| Chain sequence(s) |
A: MAITNKLIITLLLLISIAVVHCLSFRVEIDEFEPPQQGEQEGPRRRPGGGSGEGWEEESTNHPYHFRKRSFSDWFQSKEGFVRVLPKFTKHAPALFRGIENYRFSLVEMEPTTFFVPHHLDADAVFIVLQGKGVIEFVTDKTKESFHITKGDVVRIPSGVTNFITNTNQTVPLRLAQITVPVNNPGNYKDYFPAASQFQQSYFNGFTKEVLSTSFNVPEELLGRLVTRSKEIGQGIIRRISPDQIKELAEHATSPSNKHKAKKEKEEDKDLRTLWTPFNLFAIDPIYSNDFGHFHEAHPKNYNQLQDLHIAAAWANMTQGSLFLPHFNSKTTFVTFVENGCARFEMATPYKFQRGQQQWPGQGQEEEEDMSENVHKVVSRVCKGEVFIVPAGHPFTILSQDQDFIAVGFGIYATNSKRTFLAGEENLLSNLNPAATRVTFGVGSKVAEKLFTSQNYSYFAPTSRSQQQIPEKHKPSFQSILDFAGF
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MAITNKLIITLLLLISIAVVHCLSFRVEIDEFEPPQQGEQEGPRRRPGGGSGEG WEEESTNHPYHFRKRSFSDWFQSKEGFVRVLPKFTKHAPALFRGIENYRFSLVEMEPTTFFVPHHLDADAVFIVLQGKGVIEFVTDKTKESFHITKGDVVRIPSGVTNFITNTNQTVPLRLAQITVPVNNPGNYKDYFPAASQFQQSYFNGFTKEVLSTSFNVPEELLGRLVTRSKEIGQGIIRRISPDQIKELAEHATSPSNKHKAKKEKEEDKDLRTLWTPFNLFAIDPIYSNDFGHFHEAHPKNYNQLQDLHIAAAWANMTQGSLFLPHFNSKTTFVTFVENGCARFEMATPYKFQRGQQQWPGQGQEEEEDMSENVHKVVSRVCKGEVFIVPAGHPFTILSQDQDFIAVGFGIYATNSKRTFLAGEENLLSNLNPAATRVTFGVGSKVAEKLFTSQNYSYFAPTSRSQQQIPEKHKPSFQSILDFAGF(Red indicates removed residues) |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:01)
[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: Running AlphaCutter (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:21)
[INFO] FoldX: Starting FoldX energy minimization (00:00:22)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:15:41)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/6225f10dfd42bca/tmp/folded.pdb (00:15:41)
[INFO] Main: Simulation completed successfully. (00:22:06)
|
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 |
|---|---|---|---|---|
| 55 | W | A | -0.4905 | |
| 56 | E | A | -2.4386 | |
| 57 | E | A | -2.8597 | |
| 58 | E | A | -2.3493 | |
| 59 | S | A | -1.8796 | |
| 60 | T | A | -1.6651 | |
| 61 | N | A | -1.8423 | |
| 62 | H | A | -1.2620 | |
| 63 | P | A | 0.0000 | |
| 64 | Y | A | 0.0000 | |
| 65 | H | A | 0.0000 | |
| 66 | F | A | 0.0000 | |
| 67 | R | A | -2.6422 | |
| 68 | K | A | -3.0568 | |
| 69 | R | A | -2.8751 | |
| 70 | S | A | -1.9349 | |
| 71 | F | A | -1.6377 | |
| 72 | S | A | -1.6916 | |
| 73 | D | A | -2.1072 | |
| 74 | W | A | -0.7862 | |
| 75 | F | A | 0.0000 | |
| 76 | Q | A | -1.9394 | |
| 77 | S | A | -1.8658 | |
| 78 | K | A | -2.5421 | |
| 79 | E | A | -2.2386 | |
| 80 | G | A | 0.0000 | |
| 81 | F | A | -1.3581 | |
