| Chain sequence(s) |
A: NKPQSWEARAETYSLYGFTDPSLHQRGTVVVTHGEGPYIVDVNGRRYLDANSGLWNVAGFDHKGLIDAAKAQYERFPGYHAFFGRSDQTVLSEKLVEVSPFDSGRVFYTNSGSEANDTVKLWFLHAAEGKPQKRKILTRWNAYHGVTAVSASTGKPYNSVFGLPLPGFVHLTCPHYWRYGEEGETEEQFVARLARELEETIQREGADTIAGFFAEPVGAGGVIPPAKGYFQAILPILRKYDIPVISDEVICGFGRTGNTWGCVTYDFTPDAIISSKNLTAGFFPGAVILGPELSKRLETAIEAIEEFPHGFTASGHPVGCAIALKAIDVVNEGLAENVRRLAPRFEERLKHIAERPNIGEYRGIGFWALEAVKDKASKTPFDGNLSVSERIANTCTDLGLICRPLGQSVVLCPPFILTEAQDEFDKLEKALDKVFAEVA
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 (00:04:32)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/99487198270b31d/tmp/folded.pdb (00:04:32)
[INFO] Main: Simulation completed successfully. (00:06:43)
|
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 |
|---|---|---|---|---|
| 2 | N | A | -2.2456 | |
| 3 | K | A | -2.9156 | |
| 4 | P | A | -2.4782 | |
| 5 | Q | A | -2.2447 | |
| 6 | S | A | -1.2975 | |
| 7 | W | A | -0.7278 | |
| 8 | E | A | -1.6805 | |
| 9 | A | A | -2.0864 | |
| 10 | R | A | -2.6826 | |
| 11 | A | A | -1.1659 | |
| 12 | E | A | -1.9488 | |
| 13 | T | A | -1.0776 | |
| 14 | Y | A | 0.6403 | |
| 15 | S | A | 0.5368 | |
| 16 | L | A | 1.5986 | |
| 17 | Y | A | 1.0956 | |
| 18 | G | A | 0.8000 | |
| 19 | F | A | 1.4007 | |
| 20 | T | A | 0.2010 | |
| 21 | D | A | -1.5742 | |
| 23 | P | A | -1.6305 | |
| 24 | S | A | -1.9757 | |
| 25 | L | A | -1.8898 | |
| 26 | H | A | -2.6831 | |
| 27 | Q | A | -2.5638 | |
| 28 | R | A | -2.5237 | |
| 29 | G | A | -1.5727 | |
| 30 | T | A | -0.3531 | |
| 31 | V | A | 1.4378 | |
| 32 | V | A | 1.3962 | |
| 33 | V | A | 0.9398 | |
| 34 | T | A | 0.2086 | |
| 35 | H | A | -1.1720 | |
| 36 | G | A | 0.0000 | |
| 37 | E | A | -2.3832 | |
| 38 | G | A | -0.9742 | |
| 39 | P | A | 0.0000 | |
| 40 | Y | A | 0.0000 | |
| 41 | I | A | -1.0495 | |
| 42 | V | A | -1.3098 | |
| 43 | D | A | 0.0000 | |
| 44 | V | A | -0.3441 | |
| 45 | N | A | -1.6535 | |
| 46 | G | A | -2.1943 | |
| 47 | R | A | -2.8400 | |
| 48 | R | A | -2.9756 | |
| 49 | Y | A | 0.0000 | |
| 50 | L | A | 0.0000 | |
| 51 | D | A | 0.0000 | |
| 52 | A | A | 0.0000 | |
| 53 | N | A | 0.0000 | |
| 54 | S | A | 0.0000 | |
| 55 | G | A | 0.5333 | |
| 56 | L | A | 1.2049 | |
| 57 | W | A | 0.6091 | |
| 58 | N | A | 0.0475 | |
| 60 | V | A | 0.0000 | |
| 61 | A | A | 0.0000 | |
| 62 | G | A | -0.6143 | |
| 63 | F | A | -0.8037 | |
| 64 | D | A | -1.9222 | |
| 65 | H | A | -1.4855 | |
| 66 | K | A | -2.0474 | |
| 67 | G | A | -1.5034 | |
| 68 | L | A | 0.0000 | |
| 69 | I | A | -0.9418 | |
| 70 | D | A | -1.6399 | |
| 71 | A | A | -1.0595 | |
| 72 | A | A | -0.9671 | |
| 73 | K | A | -2.1722 | |
| 74 | A | A | -1.6009 | |
| 75 | Q | A | 0.0000 | |
