| Chain sequence(s) |
A: KFPKNFMFGYSWSGFQFEMGLPGSEVESDWWVWVHDKENIASGLVSGDLPENGPAYWHLYKQDHDIAEKLGMDCIRGGIEWARIFPKPTFDVKVDVEKDEEGNIISVDVPESTIKELEKIANMEALEHYRKIYSDWKERGKTFILNLYHWPLPLWIHDPIAVRKLGPDAAPAGWLDEKTVVEFVKFAAFVAYHLDDLVDMWSTMNEPNVVYNQGYINLASGFPPGFLSFEAAEKAKFNLIQAHIGAYDAIKEYSEKSVGVIYAFAWHDPLAEEYKDEVEEIRKKDYEFVTILHSKGKLDWIGVNYYSRLVYGAKDGHLVPLPGYGFMSERGGFAKSGRPASDFGWEMYPEGLENLLKYLNNAYELPMIITENGMADAADRYRPHYLVSHLKAVYNAMKEGADVRGYLHWSLTDNYEWAQGFRMRFGLVYVDFETKKRYLRPSALVSVK
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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:08)
[INFO] FoldX: Starting FoldX energy minimization (00:00:08)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:17:11)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e709064a7e85a32/tmp/folded.pdb (00:17:11)
[INFO] Main: Simulation completed successfully. (00:25:46)
|
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 | K | A | -1.7763 | |
| 3 | F | A | -1.3273 | |
| 4 | P | A | -1.8264 | |
| 5 | K | A | -2.5786 | |
| 6 | N | A | -2.2057 | |
| 7 | F | A | -1.5440 | |
| 8 | M | A | -0.7944 | |
| 9 | F | A | -0.1268 | |
| 10 | G | A | 0.0000 | |
| 11 | Y | A | 0.0000 | |
| 12 | S | A | 0.0000 | |
| 13 | W | A | 0.0000 | |
| 14 | S | A | 0.0000 | |
| 15 | G | A | -0.0975 | |
| 16 | F | A | 0.0000 | |
| 17 | Q | A | 0.0000 | |
| 18 | F | A | 0.0000 | |
| 19 | E | A | 0.0000 | |
| 20 | M | A | 0.0000 | |
| 21 | G | A | -1.1350 | |
| 22 | L | A | -0.6917 | |
| 23 | P | A | -0.9317 | |
| 24 | G | A | -0.8569 | |
| 25 | S | A | -1.0693 | |
| 26 | E | A | -1.7898 | |
| 27 | V | A | -1.3735 | |
| 28 | E | A | -1.8687 | |
| 29 | S | A | 0.0000 | |
| 30 | D | A | 0.0000 | |
| 31 | W | A | 0.0000 | |
| 32 | W | A | 0.0000 | |
| 33 | V | A | -0.2039 | |
| 34 | W | A | 0.0000 | |
| 35 | V | A | 0.0000 | |
| 36 | H | A | -1.0561 | |
| 37 | D | A | -1.5040 | |
| 38 | K | A | -2.6246 | |
| 39 | E | A | -2.5873 | |
| 40 | N | A | 0.0000 | |
| 41 | I | A | -1.1037 | |
| 42 | A | A | -1.0047 | |
| 43 | S | A | -0.9063 | |
| 44 | G | A | -0.7638 | |
| 45 | L | A | -0.4500 | |
| 46 | V | A | 0.0000 | |
| 47 | S | A | -0.9062 | |
| 48 | G | A | -1.2981 | |
| 49 | D | A | -1.6678 | |
| 50 | L | A | -0.8569 | |
| 51 | P | A | 0.0000 | |
| 52 | E | A | -1.5304 | |
| 53 | N | A | -1.9905 | |
| 54 | G | A | 0.0000 | |
| 55 | P | A | 0.0000 | |
| 56 | A | A | 0.0000 | |
| 57 | Y | A | 0.0000 | |
| 58 | W | A | -0.3205 | |
| 59 | H | A | -0.7794 | |
| 60 | L | A | -0.5921 | |
| 61 | Y | A | 0.0000 | |
| 62 | K | A | -2.6176 | |
| 63 | Q | A | -2.6296 | |
| 64 | D | A | 0.0000 | |
| 65 | H | A | 0.0000 | |
| 66 | D | A | -2.6503 | |
| 67 | I | A | 0.0000 | |
| 68 | A | A | 0.0000 | |
| 69 | E | A | -2.3729 | |
