| Chain sequence(s) |
A: MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAMDRTTTRLYAGLKKRLAMASANKA
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] (00:00:00)
[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-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:04)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/7fad802480ccf4f/tmp/folded.pdb (00:05:04)
[INFO] Main: Simulation completed successfully. (00:07:02)
|
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 | 0.7183 | |
| 2 | S | A | 0.1440 | |
| 3 | R | A | -0.1871 | |
| 4 | T | A | 0.2480 | |
| 5 | V | A | 0.7961 | |
| 6 | M | A | 0.0000 | |
| 7 | E | A | -0.7316 | |
| 8 | R | A | -1.5265 | |
| 9 | I | A | 0.0000 | |
| 10 | E | A | -0.4984 | |
| 11 | Y | A | 0.0000 | |
| 12 | E | A | -0.2636 | |
| 13 | M | A | -0.2841 | |
| 14 | H | A | -0.7467 | |
| 15 | T | A | -0.7767 | |
| 16 | P | A | 0.0000 | |
| 17 | D | A | -2.3390 | |
| 18 | P | A | -2.0525 | |
| 19 | K | A | -2.6339 | |
| 20 | A | A | -2.3604 | |
| 21 | D | A | -2.5608 | |
| 22 | P | A | 0.0000 | |
| 23 | D | A | -2.9095 | |
| 24 | K | A | -2.9381 | |
| 25 | L | A | -1.5348 | |
| 26 | H | A | -1.0590 | |
| 27 | F | A | 0.0000 | |
| 28 | V | A | 0.0000 | |
| 29 | Q | A | -0.6032 | |
| 30 | I | A | 0.0000 | |
| 31 | D | A | -1.6258 | |
| 32 | E | A | -2.5200 | |
| 33 | A | A | -1.3984 | |
| 34 | K | A | -1.7720 | |
| 35 | C | A | -1.4120 | |
| 36 | I | A | -0.8705 | |
| 37 | G | A | 0.0000 | |
| 38 | C | A | -0.5969 | |
| 39 | D | A | -0.8710 | |
| 40 | T | A | -0.6985 | |
| 41 | C | A | 0.0000 | |
| 42 | S | A | -0.2517 | |
| 43 | Q | A | -1.1428 | |
| 44 | Y | A | -0.1496 | |
| 45 | C | A | -0.2460 | |
| 46 | P | A | -1.0361 | |
| 47 | T | A | -0.2892 | |
| 48 | A | A | 0.0732 | |
| 49 | A | A | 0.0000 | |
| 50 | I | A | 0.3527 | |
| 51 | F | A | 0.5599 | |
| 52 | G | A | -1.0778 | |
| 53 | E | A | -2.1717 | |
| 54 | M | A | -1.2598 | |
| 55 | G | A | -1.7012 | |
| 56 | E | A | -2.7049 | |
| 57 | P | A | -1.9170 | |
| 58 | H | A | 0.0000 | |
| 59 | S | A | -0.4740 | |
| 60 | I | A | 0.0000 | |
| 61 | P | A | -0.4667 | |
| 62 | H | A | -1.1314 | |
| 63 | I | A | -1.6532 | |
| 64 | E | A | -2.5264 | |
| 65 | A | A | -1.0115 | |
| 66 | C | A | -0.6946 | |
| 67 | I | A | 0.0000 | |
| 68 | N | A | 0.0000 | |
| 69 | C | A | 0.0000 | |
| 70 | G | A | 0.0000 | |
| 71 | Q | A | 0.0000 | |
| 72 | C | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.0545 | |
| 75 | H | A | -0.5695 | |
| 76 | C | A | 0.0000 | |
| 77 | P | A | 0.0000 | |
