| Chain sequence(s) |
A: RSFRGPLLPNRPFTTVWNANTQWCLERHGVDVDVSVFDVVANPGQTFRGPDMTIFYSSQLGTYPYYTPTGEPVFGGLPQNASLIAHLARTFQDILAAIPAPDFSGLAVIDWEAWRPRWAFNWDTKDIYRQRSRALVQAQHPDWPAPQVEAVAQDQFQGAARAWMAGTLQLGRALRPRGLWGFYGFPDCYNYDFLSPNYTGQCPSGIRAQNDQLGWLWGQSRALYPSIYMPAVLEGTGKSQMYVQHRVAEAFRVAVAAGDPNLPVLPYVQIFYDTTNHFLPLDELEHSLGESAAQGAAGVVLWVSWENTRTKESCQAIKEYMDTTLGPFILNVTSGALLCSQALCSGHGRCVRRTSHPKALLLLNPASFSIQLTPGGGPLSLRGALSLEDQAQMAVEFKCRCYPGWQAPWCERKSMWT
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 (00:02:35)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8b4303eea9a89f8/tmp/folded.pdb (00:02:35)
[INFO] Main: Simulation completed successfully. (00:04:22)
|
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 |
|---|---|---|---|---|
| 20 | R | A | -1.6980 | |
| 21 | S | A | 0.0000 | |
| 22 | F | A | 1.0690 | |
| 23 | R | A | -0.1701 | |
| 24 | G | A | -0.2278 | |
| 25 | P | A | -0.5455 | |
| 26 | L | A | 0.0000 | |
| 27 | L | A | -0.5831 | |
| 28 | P | A | -0.9234 | |
| 29 | N | A | -1.7165 | |
| 30 | R | A | -1.1701 | |
| 31 | P | A | 0.0000 | |
| 32 | F | A | 0.0000 | |
| 33 | T | A | 0.0000 | |
| 34 | T | A | 0.0000 | |
| 35 | V | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | N | A | 0.0000 | |
| 38 | A | A | 0.0000 | |
| 39 | N | A | -0.0810 | |
| 40 | T | A | 0.0000 | |
| 41 | Q | A | -0.8576 | |
| 42 | W | A | -1.3126 | |
| 43 | C | A | 0.0000 | |
| 44 | L | A | -1.5521 | |
| 45 | E | A | -2.5667 | |
| 46 | R | A | -3.0158 | |
| 47 | H | A | -2.7442 | |
| 48 | G | A | -1.9318 | |
| 49 | V | A | 0.0000 | |
| 50 | D | A | -2.1714 | |
| 51 | V | A | 0.0000 | |
| 52 | D | A | -1.5292 | |
| 53 | V | A | -0.0294 | |
| 54 | S | A | -0.0081 | |
| 55 | V | A | 0.2694 | |
| 56 | F | A | 0.0000 | |
| 57 | D | A | -0.2216 | |
| 58 | V | A | 0.0000 | |
| 59 | V | A | 1.1498 | |
| 60 | A | A | 0.2910 | |
| 61 | N | A | 0.0117 | |
| 62 | P | A | 0.0000 | |
| 63 | G | A | -0.3181 | |
| 64 | Q | A | -0.6513 | |
| 65 | T | A | -0.0170 | |
| 66 | F | A | 0.6794 | |
| 67 | R | A | -1.3414 | |
| 68 | G | A | -0.9365 | |
| 69 | P | A | -1.1939 | |
| 70 | D | A | -1.0905 | |
| 71 | M | A | -0.5471 | |
| 72 | T | A | -0.3568 | |
| 73 | I | A | -0.1090 | |
| 74 | F | A | 0.0000 | |
| 75 | Y | A | -0.1645 | |
| 76 | S | A | -0.4722 | |
| 77 | S | A | -0.3873 | |
| 78 | Q | A | -0.6641 | |
| 79 | L | A | 0.0000 | |
| 80 | G | A | 0.0000 | |
| 81 | T | A | 0.1007 | |
| 82 | Y | A | 0.0000 | |
| 83 | P | A | 0.0000 | |
| 84 | Y | A | 0.2949 | |
| 85 | Y | A | 0.0000 | |
| 86 | T | A | -0.6623 | |
| 87 | P | A | -0.6007 | |
