| Chain sequence(s) |
A: MSDITVTNWAGNITYTAKELLRPHSLDALRALVADSARVRVLGSGHSFNEIADPGDGGVLLSLAGLPSVVDVDTAARTVRVGGGVRYAELARVVHARGLALPNMASLPHISVAGSVATGTHGSGMGNGSLASMVREVELVTADGSTVVIARGDERFGGAVTSLGALGVVTSLTLDLEPAYEMEQHVFTELPLAGLDPATFETVMAAAYSVSLFTDWRAPGFRQVWLKRRTDRPLDGFPYAAPATEKMHPVPGMPAENCTEQFGVPGPWHERLPHFRAEFTPSSGAELGSEYLMPREHALAALHAMDAIRETLAPVLQTCEIRTVAADAQWLSPAYGRDTVAAHFTWVPDTAAVLPVVRRLEEALVPFAARPHWGKVFTVPAGELRALYPRLADFGALARALDPAGKFTNAFVRGVLAG
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:42)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/94c73d40095e2fb/tmp/folded.pdb (00:06:42)
[INFO] Main: Simulation completed successfully. (00:11:55)
|
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 |
|---|---|---|---|---|
| 1 | M | A | 0.5073 | |
| 2 | S | A | -0.7088 | |
| 3 | D | A | -2.0442 | |
| 4 | I | A | -0.6945 | |
| 5 | T | A | -0.6946 | |
| 6 | V | A | 0.0000 | |
| 7 | T | A | -0.0986 | |
| 8 | N | A | 0.0000 | |
| 9 | W | A | -0.3369 | |
| 10 | A | A | -0.5133 | |
| 11 | G | A | -0.6922 | |
| 12 | N | A | -0.9619 | |
| 13 | I | A | -0.4035 | |
| 14 | T | A | -0.5662 | |
| 15 | Y | A | 0.0000 | |
| 16 | T | A | -1.4272 | |
| 17 | A | A | 0.0000 | |
| 18 | K | A | -2.8071 | |
| 19 | E | A | -2.1133 | |
| 20 | L | A | -0.8031 | |
| 21 | L | A | -0.9664 | |
| 22 | R | A | -2.0332 | |
| 23 | P | A | 0.0000 | |
| 24 | H | A | -1.6041 | |
| 25 | S | A | -1.1283 | |
| 26 | L | A | -0.5917 | |
| 27 | D | A | -1.8329 | |
| 28 | A | A | -1.2323 | |
| 29 | L | A | 0.0000 | |
| 30 | R | A | -1.7126 | |
| 31 | A | A | -1.3374 | |
| 32 | L | A | -1.0097 | |
| 33 | V | A | 0.0000 | |
| 34 | A | A | -1.7992 | |
| 35 | D | A | -2.1957 | |
| 36 | S | A | -1.3185 | |
| 37 | A | A | -0.9199 | |
| 38 | R | A | -1.5801 | |
| 39 | V | A | 0.0000 | |
| 40 | R | A | 0.0000 | |
| 41 | V | A | 0.3547 | |
| 42 | L | A | 0.0000 | |
| 43 | G | A | -0.5390 | |
| 44 | S | A | -0.4239 | |
| 45 | G | A | -0.2403 | |
| 46 | H | A | -0.3356 | |
| 47 | S | A | -0.3697 | |
| 48 | F | A | -0.2642 | |
| 49 | N | A | 0.0000 | |
| 50 | E | A | -1.3117 | |
| 51 | I | A | 0.0000 | |
| 52 | A | A | 0.0000 | |
| 53 | D | A | -0.8258 | |
| 54 | P | A | 0.0000 | |
| 55 | G | A | -1.4680 | |
| 56 | D | A | -2.4178 | |
| 57 | G | A | -1.7235 | |
| 58 | G | A | -1.3894 | |
| 59 | V | A | -0.6729 | |
| 60 | L | A | 0.0000 | |
| 61 | L | A | 0.0000 | |
| 62 | S | A | 0.0000 | |
| 63 | L | A | 0.0000 | |
| 64 | A | A | -0.8172 | |
| 65 | G | A | -1.1786 | |
| 66 | L | A | -0.5940 | |
| 67 | P | A | -0.2231 | |
| 68 | S | A | -0.3831 | |