| 82 | V | A | 0.0000 | |
| 83 | R | A | -1.5442 | |
| 84 | V | A | 0.0000 | |
| 85 | L | A | 0.0000 | |
| 86 | P | A | -0.8513 | |
| 87 | K | A | -1.5354 | |
| 88 | F | A | 0.0000 | |
| 89 | T | A | -2.1700 | |
| 90 | K | A | -2.4830 | |
| 91 | H | A | -2.2121 | |
| 92 | A | A | 0.0000 | |
| 93 | P | A | -1.6931 | |
| 94 | A | A | -1.7151 | |
| 95 | L | A | -0.8448 | |
| 96 | F | A | 0.0000 | |
| 97 | R | A | -2.4979 | |
| 98 | G | A | -1.6015 | |
| 99 | I | A | 0.0000 | |
| 100 | E | A | -2.4360 | |
| 101 | N | A | -1.5095 | |
| 102 | Y | A | 0.0000 | |
| 103 | R | A | -0.5978 | |
| 104 | F | A | 0.0000 | |
| 105 | S | A | 0.0000 | |
| 106 | L | A | -0.3620 | |
| 107 | V | A | 0.0000 | |
| 108 | E | A | -1.0059 | |
| 109 | M | A | 0.0000 | |
| 110 | E | A | -2.0670 | |
| 111 | P | A | -1.4515 | |
| 112 | T | A | 0.0000 | |
| 113 | T | A | 0.0000 | |
| 114 | F | A | -0.5248 | |
| 115 | F | A | 0.0000 | |
| 116 | V | A | 0.0000 | |
| 117 | P | A | -0.0198 | |
| 118 | H | A | 0.0000 | |
| 119 | H | A | -0.5339 | |
| 120 | L | A | 0.0000 | |
| 121 | D | A | -0.7389 | |
| 122 | A | A | 0.0000 | |
| 123 | D | A | 0.1098 | |
| 124 | A | A | 0.0000 | |
| 125 | V | A | 0.0000 | |
| 126 | F | A | 0.0000 | |
| 127 | I | A | 0.0000 | |
| 128 | V | A | 0.0000 | |
| 129 | L | A | 0.0000 | |
| 130 | Q | A | -1.2810 | |
| 131 | G | A | -1.6380 | |
| 132 | K | A | -2.2664 | |
| 133 | G | A | 0.0000 | |
| 134 | V | A | 0.0000 | |
| 135 | I | A | 0.0000 | |
| 136 | E | A | -0.7212 | |
| 137 | F | A | 0.0000 | |
| 138 | V | A | -1.2379 | |
| 139 | T | A | -1.8266 | |
| 140 | D | A | -2.7937 | |
| 141 | K | A | -3.0427 | |
| 142 | T | A | -2.3779 | |
| 143 | K | A | -2.4627 | |
| 144 | E | A | -1.4311 | |
| 145 | S | A | -1.1896 | |
| 146 | F | A | 0.0000 | |
| 147 | H | A | -1.0676 | |
| 148 | I | A | 0.0000 | |
| 149 | T | A | -1.5652 | |
| 150 | K | A | -1.6333 | |
| 151 | G | A | 0.0000 | |
| 152 | D | A | 0.0000 | |
| 153 | V | A | 0.0000 | |
| 154 | V | A | 0.0000 | |
| 155 | R | A | 0.0000 | |
| 156 | I | A | 0.0000 | |
| 157 | P | A | 0.0000 | |
| 158 | S | A | -0.1446 | |
| 159 | G | A | -0.4137 | |
| 160 | V | A | 0.0000 | |
| 161 | T | A | -0.5131 | |
| 162 | N | A | 0.0000 | |
| 163 | F | A | 0.0000 | |
| 164 | I | A | 0.0000 | |
| 165 | T | A | 0.0000 | |
| 166 | N | A | 0.0000 | |
| 167 | T | A | -1.2213 | |
