| Chain sequence(s) |
A: MNEVSVIKEGWLHKRGEYIKTWRPRYFLLKSDGSFIGYKERPEAPDQTLPPLNNFSVAECQLMKTERPRPNTFVIRCLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQRAPGEDPMDYKCGSPSDSSTTEEMEVAVSKARAKVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIRFPRTLSPEAKSLLAGLLKKDPKQRLGGGPSDAKEVMEHRFFLSINWQDVVQKKLLPPFKPQVTSEVDTRYFDDEFTAQSITITPPDRYDSLGLLELDQRTHFPQFSYSASIRE
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: MNEVSVIKEGWLHKRGEYIKTWRPRYFLLKSDGSFIGYKERPEAPDQTLPPLNNFSVAECQLMKTERPRPNTFVIRCLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQR APGEDPMDYKCGSPSDSSTTEEMEVAVSKA RAKVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEIRFPRTLSPEAKSLLAGLLKKDPKQRLGGGPSDAKEVMEHRFFLSINWQDVVQKKLLPPFKPQVTSEVDTRYFDDEFTAQSITITPPDRYDSLGLLELDQRTHFPQFSYSASIRE(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 (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:37)
[INFO] FoldX: Starting FoldX energy minimization (00:00:37)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:40)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/dc1e3b3cc5d1537/tmp/folded.pdb (00:11:40)
[INFO] Main: Simulation completed successfully. (00:14:56)
|
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 | 0.0676 | |
| 2 | N | A | -1.5983 | |
| 3 | E | A | -1.8467 | |
| 4 | V | A | -0.4443 | |
| 5 | S | A | -0.2192 | |
| 6 | V | A | 0.3937 | |
| 7 | I | A | 0.5517 | |
| 8 | K | A | -0.7609 | |
| 9 | E | A | -1.4359 | |
| 10 | G | A | -0.9442 | |
| 11 | W | A | -0.9173 | |
| 12 | L | A | 0.0000 | |
| 13 | H | A | -0.6951 | |
| 14 | K | A | -0.9940 | |
| 15 | R | A | -1.3221 | |
| 16 | G | A | 0.0000 | |
| 17 | E | A | -2.0062 | |
| 18 | Y | A | -0.5516 | |
| 19 | I | A | 0.0000 | |
| 20 | K | A | -2.2052 | |
| 21 | T | A | -1.3103 | |
| 22 | W | A | -0.8048 | |
| 23 | R | A | -0.8676 | |
| 24 | P | A | -0.9491 | |
| 25 | R | A | -1.4971 | |
| 26 | Y | A | 0.0000 | |
| 27 | F | A | 0.0000 | |
| 28 | L | A | -0.6541 | |
| 29 | L | A | 0.0000 | |
| 30 | K | A | -0.3125 | |
| 31 | S | A | -0.5169 | |
| 32 | D | A | -1.3240 | |
| 33 | G | A | 0.0000 | |
| 34 | S | A | -0.6672 | |
| 35 | F | A | 0.0000 | |
| 36 | I | A | 0.0000 | |
| 37 | G | A | 0.0000 | |
| 38 | Y | A | 0.0000 | |
| 39 | K | A | -2.8061 | |
| 40 | E | A | -3.6177 | |
| 41 | R | A | -3.5152 | |
| 42 | P | A | -2.9298 | |
| 43 | E | A | -3.0196 | |
| 44 | A | A | -2.1335 | |
| 45 | P | A | -1.7042 | |
| 46 | D | A | -2.7093 | |
| 47 | Q | A | -2.4864 | |
| 48 | T | A | -1.0786 | |
| 49 | L | A | -1.3089 | |
| 50 | P | A | -0.7863 | |
| 51 | P | A | -1.0580 | |
| 52 | L | A | -1.0400 | |
| 53 | N | A | -1.2501 | |
| 54 | N | A | -1.5329 | |
| 55 | F | A | 0.0000 | |
| 56 | S | A | -0.9289 | |
| 57 | V | A | 0.0000 | |
| 58 | A | A | -1.5831 | |
| 59 | E | A | -2.3582 | |
| 60 | C | A | -1.3823 | |
| 61 | Q | A | -1.5709 | |