| 69 | V | A | -0.0181 | |
| 70 | V | A | -0.4780 | |
| 71 | D | A | -1.8030 | |
| 72 | V | A | -1.6765 | |
| 73 | D | A | -2.3025 | |
| 74 | T | A | -1.7151 | |
| 75 | A | A | -0.6712 | |
| 76 | A | A | -0.9016 | |
| 77 | R | A | -1.8640 | |
| 78 | T | A | -1.5993 | |
| 79 | V | A | 0.0000 | |
| 80 | R | A | -1.3054 | |
| 81 | V | A | 0.0000 | |
| 82 | G | A | -0.3482 | |
| 83 | G | A | 0.0000 | |
| 84 | G | A | -0.4911 | |
| 85 | V | A | 0.0000 | |
| 86 | R | A | -1.1668 | |
| 87 | Y | A | 0.0000 | |
| 88 | A | A | -1.4643 | |
| 89 | E | A | -1.6444 | |
| 90 | L | A | 0.0000 | |
| 91 | A | A | 0.0000 | |
| 92 | R | A | -2.4860 | |
| 93 | V | A | -1.4955 | |
| 94 | V | A | 0.0000 | |
| 95 | H | A | -1.6740 | |
| 96 | A | A | -1.4791 | |
| 97 | R | A | -2.5590 | |
| 98 | G | A | -1.5822 | |
| 99 | L | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | L | A | 0.0000 | |
| 102 | P | A | -0.2340 | |
| 103 | N | A | 0.0000 | |
| 104 | M | A | 0.0000 | |
| 105 | A | A | 0.0000 | |
| 106 | S | A | 0.0563 | |
| 107 | L | A | 0.2105 | |
| 108 | P | A | 0.0000 | |
| 109 | H | A | 0.0000 | |
| 110 | I | A | -0.3694 | |
| 111 | S | A | 0.0000 | |
| 112 | V | A | 0.0000 | |
| 113 | A | A | -0.2670 | |
| 114 | G | A | -0.4719 | |
| 115 | S | A | 0.0000 | |
| 116 | V | A | 0.0000 | |
| 117 | A | A | -0.0889 | |
| 118 | T | A | 0.0000 | |
| 119 | G | A | 0.0000 | |
| 120 | T | A | -0.0618 | |
| 121 | H | A | 0.0000 | |
| 122 | G | A | 0.0000 | |
| 123 | S | A | 0.0000 | |
| 124 | G | A | 0.0000 | |
| 125 | M | A | -0.4482 | |
| 126 | G | A | -0.4824 | |
| 127 | N | A | 0.0000 | |
| 128 | G | A | -0.3318 | |
| 129 | S | A | 0.0000 | |
| 130 | L | A | 0.0000 | |
| 131 | A | A | 0.0000 | |
| 132 | S | A | -0.3551 | |
| 133 | M | A | 0.0000 | |
| 134 | V | A | 0.0000 | |
| 135 | R | A | -1.7646 | |
| 136 | E | A | -1.1068 | |
| 137 | V | A | 0.0000 | |
| 138 | E | A | 0.2742 | |
| 139 | L | A | 0.0000 | |
| 140 | V | A | 0.0000 | |
| 141 | T | A | 0.0000 | |
| 142 | A | A | -1.3553 | |
| 143 | D | A | -2.1974 | |
| 144 | G | A | 0.0000 | |
| 145 | S | A | -0.7348 | |
| 146 | T | A | -0.0208 | |
| 147 | V | A | 0.8636 | |
| 148 | V | A | 1.2245 | |
| 149 | I | A | 0.0000 | |
| 150 | A | A | -1.3871 | |
| 151 | R | A | -2.5995 | |
| 152 | G | A | -2.1414 | |
| 153 | D | A | -2.1774 | |
| 154 | E | A | -2.6757 | |
| 155 | R | A | -1.9144 | |
| 156 | F | A | -1.4308 | |
| 157 | G | A | -1.0693 | |
| 158 | G | A | 0.0000 | |
| 159 | A | A | 0.0000 | |
| 160 | V | A | 0.0000 | |
| 161 | T | A | 0.0000 | |
| 162 | S | A | 0.0000 | |
