| 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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:02:57)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/14a9bdd613c7e7c/tmp/folded.pdb (00:02:57)
[INFO] Main: Simulation completed successfully. (00:05:03)
|
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 | -0.3706 | |
| 26 | T | A | -0.4025 | |
| 27 | L | A | -0.7439 | |
| 28 | D | A | -1.8501 | |
| 29 | S | A | -1.1051 | |
| 30 | W | A | -0.8852 | |
| 31 | L | A | 0.0000 | |
| 32 | S | A | -1.2004 | |
| 33 | N | A | -1.2536 | |
| 34 | E | A | -0.7165 | |
| 35 | A | A | 0.0000 | |
| 36 | T | A | -0.0107 | |
| 37 | V | A | 1.0467 | |
| 38 | A | A | 0.0000 | |
| 39 | R | A | -0.0446 | |
| 40 | T | A | 0.2476 | |
| 41 | A | A | 0.1543 | |
| 42 | I | A | 0.0000 | |
| 43 | L | A | -0.2979 | |
| 44 | N | A | -0.5597 | |
| 45 | N | A | 0.0000 | |
| 46 | I | A | 0.0000 | |
| 47 | G | A | 0.0000 | |
| 48 | A | A | -1.6387 | |
| 49 | D | A | -1.9152 | |
| 50 | G | A | 0.0000 | |
| 51 | A | A | -0.0024 | |
| 52 | W | A | 0.7817 | |
| 53 | V | A | 0.0000 | |
| 54 | S | A | -0.5211 | |
| 55 | G | A | -1.1954 | |
| 56 | A | A | 0.0000 | |
| 57 | D | A | -2.4880 | |
| 58 | S | A | -1.3484 | |
| 59 | G | A | 0.0000 | |
| 60 | I | A | -0.4668 | |
| 61 | V | A | 0.0000 | |
| 62 | V | A | 0.0000 | |
| 63 | A | A | 0.0000 | |
| 64 | S | A | 0.0000 | |
| 65 | P | A | -0.2838 | |
| 66 | S | A | -1.0827 | |
| 67 | T | A | -1.4710 | |
| 68 | D | A | -2.8193 | |
| 69 | N | A | -2.7086 | |
| 70 | P | A | -1.9573 | |
| 71 | D | A | -2.1409 | |
| 72 | Y | A | -0.8067 | |
| 73 | F | A | -0.2257 | |
| 74 | Y | A | -0.0209 | |
| 75 | T | A | -0.0199 | |
| 76 | W | A | 0.0000 | |
| 77 | T | A | 0.0000 | |
| 78 | R | A | 0.0000 | |
| 79 | D | A | -0.2548 | |
| 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 | -0.2573 | |
| 86 | T | A | 0.0000 | |
| 87 | L | A | 0.0000 | |
| 88 | V | A | 0.0000 | |
| 89 | D | A | -0.7223 | |
| 90 | L | A | -0.6842 | |
| 91 | F | A | 0.0000 | |
| 92 | R | A | -1.5926 | |
| 93 | N | A | -1.5998 | |
| 94 | G | A | -1.4696 | |
| 95 | D | A | -1.1494 | |
| 96 | T | A | -0.7225 | |
| 97 | S | A | -0.3839 | |
| 98 | L | A | 0.0000 | |
| 99 | L | A | -0.2246 | |
| 100 | S | A | -0.5616 | |
| 101 | T | A | -0.4351 | |
| 102 | I | A | 0.0000 | |
| 103 | E | A | -0.9959 | |
| 104 | N | A | -1.1258 | |
| 105 | Y | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | S | A | 0.2302 | |
| 108 | A | A | 0.0000 | |
| 109 | Q | A | 0.0000 | |
| 110 | A | A | 0.0000 | |
| 111 | I | A | 1.9309 | |
| 112 | V | A | 0.8463 | |
| 113 | Q | A | 0.0000 | |
| 114 | G | A | 0.6515 | |
| 115 | I | A | 0.3876 | |
| 116 | S | A | -0.2364 | |
| 117 | N | A | -0.3643 | |
| 118 | P | A | -0.5345 | |
| 119 | S | A | -0.4765 | |
| 120 | G | A | -0.5805 | |
| 121 | D | A | -0.7159 | |
| 122 | L | A | 0.0000 | |
| 123 | S | A | -0.4359 | |
| 124 | S | A | -0.4702 | |
| 125 | G | A | -0.0729 | |
| 126 | A | A | -0.3423 | |