| 88 | T | A | -0.7480 | |
| 89 | G | A | -0.9960 | |
| 90 | E | A | -1.6764 | |
| 91 | P | A | -0.5326 | |
| 92 | V | A | 0.8146 | |
| 93 | F | A | 1.5136 | |
| 94 | G | A | 0.2309 | |
| 95 | G | A | 0.0000 | |
| 96 | L | A | 0.0000 | |
| 97 | P | A | 0.0000 | |
| 98 | Q | A | -1.1666 | |
| 99 | N | A | -1.0549 | |
| 100 | A | A | 0.1872 | |
| 101 | S | A | 0.6707 | |
| 102 | L | A | 0.9903 | |
| 103 | I | A | 2.0325 | |
| 104 | A | A | 0.7530 | |
| 105 | H | A | 0.0000 | |
| 106 | L | A | 0.7808 | |
| 107 | A | A | 0.0716 | |
| 108 | R | A | -1.3712 | |
| 109 | T | A | 0.0000 | |
| 110 | F | A | 0.4185 | |
| 111 | Q | A | -0.9273 | |
| 112 | D | A | 0.0000 | |
| 113 | I | A | 0.0000 | |
| 114 | L | A | 0.4674 | |
| 115 | A | A | -0.0420 | |
| 116 | A | A | -0.4386 | |
| 117 | I | A | 0.0000 | |
| 118 | P | A | -0.6347 | |
| 119 | A | A | -0.7386 | |
| 120 | P | A | -1.3655 | |
| 121 | D | A | -2.5197 | |
| 122 | F | A | 0.0000 | |
| 123 | S | A | -1.6162 | |
| 124 | G | A | 0.0000 | |
| 125 | L | A | 0.0000 | |
| 126 | A | A | 0.0000 | |
| 127 | V | A | 0.0000 | |
| 128 | I | A | 0.0000 | |
| 129 | D | A | -0.6620 | |
| 130 | W | A | 0.0000 | |
| 131 | E | A | -1.8942 | |
| 132 | A | A | -0.9485 | |
| 133 | W | A | 0.0000 | |
| 134 | R | A | -0.9046 | |
| 135 | P | A | 0.0000 | |
| 136 | R | A | -0.8634 | |
| 137 | W | A | 0.0000 | |
| 138 | A | A | -0.2290 | |
| 139 | F | A | 0.0000 | |
| 140 | N | A | 0.0000 | |
| 141 | W | A | -0.7771 | |
| 142 | D | A | -1.7974 | |
| 143 | T | A | -1.0465 | |
| 144 | K | A | -1.2795 | |
| 145 | D | A | -1.3203 | |
| 146 | I | A | -0.9167 | |
| 147 | Y | A | 0.0000 | |
| 148 | R | A | -1.3772 | |
| 149 | Q | A | -1.7871 | |
| 150 | R | A | -1.3601 | |
| 151 | S | A | 0.0000 | |
| 152 | R | A | -1.3860 | |
| 153 | A | A | -0.9642 | |
| 154 | L | A | -0.7536 | |
| 155 | V | A | 0.0000 | |
| 156 | Q | A | -1.3493 | |
| 157 | A | A | -1.0018 | |
| 158 | Q | A | -1.5846 | |
| 159 | H | A | -1.5471 | |
| 160 | P | A | -1.5989 | |
| 161 | D | A | -2.1021 | |
| 162 | W | A | -1.2035 | |
| 163 | P | A | -0.9282 | |
| 164 | A | A | -0.7922 | |
| 165 | P | A | -0.7619 | |
| 166 | Q | A | -0.9773 | |
| 167 | V | A | 0.0000 | |
| 168 | E | A | -1.5916 | |
| 169 | A | A | -1.0878 | |
| 170 | V | A | -0.9288 | |
| 171 | A | A | 0.0000 | |
| 172 | Q | A | -1.8914 | |
| 173 | D | A | -2.4841 | |
| 174 | Q | A | -2.2844 | |
| 175 | F | A | 0.0000 | |
| 176 | Q | A | -1.8403 | |
| 177 | G | A | -1.8221 | |
| 178 | A | A | 0.0000 | |
| 179 | A | A | 0.0000 | |
| 180 | R | A | -1.8223 | |