| 76 | Y | A | -0.8593 | |
| 77 | E | A | -2.4664 | |
| 78 | R | A | -2.3286 | |
| 79 | F | A | -0.6098 | |
| 80 | P | A | -0.4483 | |
| 81 | G | A | 0.1436 | |
| 82 | Y | A | 0.3362 | |
| 83 | H | A | 0.1200 | |
| 84 | A | A | 0.2828 | |
| 85 | F | A | 0.8276 | |
| 86 | F | A | 1.2064 | |
| 87 | G | A | -0.2563 | |
| 88 | R | A | -1.4393 | |
| 90 | S | A | -0.7804 | |
| 91 | D | A | -1.4348 | |
| 92 | Q | A | -0.3990 | |
| 93 | T | A | -0.0522 | |
| 94 | V | A | 0.5917 | |
| 96 | L | A | 0.0000 | |
| 97 | S | A | -0.7492 | |
| 98 | E | A | -2.1276 | |
| 99 | K | A | -1.5183 | |
| 100 | L | A | 0.0000 | |
| 101 | V | A | -1.8629 | |
| 102 | E | A | -2.5899 | |
| 103 | V | A | -0.9942 | |
| 104 | S | A | 0.0000 | |
| 105 | P | A | -0.5441 | |
| 106 | F | A | 0.0000 | |
| 107 | D | A | -2.2002 | |
| 108 | S | A | -1.9782 | |
| 109 | G | A | -1.9002 | |
| 110 | R | A | -1.3896 | |
| 111 | V | A | -0.0918 | |
| 112 | F | A | 0.2122 | |
| 113 | Y | A | 0.0000 | |
| 114 | T | A | 0.0000 | |
| 115 | N | A | -0.4488 | |
| 116 | S | A | -0.4904 | |
| 117 | G | A | -0.1521 | |
| 118 | S | A | 0.1932 | |
| 119 | E | A | -0.2642 | |
| 120 | A | A | 0.0000 | |
| 121 | N | A | 0.0000 | |
| 122 | D | A | -0.4145 | |
| 123 | T | A | -0.5174 | |
| 125 | V | A | 0.0000 | |
| 126 | K | A | -0.9656 | |
| 128 | L | A | -0.1957 | |
| 129 | W | A | -0.6600 | |
| 130 | F | A | -0.0878 | |
| 131 | L | A | 0.0000 | |
| 132 | H | A | 0.0000 | |
| 133 | A | A | -1.2044 | |
| 134 | A | A | -0.5272 | |
| 135 | E | A | -1.7531 | |
| 136 | G | A | -1.6752 | |
| 137 | K | A | -2.3250 | |
| 138 | P | A | -1.8816 | |
| 139 | Q | A | -2.3432 | |
| 140 | K | A | 0.0000 | |
| 141 | R | A | -2.3677 | |
| 142 | K | A | -1.4280 | |
| 143 | I | A | 0.0000 | |
| 144 | L | A | 0.0000 | |
| 145 | T | A | 0.0000 | |
| 146 | R | A | 0.0000 | |
| 147 | W | A | 0.3389 | |
| 148 | N | A | -0.0453 | |
| 149 | A | A | 0.0000 | |
| 150 | Y | A | 0.4844 | |
| 151 | H | A | 0.0000 | |
| 152 | G | A | 0.0000 | |
| 153 | V | A | 1.6224 | |
| 154 | T | A | 0.7227 | |
| 155 | A | A | 0.8353 | |
| 156 | V | A | 0.3897 | |
| 157 | S | A | 0.0000 | |
| 158 | A | A | 0.0000 | |
| 159 | S | A | 0.0000 | |
| 161 | T | A | 0.0000 | |
| 162 | G | A | 0.0000 | |
| 163 | K | A | -0.2129 | |
| 164 | P | A | 0.0538 | |
| 165 | Y | A | 0.9289 | |
| 166 | N | A | 0.0000 | |
| 167 | S | A | 1.1571 | |
| 168 | V | A | 2.5857 | |
| 169 | F | A | 2.6546 | |
| 170 | G | A | 1.1221 | |
| 171 | L | A | 0.9627 | |
| 172 | P | A | 0.2384 | |
| 173 | L | A | 0.5220 | |
| 174 | P | A | -0.2148 | |
| 175 | G | A | -0.5881 | |
| 176 | F | A | -0.0254 | |
| 177 | V | A | 0.1775 | |
| 178 | H | A | 0.1200 | |