| 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 | -0.2338 | |
| 134 | N | A | -1.1216 | |
| 135 | V | A | 0.0000 | |
| 136 | D | A | -3.0449 | |
| 137 | E | A | -2.7589 | |
| 138 | T | A | -1.3181 | |
| 139 | A | A | -0.6392 | |
| 140 | Y | A | -0.1962 | |
| 141 | T | A | -0.2043 | |
| 142 | G | A | -0.3474 | |
| 143 | S | A | -0.1978 | |
| 144 | W | A | -0.1383 | |
| 145 | G | A | -0.6456 | |
| 146 | R | A | -0.6926 | |
| 147 | P | A | -0.5137 | |
| 148 | Q | A | 0.0000 | |
| 149 | R | A | -0.3592 | |
| 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 | -1.1632 | |
| 165 | W | A | -1.2702 | |
| 166 | L | A | 0.0000 | |
| 167 | L | A | -1.0045 | |
| 168 | D | A | -2.3439 | |
| 169 | N | A | -1.8828 | |
| 170 | G | A | -1.0260 | |
| 171 | Y | A | -0.1657 | |
| 172 | T | A | -0.5964 | |
| 173 | S | A | -0.5662 | |
| 174 | T | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | T | A | -0.8703 | |
| 177 | D | A | -1.8863 | |
| 178 | I | A | 0.0000 | |
| 179 | V | A | 0.0000 | |
| 180 | W | A | 0.0000 | |
| 181 | P | A | -0.5463 | |
| 182 | L | A | 0.0000 | |
| 183 | V | A | 0.0000 | |
| 184 | R | A | -0.3706 | |
| 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 | 0.3587 | |
| 193 | Y | A | -0.0509 | |
| 194 | W | A | 0.0000 | |
| 195 | N | A | -0.9107 | |
| 196 | Q | A | -0.9472 | |
| 197 | T | A | -0.9138 | |
| 198 | G | A | 0.0000 | |
| 199 | Y | A | -0.8141 | |
| 200 | D | A | 0.0000 | |
| 201 | L | A | -0.1010 | |
| 202 | W | A | -0.3272 | |
| 203 | E | A | -1.0284 | |
| 204 | E | A | -1.7967 | |
| 205 | V | A | -1.1755 | |
| 206 | N | A | -1.5617 | |
| 207 | G | A | 0.0000 | |
| 208 | S | A | 0.0000 | |
| 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 | 0.0000 | |
| 222 | E | A | -0.3424 | |
| 223 | G | A | 0.0000 | |
| 224 | S | A | -0.6392 | |
| 225 | A | A | -0.3961 | |
| 226 | F | A | 0.0000 | |
| 227 | A | A | 0.0000 | |
| 228 | T | A | -0.2143 | |
| 229 | A | A | -0.1138 | |
| 230 | V | A | -0.3148 | |
| 231 | G | A | -0.4333 | |
| 232 | S | A | -0.3424 | |
| 233 | S | A | -0.5450 | |
| 234 | C | A | -0.6662 | |
| 235 | S | A | -0.5940 | |
| 236 | W | A | -0.1832 | |
| 237 | C | A | 0.0000 | |
| 238 | D | A | -1.9557 | |
| 239 | S | A | -1.1181 | |
| 240 | Q | A | 0.0000 | |
| 241 | A | A | -0.6904 | |
| 242 | P | A | -0.4920 | |
| 243 | E | A | -0.4365 | |
| 244 | I | A | 0.0000 | |
| 245 | L | A | 0.0000 | |
| 246 | C | A | 0.0000 | |
| 247 | Y | A | 0.0979 | |
| 248 | L | A | 0.0000 | |
| 249 | Q | A | -0.3095 | |
| 250 | S | A | -0.0828 | |
| 251 | F | A | 0.0000 | |
| 252 | W | A | -0.0850 | |
| 253 | T | A | -0.2012 | |
| 254 | G | A | -0.4287 | |
| 255 | S | A | -0.3046 | |
| 256 | F | A | -0.0676 | |
| 257 | I | A | 0.0000 | |
| 258 | L | A | 0.2336 | |
| 259 | A | A | 0.0000 | |
| 260 | N | A | -0.3989 | |
| 261 | F | A | -0.5115 | |
| 262 | D | A | -1.7856 | |
| 263 | S | A | -1.1179 | |
| 264 | S | A | -0.7452 | |
| 265 | R | A | -1.2003 | |
| 266 | S | A | -0.8054 | |
| 267 | G | A | -0.4119 | |