| 78 | E | A | -0.7135 | |
| 79 | N | A | -0.9950 | |
| 80 | A | A | 0.0000 | |
| 81 | I | A | 0.0000 | |
| 82 | Y | A | 0.0000 | |
| 83 | E | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | Q | A | 0.0000 | |
| 86 | S | A | 0.0000 | |
| 87 | W | A | 0.0000 | |
| 88 | V | A | 0.0000 | |
| 89 | P | A | -0.9324 | |
| 90 | E | A | -1.3958 | |
| 91 | V | A | 0.0000 | |
| 92 | E | A | -1.8609 | |
| 93 | K | A | -2.8434 | |
| 94 | K | A | -2.5439 | |
| 95 | L | A | -2.0770 | |
| 96 | K | A | -2.9780 | |
| 97 | D | A | -2.6650 | |
| 98 | G | A | -2.1172 | |
| 99 | K | A | -2.4601 | |
| 100 | V | A | -2.1004 | |
| 101 | K | A | -1.4244 | |
| 102 | C | A | 0.0000 | |
| 103 | I | A | 0.0000 | |
| 104 | A | A | 0.0000 | |
| 105 | M | A | 0.0000 | |
| 106 | P | A | 0.0000 | |
| 107 | A | A | 0.0000 | |
| 108 | P | A | 0.0000 | |
| 109 | A | A | 0.0000 | |
| 110 | V | A | 0.0000 | |
| 111 | R | A | 0.0000 | |
| 112 | Y | A | 1.2739 | |
| 113 | A | A | 0.0000 | |
| 114 | L | A | 0.0000 | |
| 115 | G | A | 0.0000 | |
| 116 | D | A | 0.1817 | |
| 117 | A | A | -0.0256 | |
| 118 | F | A | -0.1666 | |
| 119 | G | A | -0.1329 | |
| 120 | M | A | 0.3934 | |
| 121 | P | A | 0.6241 | |
| 122 | V | A | 1.6923 | |
| 123 | G | A | 1.0392 | |
| 124 | S | A | 1.2160 | |
| 125 | V | A | 1.9867 | |
| 126 | T | A | 0.0000 | |
| 127 | T | A | -0.1855 | |
| 128 | G | A | 0.0000 | |
| 129 | K | A | -1.5633 | |
| 130 | M | A | 0.0000 | |
| 131 | L | A | 0.0000 | |
| 132 | A | A | -1.8898 | |
| 133 | A | A | 0.0000 | |
| 134 | L | A | 0.0000 | |
| 135 | Q | A | -2.3419 | |
| 136 | K | A | -2.2742 | |
| 137 | L | A | -1.3642 | |
| 138 | G | A | -1.7913 | |
| 139 | F | A | 0.0000 | |
| 140 | A | A | -0.6995 | |
| 141 | H | A | -0.5943 | |
| 142 | C | A | -0.5696 | |
| 143 | W | A | 0.0000 | |
| 144 | D | A | 0.0000 | |
| 145 | T | A | 0.0000 | |
| 146 | E | A | 0.0000 | |
| 147 | F | A | -0.1481 | |
| 148 | T | A | 0.0000 | |
| 149 | A | A | 0.0000 | |
| 150 | D | A | 0.0000 | |
| 151 | V | A | 0.2021 | |
| 152 | T | A | 0.0000 | |
| 153 | I | A | 0.0000 | |
| 154 | W | A | 0.3471 | |
| 155 | E | A | -1.0372 | |
| 156 | E | A | 0.0000 | |
| 157 | G | A | 0.0000 | |
| 158 | S | A | -0.4757 | |
| 159 | E | A | -0.9681 | |
| 160 | F | A | 0.0000 | |
| 161 | V | A | -0.8126 | |
| 162 | E | A | -2.3643 | |
| 163 | R | A | 0.0000 | |
| 164 | L | A | -1.0991 | |
| 165 | T | A | -1.7331 | |
| 166 | K | A | -3.1653 | |
| 167 | K | A | -3.2731 | |
| 168 | S | A | -2.5398 | |
| 169 | D | A | -2.5334 | |