| 181 | A | A | -0.8105 | |
| 182 | W | A | 0.0000 | |
| 183 | M | A | 0.0000 | |
| 184 | A | A | -0.7660 | |
| 185 | G | A | -0.5838 | |
| 186 | T | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | Q | A | -1.0755 | |
| 189 | L | A | -0.0407 | |
| 190 | G | A | 0.0000 | |
| 191 | R | A | -1.0316 | |
| 192 | A | A | -0.3403 | |
| 193 | L | A | -0.1907 | |
| 194 | R | A | 0.0000 | |
| 195 | P | A | -1.7331 | |
| 196 | R | A | -2.6542 | |
| 197 | G | A | 0.0000 | |
| 198 | L | A | 0.0000 | |
| 199 | W | A | 0.0000 | |
| 200 | G | A | 0.0000 | |
| 201 | F | A | 0.0000 | |
| 202 | Y | A | -0.2771 | |
| 203 | G | A | -0.4049 | |
| 204 | F | A | 0.0000 | |
| 205 | P | A | 0.0000 | |
| 206 | D | A | -0.3243 | |
| 207 | C | A | 0.0000 | |
| 208 | Y | A | 0.0000 | |
| 209 | N | A | 0.0000 | |
| 210 | Y | A | 0.1811 | |
| 211 | D | A | -1.2382 | |
| 212 | F | A | 0.0000 | |
| 213 | L | A | 1.0843 | |
| 214 | S | A | -0.1740 | |
| 215 | P | A | -0.7050 | |
| 216 | N | A | -1.3621 | |
| 217 | Y | A | -0.7808 | |
| 218 | T | A | -0.8897 | |
| 219 | G | A | 0.0000 | |
| 220 | Q | A | -1.1009 | |
| 221 | C | A | 0.0000 | |
| 222 | P | A | -0.7433 | |
| 223 | S | A | -0.6204 | |
| 224 | G | A | -0.7783 | |
| 225 | I | A | 0.0000 | |
| 226 | R | A | -1.6249 | |
| 227 | A | A | -1.4105 | |
| 228 | Q | A | -1.5714 | |
| 229 | N | A | 0.0000 | |
| 230 | D | A | -2.6957 | |
| 231 | Q | A | -2.2663 | |
| 232 | L | A | 0.0000 | |
| 233 | G | A | -1.1291 | |
| 234 | W | A | -0.6599 | |
| 235 | L | A | 0.0000 | |
| 236 | W | A | 0.0000 | |
| 237 | G | A | -0.6436 | |
| 238 | Q | A | -0.5602 | |
| 239 | S | A | 0.0000 | |
| 240 | R | A | -0.9174 | |
| 241 | A | A | 0.0000 | |
| 242 | L | A | 0.0000 | |
| 243 | Y | A | 0.0000 | |
| 244 | P | A | 0.0000 | |
| 245 | S | A | -0.0207 | |
| 246 | I | A | 0.0000 | |
| 247 | Y | A | 0.0297 | |
| 248 | M | A | 0.0000 | |
| 249 | P | A | 0.3170 | |
| 250 | A | A | 0.0822 | |
| 251 | V | A | 1.5108 | |
| 252 | L | A | 0.0000 | |
| 253 | E | A | -1.0204 | |
| 254 | G | A | -0.8908 | |
| 255 | T | A | -0.6466 | |
| 256 | G | A | -0.9403 | |
| 257 | K | A | -0.6122 | |
| 258 | S | A | 0.0000 | |
| 259 | Q | A | -0.9105 | |
| 260 | M | A | -0.4567 | |
| 261 | Y | A | 0.0000 | |
| 262 | V | A | 0.0000 | |
| 263 | Q | A | -0.6380 | |
| 264 | H | A | -0.5050 | |
| 265 | R | A | 0.0000 | |
| 266 | V | A | 0.0000 | |
| 267 | A | A | -0.2792 | |
| 268 | E | A | 0.0000 | |
| 269 | A | A | 0.0000 | |
| 270 | F | A | 0.3143 | |
| 271 | R | A | -0.1669 | |
| 272 | V | A | 0.0000 | |