| 168 | N | A | -1.2893 | |
| 169 | Q | A | -1.5671 | |
| 170 | T | A | -0.6187 | |
| 171 | V | A | -0.4382 | |
| 172 | P | A | -1.0358 | |
| 173 | L | A | 0.0000 | |
| 174 | R | A | -1.0378 | |
| 175 | L | A | 0.0000 | |
| 176 | A | A | 0.0000 | |
| 177 | Q | A | 0.0000 | |
| 178 | I | A | 0.0000 | |
| 179 | T | A | 0.0000 | |
| 180 | V | A | -0.0569 | |
| 181 | P | A | 0.0000 | |
| 182 | V | A | 0.5762 | |
| 183 | N | A | -1.3710 | |
| 184 | N | A | -1.7631 | |
| 185 | P | A | -1.3842 | |
| 186 | G | A | 0.0000 | |
| 187 | N | A | -1.5698 | |
| 188 | Y | A | -1.0769 | |
| 189 | K | A | -1.5982 | |
| 190 | D | A | 0.0000 | |
| 191 | Y | A | -0.1488 | |
| 192 | F | A | 0.0000 | |
| 193 | P | A | 0.0131 | |
| 194 | A | A | -0.4898 | |
| 195 | A | A | 0.0000 | |
| 196 | S | A | -1.5845 | |
| 197 | Q | A | -1.8060 | |
| 198 | F | A | -0.3587 | |
| 199 | Q | A | -0.5677 | |
| 200 | Q | A | -1.2882 | |
| 201 | S | A | 0.0000 | |
| 202 | Y | A | 0.3722 | |
| 203 | F | A | 0.3505 | |
| 204 | N | A | -0.5262 | |
| 205 | G | A | -0.1270 | |
| 206 | F | A | 0.7641 | |
| 207 | T | A | -0.4633 | |
| 208 | K | A | -2.3324 | |
| 209 | E | A | -2.1917 | |
| 210 | V | A | -0.1143 | |
| 211 | L | A | 0.0000 | |
| 212 | S | A | -1.6698 | |
| 213 | T | A | -1.0196 | |
| 214 | S | A | -0.3971 | |
| 215 | F | A | 0.0531 | |
| 216 | N | A | -1.0446 | |
| 217 | V | A | -0.8581 | |
| 218 | P | A | -1.9375 | |
| 219 | E | A | -3.4843 | |
| 220 | E | A | -2.9099 | |
| 221 | L | A | -1.3399 | |
| 222 | L | A | 0.0000 | |
| 223 | G | A | -2.1760 | |
| 224 | R | A | -2.5968 | |
| 225 | L | A | -0.8845 | |
| 226 | V | A | 0.0000 | |
| 227 | T | A | -2.0513 | |
| 228 | R | A | -2.9909 | |
| 229 | S | A | -2.7010 | |
| 230 | K | A | -3.2689 | |
| 231 | E | A | -2.9443 | |
| 232 | I | A | -1.3838 | |
| 233 | G | A | -1.5426 | |
| 234 | Q | A | -1.6955 | |
| 235 | G | A | 0.0000 | |
| 236 | I | A | 0.0000 | |
| 237 | I | A | 0.0000 | |
| 238 | R | A | -1.6139 | |
| 239 | R | A | -2.3987 | |
| 240 | I | A | -1.2531 | |
| 241 | S | A | -1.5148 | |
| 242 | P | A | -2.3410 | |
| 243 | D | A | -3.2648 | |
| 244 | Q | A | -2.9108 | |
| 245 | I | A | -2.3837 | |
| 246 | K | A | -3.9831 | |
| 247 | E | A | -3.9678 | |
| 248 | L | A | -2.2198 | |
| 249 | A | A | -2.5415 | |
| 250 | E | A | -3.3552 | |
| 251 | H | A | -2.4453 | |
| 252 | A | A | -1.4839 | |