| 62 | L | A | -1.3434 | |
| 63 | M | A | -0.9515 | |
| 64 | K | A | -2.3397 | |
| 65 | T | A | -2.6131 | |
| 66 | E | A | -3.7449 | |
| 67 | R | A | -3.7495 | |
| 68 | P | A | -2.7776 | |
| 69 | R | A | -3.2317 | |
| 70 | P | A | -2.8658 | |
| 71 | N | A | -2.8042 | |
| 72 | T | A | 0.0000 | |
| 73 | F | A | 0.0000 | |
| 74 | V | A | 0.0000 | |
| 75 | I | A | 0.0000 | |
| 76 | R | A | -0.8488 | |
| 77 | C | A | 0.0000 | |
| 78 | L | A | 1.2705 | |
| 79 | Q | A | 0.8325 | |
| 80 | W | A | 1.5213 | |
| 81 | T | A | 1.0598 | |
| 82 | T | A | 1.3114 | |
| 83 | V | A | 2.0648 | |
| 84 | I | A | 0.7675 | |
| 85 | E | A | -0.8170 | |
| 86 | R | A | -1.1509 | |
| 87 | T | A | 0.0000 | |
| 88 | F | A | 0.0000 | |
| 89 | H | A | -1.5962 | |
| 90 | V | A | 0.0000 | |
| 91 | D | A | -2.4434 | |
| 92 | S | A | -2.0384 | |
| 93 | P | A | -2.4003 | |
| 94 | D | A | -3.1285 | |
| 95 | E | A | -2.7982 | |
| 96 | R | A | 0.0000 | |
| 97 | E | A | -3.2840 | |
| 98 | E | A | -3.0632 | |
| 99 | W | A | 0.0000 | |
| 100 | M | A | -1.9792 | |
| 101 | R | A | -2.5187 | |
| 102 | A | A | -1.3651 | |
| 103 | I | A | 0.0000 | |
| 104 | Q | A | -1.6073 | |
| 105 | M | A | -0.3016 | |
| 106 | V | A | 0.0000 | |
| 107 | A | A | 0.0000 | |
| 108 | N | A | -2.4803 | |
| 109 | S | A | -1.9347 | |
| 110 | L | A | -2.3754 | |
| 111 | K | A | -3.4855 | |
| 112 | Q | A | -3.1466 | |
| 113 | R | A | -3.0406 | |
| 144 | R | A | -2.2797 | |
| 145 | A | A | -1.6635 | |
| 146 | K | A | -2.2640 | |
| 147 | V | A | 0.0000 | |
| 148 | T | A | -1.1238 | |
| 149 | M | A | -0.8272 | |
| 150 | N | A | -1.8923 | |
| 151 | D | A | -2.2797 | |
| 152 | F | A | 0.0000 | |
| 153 | D | A | -1.2152 | |
| 154 | Y | A | 0.1186 | |
| 155 | L | A | 0.4133 | |
| 156 | K | A | -0.0920 | |
| 157 | L | A | 0.0000 | |
| 158 | L | A | 0.0000 | |
| 159 | G | A | -1.1662 | |
| 160 | K | A | -1.2909 | |
| 161 | G | A | -0.9725 | |
| 162 | T | A | -0.5060 | |
| 163 | F | A | -0.4642 | |
| 164 | G | A | -0.4871 | |
| 165 | K | A | -0.6501 | |
| 166 | V | A | -0.2587 | |
| 167 | I | A | 0.0000 | |
| 168 | L | A | 0.0000 | |
| 169 | V | A | 0.0000 | |
| 170 | R | A | -1.6877 | |
| 171 | E | A | 0.0000 | |
| 172 | K | A | -2.7520 | |
| 173 | A | A | -1.3875 | |
| 174 | T | A | -1.3352 | |
| 175 | G | A | -1.7570 | |
| 176 | R | A | -2.3304 | |
| 177 | Y | A | -1.2632 | |
| 178 | Y | A | 0.0000 | |
| 179 | A | A | 0.0000 | |
| 180 | M | A | 0.0000 | |
| 181 | K | A | -0.4198 | |
| 182 | I | A | 0.0000 | |
| 183 | L | A | 0.0000 | |
| 184 | R | A | -0.8960 | |
| 185 | K | A | 0.0000 | |
| 186 | E | A | -1.8959 | |
| 187 | V | A | -1.0644 | |
| 188 | I | A | 0.0000 | |
| 189 | I | A | -1.1779 | |
| 190 | A | A | -1.3065 | |
| 191 | K | A | -2.2480 | |
| 192 | D | A | -2.5295 | |
| 193 | E | A | -1.3697 | |
| 194 | V | A | -0.5509 | |
| 195 | A | A | -0.2554 | |