| 163 | L | A | 0.0000 | |
| 164 | G | A | -0.0067 | |
| 165 | A | A | 0.0000 | |
| 166 | L | A | 0.0000 | |
| 167 | G | A | 0.0000 | |
| 168 | V | A | 0.0000 | |
| 169 | V | A | 0.2423 | |
| 170 | T | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | L | A | 0.0000 | |
| 173 | T | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | D | A | -1.2087 | |
| 176 | L | A | 0.0000 | |
| 177 | E | A | -0.8313 | |
| 178 | P | A | -0.9653 | |
| 179 | A | A | -1.0937 | |
| 180 | Y | A | 0.0000 | |
| 181 | E | A | -2.5290 | |
| 182 | M | A | 0.0000 | |
| 183 | E | A | -0.3537 | |
| 184 | Q | A | 0.0000 | |
| 185 | H | A | 0.3906 | |
| 186 | V | A | 0.0000 | |
| 187 | F | A | -0.2457 | |
| 188 | T | A | -0.7953 | |
| 189 | E | A | -1.6913 | |
| 190 | L | A | 0.0000 | |
| 191 | P | A | -0.7265 | |
| 192 | L | A | 0.0000 | |
| 193 | A | A | -0.5786 | |
| 194 | G | A | -0.9319 | |
| 195 | L | A | 0.0000 | |
| 196 | D | A | -1.8184 | |
| 197 | P | A | -1.6594 | |
| 198 | A | A | -1.1057 | |
| 199 | T | A | -1.1031 | |
| 200 | F | A | 0.0000 | |
| 201 | E | A | -2.2565 | |
| 202 | T | A | -0.9853 | |
| 203 | V | A | 0.0000 | |
| 204 | M | A | 0.0000 | |
| 205 | A | A | -0.4235 | |
| 206 | A | A | -0.5084 | |
| 207 | A | A | -0.4380 | |
| 208 | Y | A | -0.1415 | |
| 209 | S | A | 0.0000 | |
| 210 | V | A | 0.0000 | |
| 211 | S | A | 0.0000 | |
| 212 | L | A | 0.0000 | |
| 213 | F | A | 0.0000 | |
| 214 | T | A | 0.0000 | |
| 215 | D | A | -1.0708 | |
| 216 | W | A | 0.0000 | |
| 217 | R | A | -2.6243 | |
| 218 | A | A | -1.4440 | |
| 219 | P | A | -1.0954 | |
| 220 | G | A | 0.0000 | |
| 221 | F | A | 0.0000 | |
| 222 | R | A | -1.2258 | |
| 223 | Q | A | 0.0000 | |
| 224 | V | A | 0.0000 | |
| 225 | W | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | K | A | 0.0000 | |
| 228 | R | A | -1.2248 | |
| 229 | R | A | -2.0146 | |
| 230 | T | A | -2.2340 | |
| 231 | D | A | -3.0611 | |
| 232 | R | A | -2.9433 | |
| 233 | P | A | -1.8350 | |
| 234 | L | A | -1.2390 | |
| 235 | D | A | -1.9896 | |
| 236 | G | A | -1.1508 | |
| 237 | F | A | -0.4088 | |
| 238 | P | A | -0.2795 | |
| 239 | Y | A | 0.0659 | |
| 240 | A | A | -0.3623 | |
| 241 | A | A | -0.3374 | |
| 242 | P | A | -0.3287 | |
| 243 | A | A | -0.6020 | |
| 244 | T | A | -0.7981 | |
| 245 | E | A | -1.7816 | |
| 246 | K | A | -1.3786 | |
| 247 | M | A | -0.7134 | |
| 248 | H | A | 0.0000 | |
| 249 | P | A | 0.0000 | |
| 250 | V | A | 0.0076 | |
| 251 | P | A | -0.3422 | |
| 252 | G | A | -0.3405 | |
| 253 | M | A | -0.0919 | |
| 254 | P | A | -0.7132 | |