| 70 | K | A | -2.3805 | |
| 71 | L | A | -1.1242 | |
| 72 | G | A | -1.4492 | |
| 73 | M | A | 0.0000 | |
| 74 | D | A | -1.6886 | |
| 75 | C | A | 0.0000 | |
| 76 | I | A | 0.0000 | |
| 77 | R | A | 0.0000 | |
| 78 | G | A | 0.0000 | |
| 79 | G | A | -0.1349 | |
| 80 | I | A | 0.0000 | |
| 81 | E | A | -0.2116 | |
| 82 | W | A | 0.0000 | |
| 83 | A | A | -0.6138 | |
| 84 | R | A | 0.0000 | |
| 85 | I | A | 0.0000 | |
| 86 | F | A | 0.0000 | |
| 87 | P | A | -1.1108 | |
| 88 | K | A | -1.3700 | |
| 89 | P | A | -0.5689 | |
| 90 | T | A | 0.0000 | |
| 91 | F | A | -0.1524 | |
| 92 | D | A | -1.4873 | |
| 93 | V | A | -1.3352 | |
| 94 | K | A | -2.2343 | |
| 95 | V | A | 0.0000 | |
| 96 | D | A | -3.0465 | |
| 97 | V | A | -1.8071 | |
| 98 | E | A | -2.5572 | |
| 99 | K | A | -2.9676 | |
| 100 | D | A | -3.1432 | |
| 101 | E | A | -3.5696 | |
| 102 | E | A | -3.3679 | |
| 103 | G | A | -2.6498 | |
| 104 | N | A | -1.7373 | |
| 105 | I | A | -0.6628 | |
| 106 | I | A | 0.7593 | |
| 107 | S | A | -0.6233 | |
| 108 | V | A | -1.5245 | |
| 109 | D | A | -2.7854 | |
| 110 | V | A | 0.0000 | |
| 111 | P | A | -2.0895 | |
| 112 | E | A | -2.5380 | |
| 113 | S | A | -2.1303 | |
| 114 | T | A | -2.2595 | |
| 115 | I | A | 0.0000 | |
| 116 | K | A | -3.2918 | |
| 117 | E | A | -3.0234 | |
| 118 | L | A | 0.0000 | |
| 119 | E | A | -1.9389 | |
| 120 | K | A | -2.2817 | |
| 121 | I | A | -0.9878 | |
| 122 | A | A | -1.2907 | |
| 123 | N | A | -1.3990 | |
| 124 | M | A | -1.4527 | |
| 125 | E | A | -2.4770 | |
| 126 | A | A | 0.0000 | |
| 127 | L | A | 0.0000 | |
| 128 | E | A | -3.0389 | |
| 129 | H | A | -2.2979 | |
| 130 | Y | A | 0.0000 | |
| 131 | R | A | -2.4503 | |
| 132 | K | A | -2.6117 | |
| 133 | I | A | 0.0000 | |
| 134 | Y | A | 0.0000 | |
| 135 | S | A | -2.2090 | |
| 136 | D | A | -2.7398 | |
| 137 | W | A | 0.0000 | |
| 138 | K | A | -2.5088 | |
| 139 | E | A | -2.9149 | |
| 140 | R | A | -2.5051 | |
| 141 | G | A | -1.9679 | |
| 142 | K | A | -1.9970 | |
| 143 | T | A | -1.1505 | |
| 144 | F | A | 0.0000 | |
| 145 | I | A | 0.0000 | |
| 146 | L | A | 0.0000 | |
| 147 | N | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | Y | A | 0.0000 | |
| 150 | H | A | -0.2170 | |
| 151 | W | A | 0.0000 | |
| 152 | P | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | P | A | 0.0000 | |
| 155 | L | A | -0.2398 | |
| 156 | W | A | -0.1071 | |
| 157 | I | A | 0.0000 | |
| 158 | H | A | 0.0000 | |
| 159 | D | A | -0.3973 | |
| 160 | P | A | 0.0000 | |
| 161 | I | A | -0.3515 | |
| 162 | A | A | -0.2918 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | -0.4866 | |
| 165 | K | A | -1.0754 | |
| 166 | L | A | 0.3304 | |
| 167 | G | A | -0.2193 | |