| 170 | M | A | -1.1239 | |
| 171 | P | A | -0.4086 | |
| 172 | L | A | 0.1308 | |
| 173 | P | A | 0.0000 | |
| 174 | Q | A | 0.0000 | |
| 175 | F | A | 0.0000 | |
| 176 | T | A | 0.0000 | |
| 177 | S | A | -0.1491 | |
| 178 | C | A | 0.0000 | |
| 179 | C | A | 0.0000 | |
| 180 | P | A | 0.0000 | |
| 181 | G | A | 0.0000 | |
| 182 | W | A | 0.0000 | |
| 183 | Q | A | -0.3492 | |
| 184 | K | A | 0.0000 | |
| 185 | Y | A | 0.0000 | |
| 186 | A | A | 0.0000 | |
| 187 | E | A | -0.8007 | |
| 188 | T | A | -0.5591 | |
| 189 | Y | A | -0.1525 | |
| 190 | Y | A | 0.0000 | |
| 191 | P | A | -0.7488 | |
| 192 | E | A | -1.3928 | |
| 193 | L | A | 0.0000 | |
| 194 | L | A | -0.1401 | |
| 195 | P | A | -0.0787 | |
| 196 | H | A | 0.0025 | |
| 197 | F | A | 0.0000 | |
| 198 | S | A | 0.0000 | |
| 199 | T | A | -0.3341 | |
| 200 | C | A | -0.5033 | |
| 201 | K | A | -0.7143 | |
| 202 | S | A | 0.0000 | |
| 203 | P | A | 0.0000 | |
| 204 | I | A | 0.0000 | |
| 205 | G | A | 0.0000 | |
| 206 | M | A | 0.0000 | |
| 207 | N | A | 0.0000 | |
| 208 | G | A | 0.0000 | |
| 209 | A | A | -0.3092 | |
| 210 | L | A | 0.2386 | |
| 211 | A | A | 0.0000 | |
| 212 | K | A | 0.0000 | |
| 213 | T | A | -0.5853 | |
| 214 | Y | A | -0.6244 | |
| 215 | G | A | 0.0000 | |
| 216 | A | A | 0.0000 | |
| 217 | E | A | -2.9217 | |
| 218 | R | A | -2.4862 | |
| 219 | M | A | -1.6916 | |
| 220 | K | A | -2.6720 | |
| 221 | Y | A | -2.0121 | |
| 222 | D | A | -2.0397 | |
| 223 | P | A | -1.8928 | |
| 224 | K | A | -2.2033 | |
| 225 | Q | A | -2.0674 | |
| 226 | V | A | 0.0000 | |
| 227 | Y | A | 0.0000 | |
| 228 | T | A | 0.0000 | |
| 229 | V | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | I | A | 0.0000 | |
| 232 | M | A | 0.0000 | |
| 233 | P | A | 0.0000 | |
| 234 | C | A | 0.0000 | |
| 235 | I | A | 0.0000 | |
| 236 | A | A | 0.0000 | |
| 237 | K | A | 0.0000 | |
| 238 | K | A | 0.0000 | |
| 239 | Y | A | 0.0000 | |
| 240 | E | A | 0.0000 | |
| 241 | G | A | 0.0000 | |
| 242 | L | A | 0.0000 | |
| 243 | R | A | -1.7562 | |
| 244 | P | A | -2.0920 | |
| 245 | E | A | -2.5408 | |
| 246 | L | A | -1.9419 | |
| 247 | K | A | -2.5730 | |
| 248 | S | A | -1.4360 | |
| 249 | S | A | -0.7613 | |
| 250 | G | A | -1.0053 | |
| 251 | M | A | -1.2289 | |
| 252 | R | A | -1.8065 | |
| 253 | D | A | 0.0000 | |
| 254 | I | A | 0.0000 | |
| 255 | D | A | -0.4108 | |
| 256 | A | A | 0.0000 | |
| 257 | T | A | 0.0000 | |
| 258 | L | A | 0.0000 | |
| 259 | T | A | 0.0000 | |
| 260 | T | A | 0.0000 | |