| 273 | A | A | 0.0000 | |
| 274 | V | A | 1.3695 | |
| 275 | A | A | 0.2789 | |
| 276 | A | A | -0.2397 | |
| 277 | G | A | -0.3663 | |
| 278 | D | A | 0.0000 | |
| 279 | P | A | -0.1398 | |
| 280 | N | A | -0.3954 | |
| 281 | L | A | 0.0000 | |
| 282 | P | A | 0.0000 | |
| 283 | V | A | 0.0000 | |
| 284 | L | A | 0.0000 | |
| 285 | P | A | 0.0000 | |
| 286 | Y | A | 0.0000 | |
| 287 | V | A | 0.0000 | |
| 288 | Q | A | 0.0000 | |
| 289 | I | A | 0.0000 | |
| 290 | F | A | 0.0000 | |
| 291 | Y | A | 0.0000 | |
| 292 | D | A | -0.6164 | |
| 293 | T | A | -0.9037 | |
| 294 | T | A | -1.2921 | |
| 295 | N | A | -1.9893 | |
| 296 | H | A | -1.6270 | |
| 297 | F | A | -0.4035 | |
| 298 | L | A | 0.0000 | |
| 299 | P | A | -0.3698 | |
| 300 | L | A | 0.3641 | |
| 301 | D | A | -1.4027 | |
| 302 | E | A | 0.0000 | |
| 303 | L | A | 0.0000 | |
| 304 | E | A | -0.9214 | |
| 305 | H | A | -1.1174 | |
| 306 | S | A | 0.0000 | |
| 307 | L | A | 0.0000 | |
| 308 | G | A | 0.0000 | |
| 309 | E | A | 0.0000 | |
| 310 | S | A | 0.0000 | |
| 311 | A | A | 0.0000 | |
| 312 | A | A | 0.0000 | |
| 313 | Q | A | -0.3684 | |
| 314 | G | A | 0.0000 | |
| 315 | A | A | 0.0000 | |
| 316 | A | A | 0.0000 | |
| 317 | G | A | 0.0000 | |
| 318 | V | A | 0.0000 | |
| 319 | V | A | 0.0000 | |
| 320 | L | A | 0.0000 | |
| 321 | W | A | 0.3024 | |
| 322 | V | A | 0.0000 | |
| 323 | S | A | 0.0000 | |
| 324 | W | A | -0.6004 | |
| 325 | E | A | -2.2170 | |
| 326 | N | A | 0.0000 | |
| 327 | T | A | 0.0000 | |
| 328 | R | A | -2.9876 | |
| 329 | T | A | -2.8226 | |
| 330 | K | A | -3.3666 | |
| 331 | E | A | -3.1816 | |
| 332 | S | A | -2.5567 | |
| 333 | C | A | 0.0000 | |
| 334 | Q | A | -2.5774 | |
| 335 | A | A | -1.9410 | |
| 336 | I | A | 0.0000 | |
| 337 | K | A | -2.6011 | |
| 338 | E | A | -2.6470 | |
| 339 | Y | A | -1.3296 | |
| 340 | M | A | 0.0000 | |
| 341 | D | A | -1.9123 | |
| 342 | T | A | -0.8824 | |
| 343 | T | A | -0.2285 | |
| 344 | L | A | 0.0000 | |
| 345 | G | A | 0.0000 | |
| 346 | P | A | -0.1602 | |
| 347 | F | A | 0.0000 | |
| 348 | I | A | 0.0000 | |
| 349 | L | A | 0.3689 | |
| 350 | N | A | 0.0062 | |
| 351 | V | A | 0.0000 | |
| 352 | T | A | 0.0000 | |
| 353 | S | A | 0.0505 | |
| 354 | G | A | 0.0000 | |
| 355 | A | A | 0.0000 | |
| 356 | L | A | -0.4380 | |
| 357 | L | A | -0.1501 | |
| 358 | C | A | 0.0000 | |
| 359 | S | A | 0.0000 | |
| 360 | Q | A | -1.3342 | |
| 361 | A | A | -0.2962 | |
| 362 | L | A | -0.5416 | |
| 363 | C | A | 0.0000 | |
| 364 | S | A | -1.3254 | |
| 365 | G | A | -1.3337 | |