| 168 | P | A | -0.9696 | |
| 169 | D | A | -1.5689 | |
| 170 | A | A | -0.6498 | |
| 171 | A | A | 0.0000 | |
| 172 | P | A | -0.4748 | |
| 173 | A | A | 0.0000 | |
| 174 | G | A | 0.0000 | |
| 175 | W | A | 0.0000 | |
| 176 | L | A | 0.0000 | |
| 177 | D | A | -2.0500 | |
| 178 | E | A | -2.9796 | |
| 179 | K | A | -2.5286 | |
| 180 | T | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | V | A | -0.6448 | |
| 183 | E | A | 0.0000 | |
| 184 | F | A | 0.0000 | |
| 185 | V | A | 0.0000 | |
| 186 | K | A | 0.0000 | |
| 187 | F | A | 0.0000 | |
| 188 | A | A | 0.0000 | |
| 189 | A | A | 0.0000 | |
| 190 | F | A | 0.0000 | |
| 191 | V | A | 0.0000 | |
| 192 | A | A | 0.0000 | |
| 193 | Y | A | -0.5684 | |
| 194 | H | A | -0.6773 | |
| 195 | L | A | 0.0000 | |
| 196 | D | A | -1.6575 | |
| 197 | D | A | -2.1588 | |
| 198 | L | A | -1.6694 | |
| 199 | V | A | 0.0000 | |
| 200 | D | A | -1.3214 | |
| 201 | M | A | -0.5760 | |
| 202 | W | A | 0.0000 | |
| 203 | S | A | 0.0000 | |
| 204 | T | A | 0.0000 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | 0.0000 | |
| 207 | E | A | -0.2576 | |
| 208 | P | A | 0.0000 | |
| 209 | N | A | -0.7623 | |
| 210 | V | A | -0.4272 | |
| 211 | V | A | 0.0000 | |
| 212 | Y | A | 0.0000 | |
| 213 | N | A | -0.5404 | |
| 214 | Q | A | -0.6017 | |
| 215 | G | A | 0.0000 | |
| 216 | Y | A | 0.0000 | |
| 217 | I | A | 1.6148 | |
| 218 | N | A | -0.3399 | |
| 219 | L | A | 0.2863 | |
| 220 | A | A | -0.1630 | |
| 221 | S | A | -0.5047 | |
| 222 | G | A | -0.3340 | |
| 223 | F | A | 0.0000 | |
| 224 | P | A | 0.0000 | |
| 225 | P | A | 0.0000 | |
| 226 | G | A | 0.4702 | |
| 227 | F | A | 1.1938 | |
| 228 | L | A | 2.1023 | |
| 229 | S | A | 1.2642 | |
| 230 | F | A | 1.2213 | |
| 231 | E | A | -1.4519 | |
| 232 | A | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | E | A | -2.8004 | |
| 235 | K | A | -2.7848 | |
| 236 | A | A | 0.0000 | |
| 237 | K | A | -1.3848 | |
| 238 | F | A | -0.8672 | |
| 239 | N | A | 0.0000 | |
| 240 | L | A | 0.0000 | |
| 241 | I | A | 0.0000 | |
| 242 | Q | A | 0.0000 | |
| 243 | A | A | 0.0000 | |
| 244 | H | A | 0.0000 | |
| 245 | I | A | 0.0000 | |
| 246 | G | A | 0.0000 | |
| 247 | A | A | 0.0000 | |
| 248 | Y | A | -0.6525 | |
| 249 | D | A | -1.2306 | |
| 250 | A | A | 0.0000 | |
| 251 | I | A | 0.0000 | |
| 252 | K | A | -2.0422 | |
| 253 | E | A | -2.5809 | |
| 254 | Y | A | -1.4982 | |
| 255 | S | A | 0.0000 | |
| 256 | E | A | -2.5299 | |
| 257 | K | A | -1.5441 | |
| 258 | S | A | -0.8568 | |
| 259 | V | A | 0.0000 | |
| 260 | G | A | 0.0000 | |
| 261 | V | A | 0.0000 | |
| 262 | I | A | 0.0000 | |
| 263 | Y | A | 0.0000 | |
| 264 | A | A | -0.2616 | |
| 265 | F | A | 0.0000 | |
| 266 | A | A | -0.0207 | |
