A | 0.0000 | |
| 291 | F | A | 0.0000 | |
| 292 | Q | A | 0.0000 | |
| 293 | P | A | 0.0000 | |
| 294 | C | A | 0.0000 | |
| 295 | S | A | 0.0000 | |
| 296 | P | A | -0.4847 | |
| 297 | R | A | -0.3248 | |
| 298 | A | A | 0.0000 | |
| 299 | L | A | 0.0000 | |
| 300 | A | A | 0.0000 | |
| 301 | N | A | 0.0000 | |
| 302 | H | A | 0.0000 | |
| 303 | K | A | -1.4492 | |
| 304 | E | A | -1.0526 | |
| 305 | V | A | 0.0000 | |
| 306 | V | A | 0.0000 | |
| 307 | D | A | -1.4843 | |
| 308 | S | A | -0.7026 | |
| 309 | F | A | 0.0000 | |
| 310 | R | A | -0.8865 | |
| 311 | S | A | -0.3523 | |
| 312 | I | A | 0.3890 | |
| 313 | Y | A | 0.0000 | |
| 314 | T | A | -0.9212 | |
| 315 | L | A | -0.9173 | |
| 316 | N | A | 0.0000 | |
| 317 | D | A | -1.8191 | |
| 318 | G | A | -1.4841 | |
| 319 | L | A | -1.1390 | |
| 320 | S | A | -1.5341 | |
| 321 | D | A | -2.3646 | |
| 322 | S | A | -1.5069 | |
| 323 | E | A | -1.7332 | |
| 324 | A | A | 0.0000 | |
| 325 | V | A | 0.0000 | |
| 326 | A | A | 0.0000 | |
| 327 | V | A | 0.0000 | |
| 328 | G | A | 0.0000 | |
| 329 | R | A | 0.0000 | |
| 330 | Y | A | 0.0000 | |
| 331 | P | A | -0.3406 | |
| 332 | E | A | -0.8511 | |
| 333 | D | A | 0.0000 | |
| 334 | T | A | -0.4225 | |
| 335 | Y | A | 0.1621 | |
| 336 | Y | A | 0.1350 | |
| 337 | N | A | -1.0361 | |
| 338 | G | A | 0.0000 | |
| 339 | N | A | 0.0000 | |
| 340 | P | A | 0.0000 | |
| 341 | W | A | 0.0000 | |
| 342 | F | A | 0.0000 | |
| 343 | L | A | 0.0000 | |
| 344 | C | A | 0.0000 | |
| 345 | T | A | 0.0000 | |
| 346 | L | A | 0.0000 | |
| 347 | A | A | 0.0000 | |
| 348 | A | A | 0.0000 | |
| 349 | A | A | 0.0000 | |
| 350 | E | A | 0.0000 | |
| 351 | Q | A | 0.0000 | |
| 352 | L | A | 0.0000 | |
| 353 | Y | A | 0.0000 | |
| 354 | D | A | 0.0000 | |
| 355 | A | A | 0.0000 | |
| 356 | L | A | -0.9207 | |
| 357 | Y | A | -1.1807 | |
| 358 | Q | A | 0.0000 | |
| 359 | W | A | 0.0000 | |
| 360 | D | A | -2.9935 | |
| 361 | K | A | -3.3935 | |
| 362 | Q | A | -2.8264 | |
| 363 | G | A | -1.9037 | |
| 364 | S | A | -1.6475 | |
| 365 | L | A | 0.0000 | |
| 366 | E | A | -1.9837 | |
| 367 | V | A | 0.0000 | |
| 368 | T | A | -1.1877 | |
| 369 | D | A | -1.6370 | |
| 370 | V | A | -0.1343 | |
| 371 | S | A | 0.0000 | |
| 372 | L | A | -1.3656 | |
| 373 | D | A | -2.1088 | |
| 374 | F | A | 0.0000 | |
| 375 | F | A | 0.0000 | |
| 376 | K | A | -2.1220 | |
| 377 | A | A | -1.8044 | |
| 378 | L | A | -1.3435 | |
| 379 | Y | A | -1.1043 | |
| 380 | S | A | -1.4769 | |
| 381 | D | A | -2.0325 | |
| 382 | A | A | 0.0000 | |
| 383 | A | A | -1.2674 | |
| 384 | T | A | -0.6888 | |
| 385 | G | A | -0.8281 | |
| 386 | T | A | -0.8567 | |
| 387 | Y | A | -0.5362 | |
| 388 | S | A | -1.0023 | |
| 389 | S | A | -1.1321 | |
| 390 | S | A | -0.4135 | |
| 391 | S | A | -0.3587 | |
| 392 | S | A | -0.3663 | |
| 393 | T | A | -0.4108 | |
| 394 | Y | A | 0.0000 | |
| 395 | S | A | -0.7002 | |
| 396 | S | A | -0.8517 | |
| 397 | I | A | 0.0000 | |
| 398 | V | A | -1.0239 | |
| 399 | D | A | -1.9305 | |
| 400 | A | A | -1.1382 | |
| 401 | V | A | 0.0000 | |