| 196 | H | A | -0.6217 | |
| 197 | T | A | 0.0000 | |
| 198 | V | A | -0.1179 | |
| 199 | T | A | -0.4662 | |
| 200 | E | A | 0.0000 | |
| 201 | S | A | 0.0000 | |
| 202 | R | A | -1.4559 | |
| 203 | V | A | 0.0000 | |
| 204 | L | A | 0.0000 | |
| 205 | Q | A | -1.4280 | |
| 206 | N | A | -2.1114 | |
| 207 | T | A | 0.0000 | |
| 208 | R | A | -1.5585 | |
| 209 | H | A | -0.6250 | |
| 210 | P | A | -0.5163 | |
| 211 | F | A | 0.0000 | |
| 212 | L | A | 0.0000 | |
| 213 | T | A | 0.0000 | |
| 214 | A | A | -0.7677 | |
| 215 | L | A | 0.0000 | |
| 216 | K | A | -0.2624 | |
| 217 | Y | A | 0.0000 | |
| 218 | A | A | 0.0000 | |
| 219 | F | A | 0.0000 | |
| 220 | Q | A | -1.0263 | |
| 221 | T | A | -0.9590 | |
| 222 | H | A | -1.6412 | |
| 223 | D | A | 0.0000 | |
| 224 | R | A | -0.9928 | |
| 225 | L | A | 0.0000 | |
| 226 | C | A | 0.0000 | |
| 227 | F | A | 0.0000 | |
| 228 | V | A | 0.0000 | |
| 229 | M | A | -0.2447 | |
| 230 | E | A | -0.8551 | |
| 231 | Y | A | -0.6220 | |
| 232 | A | A | 0.0000 | |
| 233 | N | A | 0.0000 | |
| 234 | G | A | 0.0000 | |
| 235 | G | A | 0.0000 | |
| 236 | E | A | -0.0209 | |
| 237 | L | A | 0.0000 | |
| 238 | F | A | 0.7619 | |
| 239 | F | A | 0.0186 | |
| 240 | H | A | 0.0000 | |
| 241 | L | A | 0.0000 | |
| 242 | S | A | -1.3869 | |
| 243 | R | A | -2.5407 | |
| 244 | E | A | -2.6061 | |
| 245 | R | A | -2.5532 | |
| 246 | V | A | -0.7143 | |
| 247 | F | A | 0.0000 | |
| 248 | T | A | -0.7401 | |
| 249 | E | A | -1.2725 | |
| 250 | E | A | -2.1488 | |
| 251 | R | A | 0.0000 | |
| 252 | A | A | 0.0000 | |
| 253 | R | A | -1.0766 | |
| 254 | F | A | 0.0000 | |
| 255 | Y | A | 0.0000 | |
| 256 | G | A | 0.0000 | |
| 257 | A | A | 0.0000 | |
| 258 | E | A | 0.0000 | |
| 259 | I | A | 0.0000 | |
| 260 | V | A | 0.0000 | |
| 261 | S | A | 0.0000 | |
| 262 | A | A | 0.0000 | |
| 263 | L | A | 0.0000 | |
| 264 | E | A | -1.3711 | |
| 265 | Y | A | -0.8910 | |
| 266 | L | A | 0.0000 | |
| 267 | H | A | 0.0000 | |
| 268 | S | A | -1.4467 | |
| 269 | R | A | -2.1113 | |
| 270 | D | A | -2.1923 | |
| 271 | V | A | 0.0000 | |
| 272 | V | A | 0.0000 | |
| 273 | Y | A | 0.0000 | |
| 274 | R | A | 0.0000 | |
| 275 | D | A | -0.5466 | |
| 276 | I | A | 0.0000 | |
| 277 | K | A | -0.3681 | |
| 278 | L | A | 0.0000 | |
| 279 | E | A | -0.5786 | |
| 280 | N | A | 0.0000 | |
| 281 | L | A | 0.0000 | |
| 282 | M | A | -0.0802 | |
| 283 | L | A | 0.0000 | |
| 284 | D | A | -1.6540 | |
| 285 | K | A | -2.8993 | |
| 286 | D | A | -2.7988 | |
| 287 | G | A | 0.0000 | |
| 288 | H | A | 0.0000 | |
| 289 | I | A | 0.0000 | |
| 290 | K | A | -0.5264 | |
| 291 | I | A | 0.0000 | |
| 292 | T | A | -1.0624 | |
| 293 | D | A | -1.7687 | |
| 294 | F | A | 0.0000 | |
| 295 | G | A | -0.7160 | |
| 296 | L | A | -0.3704 | |
| 297 | C | A | 0.0000 | |