| 267 | W | A | -0.2349 | |
| 268 | H | A | 0.0000 | |
| 269 | D | A | -0.3559 | |
| 270 | P | A | -1.1322 | |
| 271 | L | A | 0.6288 | |
| 272 | A | A | -1.0456 | |
| 273 | E | A | -3.3659 | |
| 274 | E | A | -3.4527 | |
| 275 | Y | A | -3.0075 | |
| 276 | K | A | -4.2166 | |
| 277 | D | A | -4.5201 | |
| 278 | E | A | -4.2866 | |
| 279 | V | A | 0.0000 | |
| 280 | E | A | -3.7682 | |
| 281 | E | A | -4.3541 | |
| 282 | I | A | -2.6886 | |
| 283 | R | A | 0.0000 | |
| 284 | K | A | -3.9539 | |
| 285 | K | A | -4.0613 | |
| 286 | D | A | -3.6795 | |
| 287 | Y | A | 0.0000 | |
| 288 | E | A | -2.3548 | |
| 289 | F | A | 0.0000 | |
| 290 | V | A | 0.0000 | |
| 291 | T | A | -1.1939 | |
| 292 | I | A | -0.4237 | |
| 293 | L | A | 0.0000 | |
| 294 | H | A | -1.3204 | |
| 295 | S | A | -1.2168 | |
| 296 | K | A | -2.0276 | |
| 297 | G | A | -1.5956 | |
| 298 | K | A | -1.2877 | |
| 299 | L | A | 0.0000 | |
| 300 | D | A | -0.6352 | |
| 301 | W | A | 0.0000 | |
| 302 | I | A | 0.0000 | |
| 303 | G | A | 0.0000 | |
| 304 | V | A | 0.0000 | |
| 305 | N | A | 0.0000 | |
| 306 | Y | A | 0.0000 | |
| 307 | Y | A | 0.2986 | |
| 308 | S | A | 0.0000 | |
| 309 | R | A | 0.0000 | |
| 310 | L | A | 0.5950 | |
| 311 | V | A | 0.0000 | |
| 312 | Y | A | 0.1865 | |
| 313 | G | A | 0.0000 | |
| 314 | A | A | -1.3695 | |
| 315 | K | A | -2.7213 | |
| 316 | D | A | -2.9659 | |
| 317 | G | A | -2.1971 | |
| 318 | H | A | -2.0668 | |
| 319 | L | A | -0.7038 | |
| 320 | V | A | -0.0194 | |
| 321 | P | A | 0.4096 | |
| 322 | L | A | 0.0000 | |
| 323 | P | A | -0.3550 | |
| 324 | G | A | -0.5997 | |
| 325 | Y | A | -0.1438 | |
| 326 | G | A | 0.0000 | |
| 327 | F | A | 0.9639 | |
| 328 | M | A | 0.2778 | |
| 329 | S | A | 0.0000 | |
| 330 | E | A | -2.3328 | |
| 331 | R | A | -2.5152 | |
| 332 | G | A | -1.3742 | |
| 333 | G | A | -0.7785 | |
| 334 | F | A | 0.3512 | |
| 335 | A | A | 0.0000 | |
| 336 | K | A | -1.8572 | |
| 337 | S | A | -1.0664 | |
| 338 | G | A | -0.8303 | |
| 339 | R | A | -0.4860 | |
| 340 | P | A | -0.4203 | |
| 341 | A | A | 0.0000 | |
| 342 | S | A | 0.0000 | |
| 343 | D | A | -1.5489 | |
| 344 | F | A | -0.8667 | |
| 345 | G | A | 0.0000 | |
| 346 | W | A | 0.2507 | |
| 347 | E | A | 0.0000 | |
| 348 | M | A | 0.0000 | |
| 349 | Y | A | -0.1930 | |
| 350 | P | A | 0.0000 | |
| 351 | E | A | -1.6182 | |
| 352 | G | A | 0.0000 | |
| 353 | L | A | 0.0000 | |
| 354 | E | A | -1.9402 | |
| 355 | N | A | -1.7653 | |
| 356 | L | A | 0.0000 | |
| 357 | L | A | 0.0000 | |
| 358 | K | A | -2.2725 | |
| 359 | Y | A | -1.1068 | |
| 360 | L | A | 0.0000 | |
| 361 | N | A | -2.1440 | |
| 362 | N | A | -1.9752 | |
| 363 | A | A | -1.1099 | |
| 364 | Y | A | 0.0000 | |