| 268 | K | A | -0.5707 | |
| 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 | -0.1872 | |
| 279 | T | A | 0.0000 | |
| 280 | F | A | 0.0000 | |
| 281 | D | A | 0.0000 | |
| 282 | P | A | -1.1632 | |
| 283 | E | A | -2.3249 | |
| 284 | A | A | 0.0000 | |
| 285 | A | A | -1.4640 | |
| 286 | C | A | -1.4603 | |
| 287 | D | A | -2.5292 | |
| 288 | D | A | -2.4543 | |
| 289 | S | A | -1.2965 | |
| 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 | -1.0748 | |
| 297 | R | A | -0.9128 | |
| 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 | -0.9388 | |
| 304 | E | A | -1.1862 | |
| 305 | V | A | 0.0000 | |
| 306 | V | A | 0.0000 | |
| 307 | D | A | -1.4796 | |
| 308 | S | A | -0.9046 | |
| 309 | F | A | 0.0000 | |
| 310 | R | A | -1.4824 | |
| 311 | S | A | -0.4173 | |
| 312 | I | A | 0.4148 | |
| 313 | Y | A | 0.0000 | |
| 314 | T | A | -1.0124 | |
| 315 | L | A | -1.0034 | |
| 316 | N | A | 0.0000 | |
| 317 | D | A | -1.8385 | |
| 318 | G | A | -1.2268 | |
| 319 | L | A | -1.2035 | |
| 320 | S | A | -1.6482 | |
| 321 | D | A | -2.5591 | |
| 322 | S | A | -1.7251 | |
| 323 | E | A | -1.8321 | |
| 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 | -0.3440 | |
| 330 | Y | A | -0.7010 | |
| 331 | P | A | -1.0729 | |
| 332 | E | A | -2.0216 | |
| 333 | D | A | -1.0760 | |
| 334 | T | A | -0.5165 | |
| 335 | Y | A | 0.3717 | |
| 336 | Y | A | 0.7567 | |
| 337 | N | A | -0.9110 | |
| 338 | G | A | 0.0000 | |
| 339 | N | A | 0.0000 | |
| 340 | P | A | 0.0000 | |
| 341 | W | A | -0.0913 | |
| 342 | F | A | 0.0000 | |
| 343 | L | A | 0.1733 | |
| 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 | 0.0000 | |
| 357 | Y | A | -1.1332 | |
| 358 | Q | A | 0.0000 | |
| 359 | W | A | 0.0000 | |
| 360 | D | A | -2.9410 | |
| 361 | K | A | -3.4289 | |
| 362 | Q | A | -2.8987 | |
| 363 | G | A | -1.9668 | |
| 364 | S | A | -1.6619 | |
| 365 | L | A | 0.0000 | |
| 366 | E | A | -1.8518 | |
| 367 | V | A | 0.0000 | |
| 368 | T | A | -1.3416 | |
| 369 | D | A | -1.7377 | |
| 370 | V | A | -0.7749 | |
| 371 | S | A | 0.0000 | |
| 372 | L | A | -1.5410 | |
| 373 | D | A | -2.3309 | |
| 374 | F | A | 0.0000 | |
| 375 | F | A | 0.0000 | |
| 376 | K | A | -2.4848 | |
| 377 | A | A | -2.1284 | |
| 378 | L | A | 0.0000 | |
| 379 | Y | A | -1.4583 | |
| 380 | S | A | -1.6185 | |
| 381 | D | A | -2.0969 | |
| 382 | A | A | -1.4560 | |
| 383 | A | A | -1.2282 | |
| 384 | T | A | -0.9204 | |
| 385 | G | A | -0.9413 | |
| 386 | T | A | -0.9631 | |
| 387 | Y | A | -0.6630 | |
| 388 | S | A | -0.7635 | |
| 389 | S | A | -1.0760 | |
| 390 | S | A | -0.4374 | |
| 391 | S | A | -0.3599 | |
| 392 | S | A | -0.3702 | |
| 393 | T | A | -0.6080 | |
| 394 | Y | A | 0.0000 | |
| 395 | S | A | -0.7440 | |
| 396 | S | A | -0.9966 | |
| 397 | I | A | 0.0000 | |
| 398 | V | A | -1.1006 | |
| 399 | D | A | -1.9953 | |
| 400 | A | A | -1.2256 | |
| 401 | V | A | 0.0000 | |
| 402 | K | A | -1.5107 | |
| 403 | T | A | -1.2094 | |
| 404 | F | A | 0.0000 | |