| 298 | K | A | -1.1788 | |
| 299 | E | A | -1.6327 | |
| 300 | G | A | -1.5367 | |
| 301 | I | A | 0.0000 | |
| 302 | S | A | -1.8170 | |
| 303 | D | A | -2.3920 | |
| 304 | G | A | -1.4251 | |
| 305 | A | A | -1.1850 | |
| 306 | T | A | -1.3165 | |
| 307 | M | A | 0.0000 | |
| 308 | K | A | -2.1659 | |
| 309 | T | A | -0.9409 | |
| 310 | F | A | -0.1737 | |
| 311 | C | A | 0.0228 | |
| 312 | G | A | -0.0712 | |
| 313 | T | A | -0.2012 | |
| 314 | P | A | -0.3768 | |
| 315 | E | A | -0.1352 | |
| 316 | Y | A | 0.0089 | |
| 317 | L | A | 0.0000 | |
| 318 | A | A | 0.0000 | |
| 319 | P | A | 0.0000 | |
| 320 | E | A | 0.0000 | |
| 321 | V | A | 0.0000 | |
| 322 | L | A | 0.0000 | |
| 323 | E | A | -0.9924 | |
| 324 | D | A | -1.4525 | |
| 325 | N | A | -1.6479 | |
| 326 | D | A | -2.2497 | |
| 327 | Y | A | 0.0000 | |
| 328 | G | A | -1.1173 | |
| 329 | R | A | 0.0000 | |
| 330 | A | A | 0.0000 | |
| 331 | V | A | 0.0000 | |
| 332 | D | A | 0.0000 | |
| 333 | W | A | 0.0000 | |
| 334 | W | A | 0.0000 | |
| 335 | G | A | 0.0000 | |
| 336 | L | A | 0.0000 | |
| 337 | G | A | 0.0000 | |
| 338 | V | A | 0.0000 | |
| 339 | V | A | 0.0000 | |
| 340 | M | A | 0.0000 | |
| 341 | Y | A | 0.0000 | |
| 342 | E | A | 0.0000 | |
| 343 | M | A | 0.0000 | |
| 344 | M | A | 0.0000 | |
| 345 | C | A | -0.4841 | |
| 346 | G | A | -1.2946 | |
| 347 | R | A | -1.7882 | |
| 348 | L | A | 0.0000 | |
| 349 | P | A | 0.0000 | |
| 350 | F | A | 0.0000 | |
| 351 | Y | A | 0.0079 | |
| 352 | N | A | -1.7675 | |
| 353 | Q | A | -2.5102 | |
| 354 | D | A | -3.4642 | |
| 355 | H | A | -2.9625 | |
| 356 | E | A | -3.5961 | |
| 357 | R | A | -3.5386 | |
| 358 | L | A | 0.0000 | |
| 359 | F | A | 0.0000 | |
| 360 | E | A | -1.8159 | |
| 361 | L | A | -1.0551 | |
| 362 | I | A | 0.0000 | |
| 363 | L | A | 0.0000 | |
| 364 | M | A | -0.1250 | |
| 365 | E | A | -1.8589 | |
| 366 | E | A | -2.5779 | |
| 367 | I | A | -1.6544 | |
| 368 | R | A | -2.4343 | |
| 369 | F | A | -1.2959 | |
| 370 | P | A | -1.3052 | |
| 371 | R | A | -2.1740 | |
| 372 | T | A | -1.0462 | |
| 373 | L | A | 0.0000 | |
| 374 | S | A | -1.0645 | |
| 375 | P | A | -1.4174 | |
| 376 | E | A | -1.6515 | |
| 377 | A | A | 0.0000 | |
| 378 | K | A | -1.5878 | |
| 379 | S | A | -1.1405 | |
| 380 | L | A | 0.0000 | |
| 381 | L | A | 0.0000 | |
| 382 | A | A | -0.6971 | |
| 383 | G | A | -0.7277 | |
| 384 | L | A | 0.0000 | |
| 385 | L | A | 0.0000 | |
| 386 | K | A | -2.0934 | |
| 387 | K | A | -1.8538 | |
| 388 | D | A | -2.3257 | |
| 389 | P | A | -2.0011 | |
| 390 | K | A | -2.8019 | |
| 391 | Q | A | -2.6023 | |
| 392 | R | A | 0.0000 | |
| 393 | L | A | -0.9520 | |
| 394 | G | A | 0.0000 | |
| 395 | G | A | -1.5572 | |
| 396 | G | A | -1.5696 | |
| 397 | P | A | -1.3906 | |
| 398 | S | A | -1.2547 | |
| 399 | D | A | -1.4443 | |