| 253 | T | A | -0.8814 | |
| 254 | S | A | -0.4551 | |
| 255 | P | A | -0.6583 | |
| 256 | S | A | -0.9420 | |
| 257 | N | A | -1.6283 | |
| 258 | K | A | -2.7470 | |
| 259 | H | A | -2.5103 | |
| 260 | K | A | -3.2218 | |
| 261 | A | A | -3.1882 | |
| 262 | K | A | -3.7938 | |
| 263 | K | A | -4.3387 | |
| 264 | E | A | -4.7463 | |
| 265 | K | A | -5.2001 | |
| 266 | E | A | -5.3073 | |
| 267 | E | A | -4.9736 | |
| 268 | D | A | -4.6497 | |
| 269 | K | A | -4.6943 | |
| 270 | D | A | -4.0212 | |
| 271 | L | A | -2.0004 | |
| 272 | R | A | -2.1287 | |
| 273 | T | A | -1.8011 | |
| 274 | L | A | -0.7935 | |
| 275 | W | A | 0.0000 | |
| 276 | T | A | -0.5032 | |
| 277 | P | A | 0.0000 | |
| 278 | F | A | 0.0000 | |
| 279 | N | A | -0.0900 | |
| 280 | L | A | 0.0000 | |
| 281 | F | A | 0.4831 | |
| 282 | A | A | 0.1003 | |
| 283 | I | A | -0.1494 | |
| 284 | D | A | -1.1767 | |
| 285 | P | A | -0.1974 | |
| 286 | I | A | 0.9027 | |
| 287 | Y | A | 0.3026 | |
| 288 | S | A | -0.6955 | |
| 289 | N | A | -1.2492 | |
| 290 | D | A | -2.0170 | |
| 291 | F | A | 0.0000 | |
| 292 | G | A | 0.0000 | |
| 293 | H | A | -0.8754 | |
| 294 | F | A | 0.0000 | |
| 295 | H | A | -0.0721 | |
| 296 | E | A | 0.0003 | |
| 297 | A | A | 0.0000 | |
| 298 | H | A | -1.5272 | |
| 299 | P | A | 0.0000 | |
| 300 | K | A | -3.2064 | |
| 301 | N | A | -2.9615 | |
| 302 | Y | A | 0.0000 | |
| 303 | N | A | -2.5508 | |
| 304 | Q | A | 0.0000 | |
| 305 | L | A | 0.0000 | |
| 306 | Q | A | -2.6089 | |
| 307 | D | A | -2.5927 | |
| 308 | L | A | -1.1589 | |
| 309 | H | A | -1.4223 | |
| 310 | I | A | 0.0000 | |
| 311 | A | A | 0.0000 | |
| 312 | A | A | 0.0000 | |
| 313 | A | A | 0.0000 | |
| 314 | W | A | 0.0000 | |
| 315 | A | A | -0.1880 | |
| 316 | N | A | -0.7196 | |
| 317 | M | A | 0.0000 | |
| 318 | T | A | -2.0569 | |
| 319 | Q | A | -2.8053 | |
| 320 | G | A | -1.7357 | |
| 321 | S | A | 0.0000 | |
| 322 | L | A | 0.0505 | |
| 323 | F | A | 0.0000 | |
| 324 | L | A | 0.0000 | |
| 325 | P | A | 0.0576 | |
| 326 | H | A | 0.0000 | |
| 327 | F | A | -0.3544 | |
| 328 | N | A | 0.0000 | |
| 329 | S | A | -1.6893 | |
| 330 | K | A | -2.1784 | |
| 331 | T | A | 0.0000 | |
| 332 | T | A | -0.3077 | |
| 333 | F | A | 0.0000 | |
| 334 | V | A | 0.0000 | |
| 335 | T | A | -0.0070 | |
| 336 | F | A | 0.0000 | |
| 337 | V | A | 0.0000 | |