| 402 | K | A | -1.4071 | |
| 403 | T | A | -1.1711 | |
| 404 | F | A | 0.0000 | |
| 405 | A | A | 0.0000 | |
| 406 | D | A | -0.7784 | |
| 407 | G | A | -0.6579 | |
| 408 | F | A | 0.0000 | |
| 409 | V | A | 0.0000 | |
| 410 | S | A | -0.2968 | |
| 411 | I | A | -0.1050 | |
| 412 | V | A | 0.0000 | |
| 413 | E | A | -0.6079 | |
| 414 | T | A | -0.5765 | |
| 415 | H | A | -1.1182 | |
| 416 | A | A | -0.8157 | |
| 417 | A | A | -0.9069 | |
| 418 | S | A | -0.9089 | |
| 419 | N | A | -1.2947 | |
| 420 | G | A | 0.0000 | |
| 421 | S | A | -0.7130 | |
| 422 | M | A | 0.0000 | |
| 423 | S | A | 0.0000 | |
| 424 | E | A | 0.0000 | |
| 425 | Q | A | 0.0000 | |
| 426 | Y | A | 0.0000 | |
| 427 | D | A | -1.8559 | |
| 428 | K | A | -1.2595 | |
| 429 | S | A | -1.5965 | |
| 430 | D | A | -2.5659 | |
| 431 | G | A | 0.0000 | |
| 432 | E | A | -2.6348 | |
| 433 | Q | A | -1.6695 | |
| 434 | L | A | -0.7918 | |
| 435 | S | A | -0.8125 | |
| 436 | A | A | 0.0000 | |
| 437 | R | A | -1.9847 | |
| 438 | D | A | 0.0000 | |
| 439 | L | A | 0.0000 | |
| 440 | T | A | 0.0000 | |
| 441 | W | A | 0.0000 | |
| 442 | S | A | 0.0000 | |
| 443 | Y | A | 0.0000 | |
| 444 | A | A | 0.0000 | |
| 445 | A | A | -0.0347 | |
| 446 | L | A | 0.0000 | |
| 447 | L | A | 0.0000 | |
| 448 | T | A | -0.0575 | |
| 449 | A | A | 0.0000 | |
| 450 | N | A | -0.7826 | |
| 451 | N | A | -0.5621 | |
| 452 | R | A | 0.0000 | |
| 453 | R | A | -1.1398 | |
| 454 | N | A | -1.5126 | |
| 455 | S | A | -0.7930 | |
| 456 | V | A | -0.1927 | |
| 457 | V | A | 0.1395 | |
| 458 | P | A | 0.0000 | |
| 459 | A | A | -0.4215 | |
| 460 | S | A | -0.5412 | |
| 461 | W | A | 0.0000 | |
| 462 | G | A | -0.4709 | |
| 463 | E | A | 0.0000 | |
| 464 | T | A | -0.6688 | |
| 465 | S | A | -0.3014 | |
| 466 | A | A | -0.0553 | |
| 467 | S | A | -0.1531 | |
| 468 | S | A | 0.1373 | |
| 469 | V | A | 0.8078 | |
| 470 | P | A | 0.2182 | |
| 471 | G | A | -0.2208 | |
| 472 | T | A | 0.1444 | |
| 473 | C | A | 0.6080 | |
| 474 | A | A | 0.1309 | |
| 475 | A | A | -0.1704 | |
| 476 | T | A | -0.3927 | |
| 477 | S | A | -0.1445 | |
| 478 | A | A | 0.5916 | |
| 479 | I | A | 1.8840 | |
| 480 | G | A | 0.7579 | |
| 481 | T | A | 0.2882 | |
| 482 | Y | A | 0.0901 | |
| 483 | S | A | -0.3192 | |
| 484 | S | A | 0.0482 | |
| 485 | V | A | 0.3027 | |
| 486 | T | A | 0.7202 | |
| 487 | V | A | 1.4922 | |
| 488 | T | A | 0.4124 | |
| 489 | S | A | 0.4822 | |
| 490 | W | A | 0.9133 | |
| 491 | P | A | 0.0829 |
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 | -0.169 | 3.2978 | View | CSV | PDB |
| 4.5 | -0.2229 | 3.2978 | View | CSV | PDB |
| 5.0 | -0.2872 | 3.2978 | View | CSV | PDB |
| 5.5 | -0.3559 | 3.2978 | View | CSV | PDB |
| 6.0 | -0.4238 | 3.2978 | View | CSV | PDB |
| 6.5 | -0.4866 | 3.2978 | View | CSV | PDB |
| 7.0 | -0.5424 | 3.2978 | View | CSV | PDB |
| 7.5 | -0.5912 | 3.2978 | View | CSV | PDB |
| 8.0 | -0.6333 | 3.2978 | View | CSV | PDB |
| 8.5 | -0.6668 | 3.2978 | View | CSV | PDB |
| 9.0 | -0.6885 | 3.2978 | 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