| 405 | A | A | 0.0000 | |
| 406 | D | A | -0.6988 | |
| 407 | G | A | -0.6766 | |
| 408 | F | A | 0.0000 | |
| 409 | V | A | 0.0000 | |
| 410 | S | A | -0.3717 | |
| 411 | I | A | -0.0708 | |
| 412 | V | A | 0.0000 | |
| 413 | E | A | -0.5902 | |
| 414 | T | A | -0.6000 | |
| 415 | H | A | -1.1932 | |
| 416 | A | A | -0.8983 | |
| 417 | A | A | -1.0474 | |
| 418 | S | A | -0.9878 | |
| 419 | N | A | -1.5500 | |
| 420 | G | A | -0.9277 | |
| 421 | S | A | -0.8175 | |
| 422 | M | A | 0.0000 | |
| 423 | S | A | 0.0000 | |
| 424 | E | A | -0.5406 | |
| 425 | Q | A | 0.0000 | |
| 426 | Y | A | 0.0000 | |
| 427 | D | A | -2.1973 | |
| 428 | K | A | -1.4912 | |
| 429 | S | A | -1.9035 | |
| 430 | D | A | -2.7564 | |
| 431 | G | A | 0.0000 | |
| 432 | E | A | -2.8277 | |
| 433 | Q | A | -1.6860 | |
| 434 | L | A | -0.4779 | |
| 435 | S | A | -0.1659 | |
| 436 | A | A | -1.0856 | |
| 437 | R | A | -1.6445 | |
| 438 | D | A | -1.1407 | |
| 439 | L | A | -0.4548 | |
| 440 | T | A | 0.0000 | |
| 441 | W | A | 0.1039 | |
| 442 | S | A | 0.0000 | |
| 443 | Y | A | 0.0000 | |
| 444 | A | A | 0.0000 | |
| 445 | A | A | 0.0160 | |
| 446 | L | A | 0.0000 | |
| 447 | L | A | 0.0000 | |
| 448 | T | A | -0.2447 | |
| 449 | A | A | 0.0000 | |
| 450 | N | A | -1.0999 | |
| 451 | N | A | -0.5114 | |
| 452 | R | A | -0.5430 | |
| 453 | R | A | -1.2992 | |
| 454 | N | A | -1.5548 | |
| 455 | S | A | -0.4090 | |
| 456 | V | A | 0.4467 | |
| 457 | V | A | 0.2389 | |
| 458 | P | A | -0.1377 | |
| 459 | A | A | -0.6406 | |
| 460 | S | A | -0.6519 | |
| 461 | W | A | 0.0000 | |
| 462 | G | A | -0.5667 | |
| 463 | E | A | 0.0000 | |
| 464 | T | A | -0.6206 | |
| 465 | S | A | -0.3674 | |
| 466 | A | A | -0.4469 | |
| 467 | S | A | -0.5585 | |
| 468 | S | A | -0.2693 | |
| 469 | V | A | 0.0229 | |
| 470 | P | A | -0.1735 | |
| 471 | G | A | -0.3855 | |
| 472 | T | A | -0.0728 | |
| 473 | C | A | 0.3566 | |
| 474 | A | A | 0.2823 | |
| 475 | A | A | -0.0348 | |
| 476 | T | A | -0.1862 | |
| 477 | S | A | 0.0770 | |
| 478 | A | A | 0.8707 | |
| 479 | I | A | 1.9488 | |
| 480 | G | A | 0.8720 | |
| 481 | T | A | 0.4884 | |
| 482 | Y | A | 0.3862 | |
| 483 | S | A | -0.0448 | |
| 484 | S | A | -0.1349 | |
| 485 | V | A | 0.7864 | |
| 486 | T | A | 1.0114 | |
| 487 | V | A | 1.9746 | |
| 488 | T | A | 0.5154 | |
| 489 | S | A | -0.0331 | |
| 490 | W | A | -0.2941 | |
| 491 | P | A | -0.3799 |
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 | -0.1725 | 3.4867 | View | CSV | PDB |
| 4.5 | -0.2397 | 3.4533 | View | CSV | PDB |
| 5.0 | -0.3189 | 3.4104 | View | CSV | PDB |
| 5.5 | -0.402 | 3.3633 | View | CSV | PDB |
| 6.0 | -0.4826 | 3.3146 | View | CSV | PDB |
| 6.5 | -0.5552 | 3.2655 | View | CSV | PDB |
| 7.0 | -0.6178 | 3.2163 | View | CSV | PDB |
| 7.5 | -0.6721 | 3.1674 | View | CSV | PDB |
| 8.0 | -0.7195 | 3.1194 | View | CSV | PDB |
| 8.5 | -0.7575 | 3.0744 | View | CSV | PDB |
| 9.0 | -0.7819 | 3.0365 | 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