| 400 | A | A | 0.0000 | |
| 401 | K | A | -2.6869 | |
| 402 | E | A | -2.0426 | |
| 403 | V | A | 0.0000 | |
| 404 | M | A | -1.7336 | |
| 405 | E | A | -2.5449 | |
| 406 | H | A | -1.9610 | |
| 407 | R | A | -2.0143 | |
| 408 | F | A | 0.0000 | |
| 409 | F | A | 0.0000 | |
| 410 | L | A | 0.2086 | |
| 411 | S | A | 0.1603 | |
| 412 | I | A | -0.3427 | |
| 413 | N | A | -0.9054 | |
| 414 | W | A | -0.9799 | |
| 415 | Q | A | -1.8197 | |
| 416 | D | A | -1.8879 | |
| 417 | V | A | 0.0000 | |
| 418 | V | A | -0.5749 | |
| 419 | Q | A | -2.0771 | |
| 420 | K | A | -2.1285 | |
| 421 | K | A | -2.2166 | |
| 422 | L | A | -0.4269 | |
| 423 | L | A | 0.6641 | |
| 424 | P | A | 0.0000 | |
| 425 | P | A | -0.2252 | |
| 426 | F | A | -0.5592 | |
| 427 | K | A | -2.0083 | |
| 428 | P | A | 0.0000 | |
| 429 | Q | A | -2.0354 | |
| 430 | V | A | -1.7570 | |
| 431 | T | A | -0.9654 | |
| 432 | S | A | -1.0819 | |
| 433 | E | A | -1.8734 | |
| 434 | V | A | -0.5102 | |
| 435 | D | A | -1.1566 | |
| 436 | T | A | 0.0000 | |
| 437 | R | A | -2.1267 | |
| 438 | Y | A | 0.0000 | |
| 439 | F | A | -1.7785 | |
| 440 | D | A | -3.2386 | |
| 441 | D | A | -3.6552 | |
| 442 | E | A | -3.1664 | |
| 443 | F | A | -2.0231 | |
| 444 | T | A | -1.8091 | |
| 445 | A | A | -1.4717 | |
| 446 | Q | A | -1.0838 | |
| 447 | S | A | -0.1078 | |
| 448 | I | A | 0.4604 | |
| 449 | T | A | 0.3547 | |
| 450 | I | A | 0.5627 | |
| 451 | T | A | -0.1587 | |
| 452 | P | A | -0.9278 | |
| 453 | P | A | -1.6597 | |
| 454 | D | A | -2.5996 | |
| 455 | R | A | -2.2345 | |
| 456 | Y | A | -0.2167 | |
| 457 | D | A | -0.7660 | |
| 458 | S | A | 0.0257 | |
| 459 | L | A | 1.5505 | |
| 460 | G | A | 0.8098 | |
| 461 | L | A | 1.6237 | |
| 462 | L | A | -0.0458 | |
| 463 | E | A | -1.0249 | |
| 464 | L | A | -0.2275 | |
| 465 | D | A | -1.7790 | |
| 466 | Q | A | -2.1665 | |
| 467 | R | A | -2.8650 | |
| 468 | T | A | -1.8271 | |
| 469 | H | A | -1.4894 | |
| 470 | F | A | 0.0000 | |
| 471 | P | A | -1.4334 | |
| 472 | Q | A | -1.5846 | |
| 473 | F | A | 0.0000 | |
| 474 | S | A | -0.7949 | |
| 475 | Y | A | -0.5204 | |
| 476 | S | A | -0.5082 | |
| 477 | A | A | -0.2364 | |
| 478 | S | A | -0.6104 | |
| 479 | I | A | -0.8772 | |
| 480 | R | A | -2.4167 | |
| 481 | E | A | -2.5120 |
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 | -0.8027 | 4.0439 | View | CSV | PDB |
| 4.5 | -0.8839 | 4.0439 | View | CSV | PDB |
| 5.0 | -0.9832 | 4.0439 | View | CSV | PDB |
| 5.5 | -1.0836 | 4.0439 | View | CSV | PDB |
| 6.0 | -1.1687 | 4.0439 | View | CSV | PDB |
| 6.5 | -1.2261 | 4.0439 | View | CSV | PDB |
| 7.0 | -1.2532 | 4.0439 | View | CSV | PDB |
| 7.5 | -1.2577 | 4.0439 | View | CSV | PDB |
| 8.0 | -1.2483 | 4.0439 | View | CSV | PDB |
| 8.5 | -1.2282 | 4.0439 | View | CSV | PDB |
| 9.0 | -1.1973 | 4.0439 | View | CSV | PDB |