| 179 | L | A | 0.1450 | |
| 180 | T | A | 0.0543 | |
| 181 | C | A | 0.0000 | |
| 182 | P | A | 0.0000 | |
| 183 | H | A | 0.0000 | |
| 184 | Y | A | -0.5625 | |
| 185 | W | A | -0.6058 | |
| 186 | R | A | -1.2967 | |
| 187 | Y | A | -0.8200 | |
| 188 | G | A | -1.7549 | |
| 189 | E | A | -3.1371 | |
| 190 | E | A | -2.9834 | |
| 191 | G | A | -2.1518 | |
| 192 | E | A | -2.3267 | |
| 193 | T | A | -1.9178 | |
| 194 | E | A | -2.2456 | |
| 195 | E | A | -2.9852 | |
| 196 | Q | A | -2.5952 | |
| 197 | F | A | 0.0000 | |
| 198 | V | A | 0.0000 | |
| 199 | A | A | -1.6712 | |
| 200 | R | A | -1.8053 | |
| 201 | L | A | 0.0000 | |
| 202 | A | A | -1.7009 | |
| 203 | R | A | -2.7106 | |
| 204 | E | A | -2.2233 | |
| 205 | L | A | 0.0000 | |
| 206 | E | A | -2.6400 | |
| 207 | E | A | -3.3017 | |
| 208 | T | A | -2.3857 | |
| 209 | I | A | 0.0000 | |
| 210 | Q | A | -3.1176 | |
| 211 | R | A | -3.1962 | |
| 212 | E | A | -2.4056 | |
| 213 | G | A | -2.0781 | |
| 214 | A | A | -2.0694 | |
| 215 | D | A | -2.7227 | |
| 216 | T | A | -2.0393 | |
| 217 | I | A | 0.0000 | |
| 218 | A | A | 0.0000 | |
| 219 | G | A | 0.0000 | |
| 220 | F | A | 0.0000 | |
| 221 | F | A | 0.0000 | |
| 222 | A | A | 0.0000 | |
| 223 | E | A | 0.0000 | |
| 224 | P | A | 0.0000 | |
| 225 | V | A | 0.3222 | |
| 227 | G | A | 0.0000 | |
| 228 | A | A | -0.0337 | |
| 229 | G | A | -0.0056 | |
| 230 | G | A | 0.0000 | |
| 231 | V | A | 0.0000 | |
| 232 | I | A | 0.2957 | |
| 233 | P | A | 0.0205 | |
| 234 | P | A | -0.3301 | |
| 235 | A | A | 0.0000 | |
| 236 | K | A | -2.3617 | |
| 237 | G | A | -2.0437 | |
| 238 | Y | A | 0.0000 | |
| 239 | F | A | 0.0000 | |
| 240 | Q | A | -1.7806 | |
| 241 | A | A | -1.0861 | |
| 242 | I | A | 0.0000 | |
| 243 | L | A | 0.0000 | |
| 244 | P | A | -1.1772 | |
| 245 | I | A | -1.4757 | |
| 246 | L | A | 0.0000 | |
| 247 | R | A | -2.3444 | |
| 248 | K | A | -2.6298 | |
| 249 | Y | A | -2.2416 | |
| 250 | D | A | -2.7045 | |
| 251 | I | A | 0.0000 | |
| 252 | P | A | 0.0000 | |
| 253 | V | A | 0.0000 | |
| 254 | I | A | 0.0000 | |
| 255 | S | A | 0.0000 | |
| 256 | D | A | 0.0000 | |
| 257 | E | A | 0.0000 | |
| 258 | V | A | 0.1342 | |
| 259 | I | A | 0.3977 | |
| 260 | C | A | 0.0000 | |
| 261 | G | A | 0.0000 | |
| 262 | F | A | 0.0000 | |
| 263 | G | A | 0.0000 | |
| 264 | R | A | 0.0000 | |
| 265 | T | A | 0.0000 | |
| 266 | G | A | -1.0085 | |
| 267 | N | A | -0.5885 | |
| 268 | T | A | 0.0917 | |
| 269 | W | A | 0.0000 | |
| 270 | G | A | 0.0000 | |
| 271 | C | A | 0.0000 | |
| 272 | V | A | 0.5436 | |
| 273 | T | A | 0.0945 | |
| 274 | Y | A | -0.6874 | |
| 275 | D | A | -1.4465 | |
| 276 | F | A | 0.0000 | |
