| Chain sequence(s) |
A: MMRVRFPLLVLLGTVFLASVCVSLKVREDENNPFYLRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQQQKQKQEEEPLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDAQPQQKEEGSKGRKGPFPSILGALY
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MMRVRFPLLVLLGTVFLASVCVS LKVREDENNPFYLRSSNSFQTLFENQNGRIRLLQRFNKRSPQLENLRDYRIVQFQSKPNTILLPHHADADFLLFVLSGRAILTLVNNDDRDSYNLHPGDAQRIPAGTTYYLVNPHDHQNLKIIKLAIPVNKPGRYDDFFLSSTQAQQSYLQGFSHNILETSFHSEFEEINRVLFGEEEEQRQQEGVIVELSKEQIRQLSRRAKSSSRKTISSEDEPFNLRSRNPIYSNNFGKFFEITPEKNPQLRDLDIFLSSVDINEGALLLPHFNSKAIVILVINEGDANIELVGIKEQQQKQKQEEEPLEVQRYRAELSEDDVFVIPAAYPFVVNATSNLNFLAFGINAENNQRNFLAGEKDNVVRQIERQVQELAFPGSAQDVERLLKKQRESYFVDAQPQQKEEGSKGRKGPFPSILGALY(Red indicates removed residues) |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB: Running AlphaCutter (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:09)
[INFO] FoldX: Starting FoldX energy minimization (00:00:09)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:07:55)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/44bfff3d1473ef6/tmp/folded.pdb (00:07:55)
[INFO] Main: Simulation completed successfully. (00:13:55)
|
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 |
|---|---|---|---|---|
| 24 | L | A | 0.6692 | |
| 25 | K | A | -1.2641 | |
| 26 | V | A | -1.1164 | |
| 27 | R | A | -2.7794 | |
| 28 | E | A | -3.9003 | |
| 29 | D | A | -3.4488 | |
| 30 | E | A | -3.4856 | |
| 31 | N | A | -3.1000 | |
| 32 | N | A | 0.0000 | |
| 33 | P | A | -1.6597 | |
| 34 | F | A | 0.0000 | |
| 35 | Y | A | 0.0000 | |
| 36 | L | A | 0.0000 | |
| 37 | R | A | -2.3613 | |
| 38 | S | A | -1.5637 | |
| 39 | S | A | -1.3195 | |
| 40 | N | A | -1.9072 | |
| 41 | S | A | 0.0000 | |
| 42 | F | A | -1.0690 | |
| 43 | Q | A | -1.1455 | |
| 44 | T | A | -0.5289 | |
| 45 | L | A | 0.3260 | |
| 46 | F | A | -0.5023 | |
| 47 | E | A | -2.1504 | |
| 48 | N | A | -2.0052 | |
| 49 | Q | A | -2.2984 | |
| 50 | N | A | 0.0000 | |
| 51 | G | A | -1.9471 | |
| 52 | R | A | -1.6529 | |
| 53 | I | A | 0.0000 | |
| 54 | R | A | -0.5557 | |
| 55 | L | A | -0.1767 | |
| 56 | L | A | 0.0000 | |
| 57 | Q | A | -1.5070 | |
| 58 | R | A | -2.2166 | |
| 59 | F | A | 0.0000 | |
| 60 | N | A | -3.0094 | |
| 61 | K | A | -2.9494 | |
| 62 | R | A | -2.1427 | |
| 63 | S | A | 0.0000 | |
| 64 | P | A | -2.1707 | |
| 65 | Q | A | -2.2763 | |
| 66 | L | A | 0.0000 | |
| 67 | E | A | -3.4422 | |
| 68 | N | A | -2.6330 | |
| 69 | L | A | 0.0000 | |
| 70 | R | A | -3.0465 | |
| 71 | D | A | -1.8810 | |
| 72 | Y | A | -0.9280 | |
| 73 | R | A | 0.0000 | |
| 74 | I | A | 0.0000 | |
| 75 | V | A | 0.0000 | |
| 76 | Q | A | 0.0000 | |