| 366 | H | A | -1.5898 | |
| 367 | G | A | 0.0000 | |
| 368 | R | A | -0.6241 | |
| 369 | C | A | 0.0000 | |
| 370 | V | A | -0.4050 | |
| 371 | R | A | 0.0000 | |
| 372 | R | A | -1.0860 | |
| 373 | T | A | -0.9836 | |
| 374 | S | A | -0.7876 | |
| 375 | H | A | -1.1917 | |
| 376 | P | A | -1.5104 | |
| 377 | K | A | -2.0697 | |
| 378 | A | A | -1.0186 | |
| 379 | L | A | -0.3169 | |
| 380 | L | A | 0.0000 | |
| 381 | L | A | 0.1646 | |
| 382 | L | A | 0.0000 | |
| 383 | N | A | -0.8528 | |
| 384 | P | A | -0.5309 | |
| 385 | A | A | -0.3458 | |
| 386 | S | A | -0.6837 | |
| 387 | F | A | 0.0000 | |
| 388 | S | A | -1.0153 | |
| 389 | I | A | -0.4736 | |
| 390 | Q | A | -1.0249 | |
| 391 | L | A | -0.1918 | |
| 392 | T | A | -0.3635 | |
| 393 | P | A | -0.6705 | |
| 394 | G | A | -0.7853 | |
| 395 | G | A | -0.8136 | |
| 396 | G | A | -0.5988 | |
| 397 | P | A | -0.4471 | |
| 398 | L | A | -0.3408 | |
| 399 | S | A | -0.3445 | |
| 400 | L | A | -0.6768 | |
| 401 | R | A | -2.0038 | |
| 402 | G | A | -1.1858 | |
| 403 | A | A | -0.2420 | |
| 404 | L | A | 0.1283 | |
| 405 | S | A | -0.1719 | |
| 406 | L | A | 0.3460 | |
| 407 | E | A | -1.6493 | |
| 408 | D | A | -1.1966 | |
| 409 | Q | A | -0.6850 | |
| 410 | A | A | -0.7953 | |
| 411 | Q | A | -1.2643 | |
| 412 | M | A | 0.0000 | |
| 413 | A | A | -0.3212 | |
| 414 | V | A | 0.3650 | |
| 415 | E | A | -0.6315 | |
| 416 | F | A | 0.0000 | |
| 417 | K | A | -0.7740 | |
| 418 | C | A | -0.5671 | |
| 419 | R | A | -0.7044 | |
| 420 | C | A | -0.8153 | |
| 421 | Y | A | 0.0000 | |
| 422 | P | A | -0.2157 | |
| 423 | G | A | -0.3091 | |
| 424 | W | A | -1.4918 | |
| 425 | Q | A | -1.6183 | |
| 426 | A | A | -1.0448 | |
| 427 | P | A | -0.7152 | |
| 428 | W | A | -0.7863 | |
| 429 | C | A | 0.0000 | |
| 430 | E | A | -3.0850 | |
| 431 | R | A | -3.5001 | |
| 432 | K | A | -2.7343 | |
| 433 | S | A | -0.9416 | |
| 434 | M | A | 0.6718 | |
| 435 | W | A | 1.2878 | |
| 436 | T | A | 0.3573 |
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 | -0.0498 | 3.9007 | View | CSV | PDB |
| 4.5 | -0.0937 | 3.8783 | View | CSV | PDB |
| 5.0 | -0.1484 | 3.8425 | View | CSV | PDB |
| 5.5 | -0.2053 | 3.7986 | View | CSV | PDB |
| 6.0 | -0.2563 | 3.7539 | View | CSV | PDB |
| 6.5 | -0.2956 | 3.7153 | View | CSV | PDB |
| 7.0 | -0.3222 | 3.6892 | View | CSV | PDB |
| 7.5 | -0.3399 | 3.7373 | View | CSV | PDB |
| 8.0 | -0.3526 | 3.8086 | View | CSV | PDB |
| 8.5 | -0.3607 | 3.8808 | View | CSV | PDB |
| 9.0 | -0.3622 | 3.9529 | 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