| 261 | R | A | 0.0000 | |
| 262 | E | A | 0.0000 | |
| 263 | L | A | 0.0000 | |
| 264 | A | A | 0.0000 | |
| 265 | Y | A | -0.4236 | |
| 266 | M | A | 0.0000 | |
| 267 | I | A | 0.0000 | |
| 268 | K | A | -2.0103 | |
| 269 | K | A | -2.2027 | |
| 270 | A | A | -1.5687 | |
| 271 | G | A | -1.5425 | |
| 272 | I | A | -1.7075 | |
| 273 | D | A | -1.9786 | |
| 274 | F | A | 0.0000 | |
| 275 | A | A | -1.2041 | |
| 276 | K | A | -2.3764 | |
| 277 | L | A | 0.0000 | |
| 278 | P | A | -1.8381 | |
| 279 | D | A | -2.7488 | |
| 280 | G | A | -2.3346 | |
| 281 | K | A | -2.7127 | |
| 282 | R | A | -2.1448 | |
| 283 | D | A | -1.3555 | |
| 284 | S | A | -0.9469 | |
| 285 | L | A | -0.4351 | |
| 286 | M | A | 0.0000 | |
| 287 | G | A | 0.0000 | |
| 288 | E | A | -1.9242 | |
| 289 | S | A | -0.9470 | |
| 290 | T | A | -0.5251 | |
| 291 | G | A | -0.2416 | |
| 292 | G | A | -0.0602 | |
| 293 | A | A | 0.0000 | |
| 294 | T | A | 0.1191 | |
| 295 | I | A | 0.4322 | |
| 296 | F | A | 0.0000 | |
| 297 | G | A | 0.0000 | |
| 298 | V | A | 1.1026 | |
| 299 | T | A | 0.0000 | |
| 300 | G | A | 0.0000 | |
| 301 | G | A | 0.0000 | |
| 302 | V | A | 0.0000 | |
| 303 | M | A | 0.0000 | |
| 304 | E | A | 0.0000 | |
| 305 | A | A | 0.0000 | |
| 306 | A | A | 0.0000 | |
| 307 | L | A | 0.0000 | |
| 308 | R | A | -0.5788 | |
| 309 | F | A | 0.1181 | |
| 310 | A | A | 0.0000 | |
| 311 | Y | A | -0.9147 | |
| 312 | E | A | -2.0005 | |
| 313 | A | A | -0.5604 | |
| 314 | V | A | -0.0232 | |
| 315 | T | A | -1.2380 | |
| 316 | G | A | -1.8030 | |
| 317 | K | A | -3.2382 | |
| 318 | K | A | -3.2873 | |
| 319 | P | A | 0.0000 | |
| 320 | D | A | -2.5910 | |
| 321 | S | A | -1.7432 | |
| 322 | W | A | -1.1866 | |
| 323 | D | A | -2.1478 | |
| 324 | F | A | -1.3773 | |
| 325 | K | A | -2.3163 | |
| 326 | A | A | -1.5336 | |
| 327 | V | A | 0.0000 | |
| 328 | R | A | -1.6184 | |
| 329 | G | A | -0.5703 | |
| 330 | L | A | 0.5198 | |
| 331 | D | A | -1.2632 | |
| 332 | G | A | 0.0000 | |
| 333 | I | A | -0.3421 | |
| 334 | K | A | 0.0000 | |
| 335 | E | A | -2.0262 | |
| 336 | A | A | 0.0000 | |
| 337 | T | A | -1.3552 | |
| 338 | V | A | -1.1749 | |
| 339 | N | A | -2.2236 | |
| 340 | V | A | 0.0000 | |
| 341 | G | A | -1.4259 | |
| 342 | G | A | -1.4194 | |
| 343 | T | A | -1.6308 | |
| 344 | D | A | -2.6233 | |
| 345 | V | A | 0.0000 | |
| 346 | K | A | -1.5902 | |
| 347 | V | A | 0.0000 | |
| 348 | A | A | 0.0000 | |
| 349 | V | A | 0.0000 | |
| 350 | V | A | 0.0000 | |
| 351 | H | A | 0.0000 | |