| 77 | F | A | 0.0000 | |
| 78 | Q | A | -1.2453 | |
| 79 | S | A | 0.0000 | |
| 80 | K | A | -2.8326 | |
| 81 | P | A | -2.6472 | |
| 82 | N | A | -2.0177 | |
| 83 | T | A | 0.0000 | |
| 84 | I | A | 0.0000 | |
| 85 | L | A | 0.0000 | |
| 86 | L | A | 0.0000 | |
| 87 | P | A | 0.3555 | |
| 88 | H | A | 0.0000 | |
| 89 | H | A | -0.3556 | |
| 90 | A | A | 0.0000 | |
| 91 | D | A | -1.0627 | |
| 92 | A | A | 0.0000 | |
| 93 | D | A | 0.0687 | |
| 94 | F | A | 0.0000 | |
| 95 | L | A | 0.0000 | |
| 96 | L | A | 0.0000 | |
| 97 | F | A | 0.0000 | |
| 98 | V | A | 0.0000 | |
| 99 | L | A | 0.0000 | |
| 100 | S | A | -1.1193 | |
| 101 | G | A | -1.8629 | |
| 102 | R | A | -1.9449 | |
| 103 | A | A | 0.0000 | |
| 104 | I | A | 0.0000 | |
| 105 | L | A | 0.0000 | |
| 106 | T | A | 0.0000 | |
| 107 | L | A | 0.0000 | |
| 108 | V | A | -1.7662 | |
| 109 | N | A | -3.3099 | |
| 110 | N | A | -3.3484 | |
| 111 | D | A | -3.8488 | |
| 112 | D | A | -4.0841 | |
| 113 | R | A | -3.4533 | |
| 114 | D | A | -2.3315 | |
| 115 | S | A | 0.0000 | |
| 116 | Y | A | 0.0000 | |
| 117 | N | A | -1.2947 | |
| 118 | L | A | 0.0000 | |
| 119 | H | A | -0.9431 | |
| 120 | P | A | -0.7882 | |
| 121 | G | A | 0.0000 | |
| 122 | D | A | 0.0000 | |
| 123 | A | A | 0.0000 | |
| 124 | Q | A | 0.0000 | |
| 125 | R | A | -1.1726 | |
| 126 | I | A | 0.0000 | |
| 127 | P | A | -0.5753 | |
| 128 | A | A | -0.0944 | |
| 129 | G | A | -0.5678 | |
| 130 | T | A | -0.6717 | |
| 131 | T | A | -0.4078 | |
| 132 | Y | A | 0.0000 | |
| 133 | Y | A | 0.1793 | |
| 134 | L | A | 0.0000 | |
| 135 | V | A | 0.0000 | |
| 136 | N | A | 0.0000 | |
| 137 | P | A | -1.6893 | |
| 138 | H | A | -2.3878 | |
| 139 | D | A | -2.7538 | |
| 140 | H | A | -2.7431 | |
| 141 | Q | A | -3.1008 | |
| 142 | N | A | -3.0209 | |
| 143 | L | A | 0.0000 | |
| 144 | K | A | -1.1616 | |
| 145 | I | A | 0.0000 | |
| 146 | I | A | 0.0000 | |
| 147 | K | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | A | A | 0.0000 | |
| 150 | I | A | -0.1745 | |
| 151 | P | A | 0.0000 | |
| 152 | V | A | 0.2749 | |
| 153 | N | A | -1.7851 | |
| 154 | K | A | -2.8888 | |
| 155 | P | A | -1.9704 | |
| 156 | G | A | 0.0000 | |
| 157 | R | A | -2.9990 | |
| 158 | Y | A | -2.0335 | |
| 159 | D | A | -2.5823 | |
| 160 | D | A | -0.9193 | |
| 161 | F | A | 0.0941 | |
| 162 | F | A | 0.3515 | |
| 163 | L | A | 0.8226 | |
| 164 | S | A | 0.2490 | |
| 165 | S | A | -0.7831 | |
| 166 | T | A | 0.0000 | |
| 167 | Q | A | -3.3664 | |
| 168 | A | A | -1.4144 | |
| 169 | Q | A | -1.1592 | |
| 170 | Q | A | -1.4793 | |
| 171 | S | A | 0.0000 | |
| 172 | Y | A | 0.6567 | |
| 173 | L | A | 0.6914 | |