| 338 | E | A | 0.0000 | |
| 339 | N | A | -1.3149 | |
| 340 | G | A | 0.0000 | |
| 341 | C | A | -1.1574 | |
| 342 | A | A | 0.0000 | |
| 343 | R | A | -0.9662 | |
| 344 | F | A | 0.0000 | |
| 345 | E | A | -1.1621 | |
| 346 | M | A | 0.0000 | |
| 347 | A | A | -0.4812 | |
| 348 | T | A | 0.0000 | |
| 349 | P | A | -0.9129 | |
| 350 | Y | A | -1.2640 | |
| 351 | K | A | -2.5343 | |
| 352 | F | A | -1.7974 | |
| 353 | Q | A | -2.5590 | |
| 354 | R | A | -3.4629 | |
| 355 | G | A | -2.9309 | |
| 356 | Q | A | -2.8224 | |
| 357 | Q | A | -2.4483 | |
| 358 | Q | A | -1.9749 | |
| 359 | W | A | -0.3541 | |
| 360 | P | A | -0.7682 | |
| 361 | G | A | -1.2784 | |
| 362 | Q | A | -2.2794 | |
| 363 | G | A | -2.6046 | |
| 364 | Q | A | -3.6219 | |
| 365 | E | A | -4.3668 | |
| 366 | E | A | -4.7667 | |
| 367 | E | A | -4.5686 | |
| 368 | E | A | -3.9322 | |
| 369 | D | A | -3.4994 | |
| 370 | M | A | -1.3168 | |
| 371 | S | A | -1.7178 | |
| 372 | E | A | -2.0533 | |
| 373 | N | A | -1.9041 | |
| 374 | V | A | -0.1323 | |
| 375 | H | A | -1.4754 | |
| 376 | K | A | -2.1072 | |
| 377 | V | A | 0.0000 | |
| 378 | V | A | 0.0000 | |
| 379 | S | A | 0.0000 | |
| 380 | R | A | -1.3698 | |
| 381 | V | A | 0.0000 | |
| 382 | C | A | -1.0247 | |
| 383 | K | A | -1.5579 | |
| 384 | G | A | -1.4465 | |
| 385 | E | A | 0.0000 | |
| 386 | V | A | 0.0000 | |
| 387 | F | A | 0.0000 | |
| 388 | I | A | 0.0000 | |
| 389 | V | A | 0.0000 | |
| 390 | P | A | -0.3902 | |
| 391 | A | A | -0.7095 | |
| 392 | G | A | -0.8108 | |
| 393 | H | A | 0.0000 | |
| 394 | P | A | -0.1048 | |
| 395 | F | A | 0.0000 | |
| 396 | T | A | -0.1500 | |
| 397 | I | A | 0.0000 | |
| 398 | L | A | -0.5108 | |
| 399 | S | A | 0.0000 | |
| 400 | Q | A | -2.0947 | |
| 401 | D | A | -2.9638 | |
| 402 | Q | A | -2.9541 | |
| 403 | D | A | -3.0507 | |
| 404 | F | A | 0.0000 | |
| 405 | I | A | -0.5492 | |
| 406 | A | A | 0.0000 | |
| 407 | V | A | 0.0000 | |
| 408 | G | A | 0.0000 | |
| 409 | F | A | 0.0000 | |
| 410 | G | A | 0.0000 | |
| 411 | I | A | 0.0000 | |
| 412 | Y | A | -0.0597 | |
| 413 | A | A | 0.0000 | |
| 414 | T | A | -1.8127 | |
| 415 | N | A | -2.2587 | |
| 416 | S | A | -2.0082 | |
| 417 | K | A | -2.4707 | |
| 418 | R | A | -1.2682 | |
| 419 | T | A | -0.4514 | |
| 420 | F | A | 0.0000 | |
| 421 | L | A | 0.2754 | |
| 422 | A | A | -0.2131 | |