| 352 | G | A | -0.6592 | |
| 353 | A | A | 0.0000 | |
| 354 | K | A | -2.7384 | |
| 355 | R | A | -2.5591 | |
| 356 | F | A | 0.0000 | |
| 357 | K | A | -3.1954 | |
| 358 | Q | A | -2.9659 | |
| 359 | V | A | 0.0000 | |
| 360 | C | A | 0.0000 | |
| 361 | D | A | -2.8738 | |
| 362 | D | A | -2.8722 | |
| 363 | V | A | 0.0000 | |
| 364 | K | A | -2.8026 | |
| 365 | A | A | -1.9909 | |
| 366 | G | A | -2.1177 | |
| 367 | K | A | -2.6311 | |
| 368 | S | A | -1.7025 | |
| 369 | P | A | -0.9133 | |
| 370 | Y | A | -0.7035 | |
| 371 | H | A | -0.4269 | |
| 372 | F | A | 0.0000 | |
| 373 | I | A | 0.0000 | |
| 374 | E | A | 0.0000 | |
| 375 | Y | A | 0.0000 | |
| 376 | M | A | 0.0000 | |
| 377 | A | A | 0.0000 | |
| 378 | C | A | 0.0000 | |
| 379 | P | A | -0.0917 | |
| 380 | G | A | 0.0000 | |
| 381 | G | A | 0.0000 | |
| 382 | C | A | 0.7678 | |
| 383 | V | A | 1.0745 | |
| 384 | C | A | 0.9536 | |
| 385 | G | A | 0.0000 | |
| 386 | G | A | 0.0000 | |
| 387 | G | A | 0.0000 | |
| 388 | Q | A | 0.0000 | |
| 389 | P | A | 0.0000 | |
| 390 | V | A | -0.0918 | |
| 391 | M | A | 0.4416 | |
| 392 | P | A | 0.4868 | |
| 393 | G | A | 0.8503 | |
| 394 | V | A | 2.0768 | |
| 395 | L | A | 1.6128 | |
| 396 | E | A | -0.1910 | |
| 397 | A | A | 0.3269 | |
| 398 | M | A | 0.3249 | |
| 399 | D | A | -1.3397 | |
| 400 | R | A | -1.0284 | |
| 401 | T | A | -0.4327 | |
| 402 | T | A | -0.3225 | |
| 403 | T | A | -0.2271 | |
| 404 | R | A | -0.3088 | |
| 405 | L | A | 1.2555 | |
| 406 | Y | A | 1.2037 | |
| 407 | A | A | 0.0000 | |
| 408 | G | A | -0.0971 | |
| 409 | L | A | 0.3804 | |
| 410 | K | A | -0.7038 | |
| 411 | K | A | -2.0687 | |
| 412 | R | A | -1.5622 | |
| 413 | L | A | 0.0725 | |
| 414 | A | A | -0.4828 | |
| 415 | M | A | -0.7283 | |
| 416 | A | A | -0.8756 | |
| 417 | S | A | -0.9451 | |
| 418 | A | A | -0.9157 | |
| 419 | N | A | -1.7750 | |
| 420 | K | A | -2.2456 | |
| 421 | A | A | -1.1751 |
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 | -0.5664 | 3.1273 | View | CSV | PDB |
| 4.5 | -0.6243 | 3.022 | View | CSV | PDB |
| 5.0 | -0.6909 | 2.8948 | View | CSV | PDB |
| 5.5 | -0.752 | 2.7617 | View | CSV | PDB |
| 6.0 | -0.791 | 2.736 | View | CSV | PDB |
| 6.5 | -0.796 | 2.7137 | View | CSV | PDB |
| 7.0 | -0.7686 | 2.6916 | View | CSV | PDB |
| 7.5 | -0.7205 | 2.6702 | View | CSV | PDB |
| 8.0 | -0.6606 | 2.6509 | View | CSV | PDB |
| 8.5 | -0.5913 | 2.6361 | View | CSV | PDB |
| 9.0 | -0.5127 | 2.6273 | 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