| 174 | Q | A | -0.0844 | |
| 175 | G | A | -0.0285 | |
| 176 | F | A | 1.0672 | |
| 177 | S | A | 0.0207 | |
| 178 | H | A | -1.4647 | |
| 179 | N | A | -1.1994 | |
| 180 | I | A | 0.9661 | |
| 181 | L | A | 0.0000 | |
| 182 | E | A | -1.7524 | |
| 183 | T | A | -0.6533 | |
| 184 | S | A | -0.0345 | |
| 185 | F | A | 0.0860 | |
| 186 | H | A | -0.9586 | |
| 187 | S | A | -1.9650 | |
| 188 | E | A | -3.3815 | |
| 189 | F | A | -2.5711 | |
| 190 | E | A | -3.3593 | |
| 191 | E | A | -3.0328 | |
| 192 | I | A | 0.0000 | |
| 193 | N | A | 0.0000 | |
| 194 | R | A | -2.4840 | |
| 195 | V | A | 0.4999 | |
| 196 | L | A | 0.7032 | |
| 197 | F | A | 0.0000 | |
| 198 | G | A | 0.0000 | |
| 199 | E | A | -4.0282 | |
| 200 | E | A | -4.1886 | |
| 201 | E | A | -4.4097 | |
| 202 | E | A | -4.9414 | |
| 203 | Q | A | -4.1136 | |
| 204 | R | A | -4.3030 | |
| 205 | Q | A | -3.6742 | |
| 206 | Q | A | -3.0256 | |
| 207 | E | A | -3.2298 | |
| 208 | G | A | 0.0000 | |
| 209 | V | A | 0.0000 | |
| 210 | I | A | 0.0000 | |
| 211 | V | A | -1.4463 | |
| 212 | E | A | -2.2257 | |
| 213 | L | A | -1.5079 | |
| 214 | S | A | -1.8098 | |
| 215 | K | A | -2.6941 | |
| 216 | E | A | -3.1528 | |
| 217 | Q | A | -2.5869 | |
| 218 | I | A | 0.0000 | |
| 219 | R | A | -3.3690 | |
| 220 | Q | A | -3.2638 | |
| 221 | L | A | -2.1570 | |
| 222 | S | A | -2.6592 | |
| 223 | R | A | -3.5264 | |
| 224 | R | A | -3.6161 | |
| 225 | A | A | -2.2556 | |
| 226 | K | A | -2.3875 | |
| 227 | S | A | -1.3104 | |
| 228 | S | A | -1.3751 | |
| 229 | S | A | -1.8992 | |
| 230 | R | A | -3.2191 | |
| 231 | K | A | -2.7325 | |
| 232 | T | A | 0.0000 | |
| 233 | I | A | 0.0000 | |
| 234 | S | A | -2.0243 | |
| 235 | S | A | -2.1510 | |
| 236 | E | A | -3.3143 | |
| 237 | D | A | -2.9933 | |
| 238 | E | A | -2.2510 | |
| 239 | P | A | 0.0000 | |
| 240 | F | A | 0.0000 | |
| 241 | N | A | -1.1997 | |
| 242 | L | A | 0.0000 | |
| 243 | R | A | -1.9892 | |
| 244 | S | A | -2.3708 | |
| 245 | R | A | -2.9885 | |
| 246 | N | A | -2.2264 | |
| 247 | P | A | -1.0402 | |
| 248 | I | A | 0.3918 | |
| 249 | Y | A | 0.0372 | |
| 250 | S | A | -0.8371 | |
| 251 | N | A | -1.3128 | |
| 252 | N | A | -1.7718 | |
| 253 | F | A | -1.4219 | |
| 254 | G | A | 0.0000 | |
| 255 | K | A | -1.3515 | |
| 256 | F | A | 0.0000 | |
| 257 | F | A | 0.0000 | |
| 258 | E | A | -0.6927 | |
| 259 | I | A | 0.0000 | |
| 260 | T | A | -1.6761 | |
| 261 | P | A | 0.0000 | |
| 262 | E | A | -2.7129 | |
| 263 | K | A | -2.1936 | |
| 264 | N | A | 0.0000 | |
| 265 | P | A | -2.7322 | |
| 266 | Q | A | 0.0000 | |
| 267 | L | A | 0.0000 | |
| 268 | R | A | -3.8871 | |
| 269 | D | A | -3.0777 | |