| 255 | A | A | -1.2911 | |
| 256 | E | A | -1.9783 | |
| 257 | N | A | -1.2872 | |
| 258 | C | A | 0.0000 | |
| 259 | T | A | 0.0000 | |
| 260 | E | A | -0.4004 | |
| 261 | Q | A | 0.0000 | |
| 262 | F | A | 1.5721 | |
| 263 | G | A | 1.0499 | |
| 264 | V | A | 1.3817 | |
| 265 | P | A | -0.2680 | |
| 266 | G | A | -0.9262 | |
| 267 | P | A | -1.3169 | |
| 268 | W | A | 0.0000 | |
| 269 | H | A | -1.3532 | |
| 270 | E | A | -1.6318 | |
| 271 | R | A | 0.0000 | |
| 272 | L | A | 0.0000 | |
| 273 | P | A | 0.0000 | |
| 274 | H | A | 0.0000 | |
| 275 | F | A | -0.5570 | |
| 276 | R | A | -1.3303 | |
| 277 | A | A | -1.3711 | |
| 278 | E | A | -1.7501 | |
| 279 | F | A | -0.8756 | |
| 280 | T | A | -0.5276 | |
| 281 | P | A | -0.3495 | |
| 282 | S | A | -0.2990 | |
| 283 | S | A | -0.4732 | |
| 284 | G | A | -0.4656 | |
| 285 | A | A | -0.4260 | |
| 286 | E | A | -0.6286 | |
| 287 | L | A | 0.0000 | |
| 288 | G | A | 0.0000 | |
| 289 | S | A | 0.0000 | |
| 290 | E | A | 0.0000 | |
| 291 | Y | A | 0.0000 | |
| 292 | L | A | 0.0000 | |
| 293 | M | A | 0.0000 | |
| 294 | P | A | 0.0000 | |
| 295 | R | A | -1.7209 | |
| 296 | E | A | -2.4313 | |
| 297 | H | A | -1.2110 | |
| 298 | A | A | 0.0000 | |
| 299 | L | A | -0.7483 | |
| 300 | A | A | -0.5477 | |
| 301 | A | A | 0.0000 | |
| 302 | L | A | 0.0000 | |
| 303 | H | A | -0.8116 | |
| 304 | A | A | -0.5717 | |
| 305 | M | A | 0.0000 | |
| 306 | D | A | -1.1659 | |
| 307 | A | A | -0.5801 | |
| 308 | I | A | -0.8415 | |
| 309 | R | A | -2.0421 | |
| 310 | E | A | -2.5063 | |
| 311 | T | A | -1.5170 | |
| 312 | L | A | 0.0000 | |
| 313 | A | A | 0.0000 | |
| 314 | P | A | -0.9650 | |
| 315 | V | A | 0.0000 | |
| 316 | L | A | 0.0000 | |
| 317 | Q | A | -0.2074 | |
| 318 | T | A | 0.0000 | |
| 319 | C | A | 0.0000 | |
| 320 | E | A | 0.0000 | |
| 321 | I | A | 0.0000 | |
| 322 | R | A | 0.0000 | |
| 323 | T | A | 0.0000 | |
| 324 | V | A | 0.0000 | |
| 325 | A | A | -0.6207 | |
| 326 | A | A | -0.6624 | |
| 327 | D | A | 0.0000 | |
| 328 | A | A | -0.0580 | |
| 329 | Q | A | 0.0000 | |
| 330 | W | A | 0.0000 | |
| 331 | L | A | 0.0000 | |
| 332 | S | A | 0.0000 | |
| 333 | P | A | 0.0000 | |
| 334 | A | A | 0.0000 | |
| 335 | Y | A | -0.3241 | |
| 336 | G | A | -0.7583 | |
| 337 | R | A | -1.0968 | |
| 338 | D | A | -1.5205 | |
| 339 | T | A | 0.0000 | |
| 340 | V | A | 0.0000 | |
| 341 | A | A | 0.0000 | |
| 342 | A | A | 0.0000 | |
| 343 | H | A | -0.1418 | |
| 344 | F | A | 0.0000 | |
| 345 | T | A | 0.0000 | |
| 346 | W | A | 0.0000 | |
| 347 | V | A | -0.1100 | |