| 423 | G | A | 0.0000 | |
| 424 | E | A | -2.6347 | |
| 425 | E | A | -2.3109 | |
| 426 | N | A | 0.0000 | |
| 427 | L | A | 0.2757 | |
| 428 | L | A | 0.1511 | |
| 429 | S | A | -1.1818 | |
| 430 | N | A | -1.4214 | |
| 431 | L | A | -0.8954 | |
| 432 | N | A | -1.6269 | |
| 433 | P | A | -1.4620 | |
| 434 | A | A | -0.4856 | |
| 435 | A | A | -0.1328 | |
| 436 | T | A | 0.0000 | |
| 437 | R | A | -0.5757 | |
| 438 | V | A | 1.1564 | |
| 439 | T | A | 0.7383 | |
| 440 | F | A | 0.7786 | |
| 441 | G | A | 0.0719 | |
| 442 | V | A | -0.1430 | |
| 443 | G | A | -0.8087 | |
| 444 | S | A | -1.7191 | |
| 445 | K | A | -2.2100 | |
| 446 | V | A | -0.8152 | |
| 447 | A | A | 0.0000 | |
| 448 | E | A | -2.5347 | |
| 449 | K | A | -2.0322 | |
| 450 | L | A | 0.1929 | |
| 451 | F | A | -0.4401 | |
| 452 | T | A | -1.5228 | |
| 453 | S | A | -1.1035 | |
| 454 | Q | A | -1.2486 | |
| 455 | N | A | -1.2281 | |
| 456 | Y | A | -1.0792 | |
| 457 | S | A | -1.1577 | |
| 458 | Y | A | -0.2070 | |
| 459 | F | A | 0.0000 | |
| 460 | A | A | 0.0000 | |
| 461 | P | A | 0.0000 | |
| 462 | T | A | -0.8640 | |
| 463 | S | A | -1.4529 | |
| 464 | R | A | -2.5622 | |
| 465 | S | A | -1.9019 | |
| 466 | Q | A | -1.8297 | |
| 467 | Q | A | -1.4552 | |
| 468 | Q | A | -1.2546 | |
| 469 | I | A | 0.2417 | |
| 470 | P | A | -1.1992 | |
| 471 | E | A | -2.9021 | |
| 472 | K | A | -3.3821 | |
| 473 | H | A | -3.3901 | |
| 474 | K | A | -2.8819 | |
| 475 | P | A | -1.2120 | |
| 476 | S | A | -0.3001 | |
| 477 | F | A | 1.6380 | |
| 478 | Q | A | 0.1695 | |
| 479 | S | A | 0.8251 | |
| 480 | I | A | 2.4584 | |
| 481 | L | A | 1.9877 | |
| 482 | D | A | 0.0166 | |
| 483 | F | A | 2.1645 | |
| 484 | A | A | 1.5161 | |
| 485 | G | A | 0.8816 | |
| 486 | F | A | 2.0230 |
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 | -0.8933 | 6.2623 | View | CSV | PDB |
| 4.5 | -0.9717 | 6.1052 | View | CSV | PDB |
| 5.0 | -1.067 | 5.9161 | View | CSV | PDB |
| 5.5 | -1.1599 | 5.7137 | View | CSV | PDB |
| 6.0 | -1.228 | 5.5067 | View | CSV | PDB |
| 6.5 | -1.2549 | 5.2983 | View | CSV | PDB |
| 7.0 | -1.2413 | 5.0901 | View | CSV | PDB |
| 7.5 | -1.2013 | 5.0216 | View | CSV | PDB |
| 8.0 | -1.1475 | 5.0216 | View | CSV | PDB |
| 8.5 | -1.084 | 5.0216 | View | CSV | PDB |
| 9.0 | -1.0108 | 5.0216 | 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