| 270 | L | A | -1.8885 | |
| 271 | D | A | -2.6201 | |
| 272 | I | A | 0.0000 | |
| 273 | F | A | 0.0000 | |
| 274 | L | A | 0.0000 | |
| 275 | S | A | 0.0000 | |
| 276 | S | A | 0.0000 | |
| 277 | V | A | 0.0000 | |
| 278 | D | A | -1.4370 | |
| 279 | I | A | 0.0000 | |
| 280 | N | A | -2.7499 | |
| 281 | E | A | -3.0995 | |
| 282 | G | A | -1.9177 | |
| 283 | A | A | 0.0000 | |
| 284 | L | A | -0.5636 | |
| 285 | L | A | 0.0000 | |
| 286 | L | A | 0.0000 | |
| 287 | P | A | 0.1834 | |
| 288 | H | A | 0.0000 | |
| 289 | F | A | 0.1034 | |
| 290 | N | A | 0.0000 | |
| 291 | S | A | -0.9810 | |
| 292 | K | A | -1.2885 | |
| 293 | A | A | 0.0000 | |
| 294 | I | A | -0.2154 | |
| 295 | V | A | 0.0000 | |
| 296 | I | A | 0.0000 | |
| 297 | L | A | 0.0000 | |
| 298 | V | A | 0.0000 | |
| 299 | I | A | 0.0000 | |
| 300 | N | A | 0.0000 | |
| 301 | E | A | -2.5072 | |
| 302 | G | A | -2.4155 | |
| 303 | D | A | -2.5283 | |
| 304 | A | A | 0.0000 | |
| 305 | N | A | -1.6055 | |
| 306 | I | A | 0.0000 | |
| 307 | E | A | -1.1023 | |
| 308 | L | A | 0.0000 | |
| 309 | V | A | 0.8941 | |
| 310 | G | A | 0.0000 | |
| 311 | I | A | 1.1516 | |
| 312 | K | A | -1.0332 | |
| 313 | E | A | -2.4990 | |
| 314 | Q | A | -2.9065 | |
| 315 | Q | A | -3.2891 | |
| 316 | Q | A | -3.6478 | |
| 317 | K | A | -4.1122 | |
| 318 | Q | A | -3.8083 | |
| 319 | K | A | -4.5090 | |
| 320 | Q | A | -3.9613 | |
| 321 | E | A | -4.5715 | |
| 322 | E | A | -3.7711 | |
| 323 | E | A | -3.4065 | |
| 324 | P | A | -1.4075 | |
| 325 | L | A | 0.2823 | |
| 326 | E | A | -0.2947 | |
| 327 | V | A | 1.0431 | |
| 328 | Q | A | 0.0000 | |
| 329 | R | A | -0.5494 | |
| 330 | Y | A | -1.4789 | |
| 331 | R | A | -2.3646 | |
| 332 | A | A | 0.0000 | |
| 333 | E | A | -2.8602 | |
| 334 | L | A | 0.0000 | |
| 335 | S | A | -2.2443 | |
| 336 | E | A | -2.7163 | |
| 337 | D | A | -1.5242 | |
| 338 | D | A | 0.0000 | |
| 339 | V | A | 0.0000 | |
| 340 | F | A | 0.0000 | |
| 341 | V | A | 0.0000 | |
| 342 | I | A | 0.0000 | |
| 343 | P | A | 0.0000 | |
| 344 | A | A | -0.0741 | |
| 345 | A | A | 0.0062 | |
| 346 | Y | A | 0.6900 | |
| 347 | P | A | 0.3804 | |
| 348 | F | A | 0.0000 | |
| 349 | V | A | -0.0153 | |
| 350 | V | A | 0.0000 | |
| 351 | N | A | -1.2550 | |
| 352 | A | A | 0.0000 | |
| 353 | T | A | -1.7518 | |
| 354 | S | A | -2.2747 | |
| 355 | N | A | -2.9721 | |
| 356 | L | A | 0.0000 | |
| 357 | N | A | -1.5771 | |
| 358 | F | A | 0.0000 | |
| 359 | L | A | 0.0000 | |
| 360 | A | A | 0.0000 | |
| 361 | F | A | 0.0000 | |
| 362 | G | A | 0.0000 | |
| 363 | I | A | 0.0000 | |
| 364 | N | A | -1.6320 | |
| 365 | A | A | 0.0000 | |