| 277 | T | A | -0.2634 | |
| 278 | P | A | 0.0000 | |
| 279 | D | A | -0.5908 | |
| 280 | A | A | 0.0000 | |
| 281 | I | A | 0.0000 | |
| 282 | I | A | 0.0000 | |
| 283 | S | A | 0.0000 | |
| 284 | S | A | 0.0000 | |
| 285 | K | A | -0.2353 | |
| 286 | N | A | 0.0000 | |
| 287 | L | A | 0.0000 | |
| 288 | T | A | 0.0000 | |
| 289 | A | A | 0.0000 | |
| 290 | G | A | -0.0287 | |
| 291 | F | A | 0.5090 | |
| 292 | F | A | 0.1785 | |
| 293 | P | A | -0.3253 | |
| 295 | G | A | -0.2863 | |
| 296 | A | A | 0.0000 | |
| 297 | V | A | 0.0000 | |
| 298 | I | A | 0.0000 | |
| 299 | L | A | -0.6183 | |
| 300 | G | A | 0.0000 | |
| 301 | P | A | -2.0469 | |
| 302 | E | A | -2.4980 | |
| 303 | L | A | 0.0000 | |
| 304 | S | A | 0.0000 | |
| 305 | K | A | -2.7714 | |
| 306 | R | A | -1.9319 | |
| 307 | L | A | -1.4158 | |
| 308 | E | A | -2.2650 | |
| 309 | T | A | -1.5492 | |
| 310 | A | A | 0.0000 | |
| 311 | I | A | -1.2917 | |
| 312 | E | A | -2.2981 | |
| 313 | A | A | -0.7408 | |
| 314 | I | A | 0.0041 | |
| 315 | E | A | -2.4254 | |
| 316 | E | A | -2.1622 | |
| 317 | F | A | -0.8022 | |
| 318 | P | A | -0.6186 | |
| 319 | H | A | -0.4548 | |
| 320 | G | A | 0.0058 | |
| 321 | F | A | 0.1715 | |
| 322 | T | A | 0.1540 | |
| 323 | A | A | 0.0471 | |
| 324 | S | A | 0.0000 | |
| 325 | G | A | 0.0000 | |
| 326 | H | A | -0.0847 | |
| 327 | P | A | 0.0000 | |
| 328 | V | A | 0.0000 | |
| 329 | G | A | -0.0685 | |
| 330 | C | A | 0.0000 | |
| 331 | A | A | 0.0000 | |
| 332 | I | A | 0.0000 | |
| 333 | A | A | 0.0000 | |
| 334 | L | A | -0.0149 | |
| 335 | K | A | -0.4725 | |
| 336 | A | A | 0.0000 | |
| 337 | I | A | -0.5671 | |
| 338 | D | A | -1.4783 | |
| 339 | V | A | 0.0000 | |
| 340 | V | A | 0.0000 | |
| 342 | N | A | -2.6616 | |
| 343 | E | A | -2.9011 | |
| 344 | G | A | -2.4498 | |
| 345 | L | A | 0.0000 | |
| 346 | A | A | -1.9954 | |
| 347 | E | A | -3.2833 | |
| 348 | N | A | -2.1496 | |
| 349 | V | A | 0.0000 | |
| 350 | R | A | -2.7836 | |
| 351 | R | A | -2.7125 | |
| 352 | L | A | 0.0000 | |
| 353 | A | A | -2.0597 | |
| 354 | P | A | -2.3545 | |
| 355 | R | A | -3.5973 | |
| 356 | F | A | 0.0000 | |
| 357 | E | A | -2.8575 | |
| 358 | E | A | -3.8917 | |
| 359 | R | A | -3.0472 | |
| 360 | L | A | 0.0000 | |
| 361 | K | A | -3.6459 | |
| 362 | H | A | -3.0362 | |
| 363 | I | A | 0.0000 | |
| 364 | A | A | -2.1729 | |
| 365 | E | A | -2.7234 | |
| 366 | R | A | -1.9852 | |
| 367 | P | A | -1.5847 | |
| 368 | N | A | 0.0000 | |
| 369 | I | A | 0.0000 | |
| 370 | G | A | -1.4767 | |
| 371 | E | A | -0.9102 | |
| 372 | Y | A | -0.6992 | |
| 373 | R | A | 0.0000 | |
| 374 | G | A | 0.1621 | |