| 348 | P | A | -0.8231 | |
| 349 | D | A | -1.0023 | |
| 350 | T | A | -0.4160 | |
| 351 | A | A | -0.1052 | |
| 352 | A | A | -0.0876 | |
| 353 | V | A | 0.0000 | |
| 354 | L | A | 0.2122 | |
| 355 | P | A | -0.4571 | |
| 356 | V | A | 0.0000 | |
| 357 | V | A | 0.0000 | |
| 358 | R | A | -1.9398 | |
| 359 | R | A | -2.5205 | |
| 360 | L | A | 0.0000 | |
| 361 | E | A | 0.0000 | |
| 362 | E | A | -2.0417 | |
| 363 | A | A | -0.9142 | |
| 364 | L | A | 0.0000 | |
| 365 | V | A | 0.9769 | |
| 366 | P | A | 0.3882 | |
| 367 | F | A | 0.3257 | |
| 368 | A | A | 0.6162 | |
| 369 | A | A | 0.3628 | |
| 370 | R | A | 0.0000 | |
| 371 | P | A | 0.0000 | |
| 372 | H | A | 0.0000 | |
| 373 | W | A | 0.0000 | |
| 374 | G | A | 0.0000 | |
| 375 | K | A | -0.1539 | |
| 376 | V | A | 0.2702 | |
| 377 | F | A | 0.3607 | |
| 378 | T | A | -0.0394 | |
| 379 | V | A | -0.4434 | |
| 380 | P | A | -0.7659 | |
| 381 | A | A | -1.0434 | |
| 382 | G | A | -1.3133 | |
| 383 | E | A | -1.8139 | |
| 384 | L | A | 0.0000 | |
| 385 | R | A | -1.0814 | |
| 386 | A | A | -0.7785 | |
| 387 | L | A | -0.3450 | |
| 388 | Y | A | 0.0000 | |
| 389 | P | A | -0.6593 | |
| 390 | R | A | -1.0548 | |
| 391 | L | A | -0.5247 | |
| 392 | A | A | -0.5784 | |
| 393 | D | A | -1.2098 | |
| 394 | F | A | 0.0000 | |
| 395 | G | A | -0.8077 | |
| 396 | A | A | -0.8607 | |
| 397 | L | A | 0.0000 | |
| 398 | A | A | 0.0000 | |
| 399 | R | A | -1.9294 | |
| 400 | A | A | -0.8281 | |
| 401 | L | A | -0.5680 | |
| 402 | D | A | 0.0000 | |
| 403 | P | A | -0.9853 | |
| 404 | A | A | -0.6061 | |
| 405 | G | A | -1.0218 | |
| 406 | K | A | -0.8430 | |
| 407 | F | A | 0.0000 | |
| 408 | T | A | -0.7729 | |
| 409 | N | A | 0.0000 | |
| 410 | A | A | -0.7838 | |
| 411 | F | A | -0.7321 | |
| 412 | V | A | 0.0000 | |
| 413 | R | A | -1.7677 | |
| 414 | G | A | -1.0253 | |
| 415 | V | A | 0.0000 | |
| 416 | L | A | -0.7216 | |
| 417 | A | A | -0.7496 | |
| 418 | G | A | -0.6871 |
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 | -0.1412 | 4.2341 | View | CSV | PDB |
| 4.5 | -0.2049 | 4.1711 | View | CSV | PDB |
| 5.0 | -0.2804 | 4.0939 | View | CSV | PDB |
| 5.5 | -0.3586 | 4.0181 | View | CSV | PDB |
| 6.0 | -0.4321 | 3.9551 | View | CSV | PDB |
| 6.5 | -0.4943 | 3.9149 | View | CSV | PDB |
| 7.0 | -0.5423 | 3.903 | View | CSV | PDB |
| 7.5 | -0.5787 | 3.9123 | View | CSV | PDB |
| 8.0 | -0.6067 | 3.9319 | View | CSV | PDB |
| 8.5 | -0.6265 | 3.9553 | View | CSV | PDB |
| 9.0 | -0.6369 | 3.9799 | 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