| 366 | E | A | -2.8704 | |
| 367 | N | A | -2.6119 | |
| 368 | N | A | -2.0792 | |
| 369 | Q | A | -2.0046 | |
| 370 | R | A | -1.1222 | |
| 371 | N | A | -0.9705 | |
| 372 | F | A | 0.0000 | |
| 373 | L | A | -0.0896 | |
| 374 | A | A | -1.2017 | |
| 375 | G | A | 0.0000 | |
| 376 | E | A | -3.8370 | |
| 377 | K | A | -3.3312 | |
| 378 | D | A | -2.6287 | |
| 379 | N | A | 0.0000 | |
| 380 | V | A | -0.4961 | |
| 381 | V | A | -0.4214 | |
| 382 | R | A | -2.1251 | |
| 383 | Q | A | -1.9219 | |
| 384 | I | A | -1.3814 | |
| 385 | E | A | -3.1607 | |
| 386 | R | A | -3.6752 | |
| 387 | Q | A | -2.3953 | |
| 388 | V | A | -0.7054 | |
| 389 | Q | A | 0.0000 | |
| 390 | E | A | -2.0024 | |
| 391 | L | A | 0.5757 | |
| 392 | A | A | 0.4263 | |
| 393 | F | A | 0.4763 | |
| 394 | P | A | -0.1833 | |
| 395 | G | A | -0.7838 | |
| 396 | S | A | -1.7347 | |
| 397 | A | A | -2.3927 | |
| 398 | Q | A | -2.4579 | |
| 399 | D | A | -1.7545 | |
| 400 | V | A | -1.4739 | |
| 401 | E | A | -2.3306 | |
| 402 | R | A | -2.3540 | |
| 403 | L | A | -0.5770 | |
| 404 | L | A | -1.5365 | |
| 405 | K | A | -3.0028 | |
| 406 | K | A | -3.0479 | |
| 407 | Q | A | -2.8741 | |
| 408 | R | A | -3.7594 | |
| 409 | E | A | -3.0245 | |
| 410 | S | A | -2.1751 | |
| 411 | Y | A | 0.0000 | |
| 412 | F | A | 0.0000 | |
| 413 | V | A | 0.0000 | |
| 414 | D | A | -1.6557 | |
| 415 | A | A | -1.3235 | |
| 416 | Q | A | -2.6167 | |
| 417 | P | A | -2.8566 | |
| 418 | Q | A | -3.8249 | |
| 419 | Q | A | -4.1621 | |
| 420 | K | A | -4.7631 | |
| 421 | E | A | -5.0265 | |
| 422 | E | A | -4.6736 | |
| 423 | G | A | -3.7189 | |
| 424 | S | A | -3.6434 | |
| 425 | K | A | -4.1215 | |
| 426 | G | A | -3.4239 | |
| 427 | R | A | -3.6447 | |
| 428 | K | A | -3.0754 | |
| 429 | G | A | -1.5867 | |
| 430 | P | A | -0.2890 | |
| 431 | F | A | 1.5411 | |
| 432 | P | A | 1.1574 | |
| 433 | S | A | 1.4791 | |
| 434 | I | A | 2.7570 | |
| 435 | L | A | 2.4172 | |
| 436 | G | A | 1.2853 | |
| 437 | A | A | 1.5484 | |
| 438 | L | A | 2.3512 | |
| 439 | Y | A | 2.0815 |
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 | -1.1202 | 5.5032 | View | CSV | PDB |
| 4.5 | -1.2088 | 5.5048 | View | CSV | PDB |
| 5.0 | -1.3252 | 5.5096 | View | CSV | PDB |
| 5.5 | -1.4474 | 5.5226 | View | CSV | PDB |
| 6.0 | -1.5514 | 5.552 | View | CSV | PDB |
| 6.5 | -1.6179 | 5.6014 | View | CSV | PDB |
| 7.0 | -1.6419 | 5.6649 | View | CSV | PDB |
| 7.5 | -1.6355 | 5.7348 | View | CSV | PDB |
| 8.0 | -1.6135 | 5.8069 | View | CSV | PDB |
| 8.5 | -1.5833 | 5.8796 | View | CSV | PDB |
| 9.0 | -1.5461 | 5.9518 | 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