| 375 | I | A | 0.1652 | |
| 376 | G | A | 0.0000 | |
| 377 | F | A | 0.0000 | |
| 379 | W | A | 0.0000 | |
| 380 | A | A | 0.0000 | |
| 381 | L | A | 0.0000 | |
| 382 | E | A | 0.0000 | |
| 383 | A | A | 0.0000 | |
| 384 | V | A | 0.0000 | |
| 385 | K | A | -2.8366 | |
| 386 | D | A | -2.7139 | |
| 387 | K | A | -2.2840 | |
| 388 | A | A | -1.2305 | |
| 389 | S | A | -1.4290 | |
| 390 | K | A | -2.1895 | |
| 391 | T | A | -1.9576 | |
| 392 | P | A | -1.9387 | |
| 393 | F | A | 0.0000 | |
| 394 | D | A | -2.6114 | |
| 395 | G | A | -1.9653 | |
| 396 | N | A | -1.9079 | |
| 397 | L | A | -1.0270 | |
| 398 | S | A | -1.1790 | |
| 399 | V | A | 0.0000 | |
| 400 | S | A | 0.0000 | |
| 401 | E | A | -1.2839 | |
| 402 | R | A | -1.0457 | |
| 403 | I | A | 0.0000 | |
| 404 | A | A | 0.0000 | |
| 405 | N | A | -1.3369 | |
| 406 | T | A | -1.3013 | |
| 407 | C | A | 0.0000 | |
| 408 | T | A | -1.0191 | |
| 409 | D | A | -1.6424 | |
| 410 | L | A | -0.9168 | |
| 411 | G | A | -1.1550 | |
| 412 | L | A | 0.0000 | |
| 413 | I | A | -0.1239 | |
| 414 | C | A | 0.0000 | |
| 415 | R | A | -0.9327 | |
| 416 | P | A | -0.8050 | |
| 417 | L | A | -0.3468 | |
| 418 | G | A | -0.6705 | |
| 419 | Q | A | -0.7054 | |
| 420 | S | A | 0.0000 | |
| 421 | V | A | 0.0000 | |
| 422 | V | A | 0.0000 | |
| 423 | L | A | 0.0000 | |
| 424 | C | A | 0.0000 | |
| 425 | P | A | 0.0000 | |
| 426 | P | A | 0.0000 | |
| 427 | F | A | 0.0000 | |
| 428 | I | A | 0.1623 | |
| 429 | L | A | 0.0954 | |
| 430 | T | A | -0.6380 | |
| 431 | E | A | -1.6418 | |
| 432 | A | A | -1.1590 | |
| 433 | Q | A | -1.2042 | |
| 435 | D | A | -2.8077 | |
| 436 | E | A | -1.8877 | |
| 438 | F | A | -1.4930 | |
| 439 | D | A | -2.2323 | |
| 440 | K | A | -1.8167 | |
| 441 | L | A | 0.0000 | |
| 442 | E | A | -1.9825 | |
| 443 | K | A | -2.4835 | |
| 444 | A | A | 0.0000 | |
| 445 | L | A | 0.0000 | |
| 446 | D | A | -3.2733 | |
| 447 | K | A | -3.2031 | |
| 448 | V | A | 0.0000 | |
| 449 | F | A | 0.0000 | |
| 450 | A | A | -1.7158 | |
| 451 | E | A | -2.3001 | |
| 452 | V | A | -0.9366 | |
| 453 | A | A | -0.7875 |
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 | -0.4597 | 5.1297 | View | CSV | PDB |
| 4.5 | -0.531 | 5.1297 | View | CSV | PDB |
| 5.0 | -0.6218 | 5.1297 | View | CSV | PDB |
| 5.5 | -0.7168 | 5.1297 | View | CSV | PDB |
| 6.0 | -0.8 | 5.1297 | View | CSV | PDB |
| 6.5 | -0.8594 | 5.1297 | View | CSV | PDB |
| 7.0 | -0.8907 | 5.1297 | View | CSV | PDB |
| 7.5 | -0.8996 | 5.1297 | View | CSV | PDB |
| 8.0 | -0.8948 | 5.1297 | View | CSV | PDB |
| 8.5 | -0.8802 | 5.1296 | View | CSV | PDB |
| 9.0 | -0.8563 | 5.1293 | 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