| 365 | E | A | -2.3355 | |
| 366 | L | A | -1.1198 | |
| 367 | P | A | -0.9052 | |
| 368 | M | A | 0.0000 | |
| 369 | I | A | 0.0000 | |
| 370 | I | A | 0.0000 | |
| 371 | T | A | 0.0000 | |
| 372 | E | A | -0.2485 | |
| 373 | N | A | 0.0000 | |
| 374 | G | A | 0.0000 | |
| 375 | M | A | 0.0000 | |
| 376 | A | A | 0.0000 | |
| 377 | D | A | 0.0000 | |
| 378 | A | A | -0.6008 | |
| 379 | A | A | -0.4778 | |
| 380 | D | A | -1.0119 | |
| 381 | R | A | -1.8546 | |
| 382 | Y | A | -0.9873 | |
| 383 | R | A | 0.0000 | |
| 384 | P | A | -0.0463 | |
| 385 | H | A | -0.6143 | |
| 386 | Y | A | 0.0000 | |
| 387 | L | A | 0.0000 | |
| 388 | V | A | 1.0631 | |
| 389 | S | A | -0.1105 | |
| 390 | H | A | 0.0000 | |
| 391 | L | A | 0.0217 | |
| 392 | K | A | -1.3246 | |
| 393 | A | A | 0.0000 | |
| 394 | V | A | 0.0000 | |
| 395 | Y | A | -1.4031 | |
| 396 | N | A | -2.1303 | |
| 397 | A | A | 0.0000 | |
| 398 | M | A | -2.1123 | |
| 399 | K | A | -2.8274 | |
| 400 | E | A | -3.1463 | |
| 401 | G | A | -2.3786 | |
| 402 | A | A | 0.0000 | |
| 403 | D | A | -1.9177 | |
| 404 | V | A | 0.0000 | |
| 405 | R | A | -1.5247 | |
| 406 | G | A | 0.0000 | |
| 407 | Y | A | 0.0000 | |
| 408 | L | A | 0.0000 | |
| 409 | H | A | 0.0000 | |
| 410 | W | A | 0.0000 | |
| 411 | S | A | 0.0000 | |
| 412 | L | A | 0.0000 | |
| 413 | T | A | 0.0000 | |
| 414 | D | A | 0.0000 | |
| 415 | N | A | 0.0000 | |
| 416 | Y | A | 0.0000 | |
| 417 | E | A | -0.4971 | |
| 418 | W | A | -0.0030 | |
| 419 | A | A | -0.6163 | |
| 420 | Q | A | -1.0493 | |
| 421 | G | A | 0.0000 | |
| 422 | F | A | -0.9974 | |
| 423 | R | A | -1.7921 | |
| 424 | M | A | 0.0000 | |
| 425 | R | A | -0.5277 | |
| 426 | F | A | 0.0000 | |
| 427 | G | A | 0.0000 | |
| 428 | L | A | 0.0000 | |
| 429 | V | A | 0.0000 | |
| 430 | Y | A | 0.9002 | |
| 431 | V | A | 0.0000 | |
| 432 | D | A | -1.5706 | |
| 433 | F | A | -1.6649 | |
| 434 | E | A | -2.5489 | |
| 435 | T | A | -1.8897 | |
| 436 | K | A | -1.7723 | |
| 437 | K | A | -2.0364 | |
| 438 | R | A | -0.5129 | |
| 439 | Y | A | 1.0668 | |
| 440 | L | A | 1.3498 | |
| 441 | R | A | 0.0000 | |
| 442 | P | A | 0.2569 | |
| 443 | S | A | 0.0000 | |
| 444 | A | A | 0.0000 | |
| 445 | L | A | 1.2133 | |
| 446 | V | A | 1.2071 | |
| 447 | S | A | 0.4881 | |
| 448 | V | A | -0.0790 | |
| 449 | K | A | -0.9559 |
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 | -0.5683 | 4.1191 | View | CSV | PDB |
| 4.5 | -0.646 | 3.8983 | View | CSV | PDB |
| 5.0 | -0.7433 | 3.6093 | View | CSV | PDB |
| 5.5 | -0.8415 | 3.4191 | View | CSV | PDB |
| 6.0 | -0.9196 | 3.3747 | View | CSV | PDB |
| 6.5 | -0.9612 | 3.3431 | View | CSV | PDB |
| 7.0 | -0.964 | 3.3264 | View | CSV | PDB |
| 7.5 | -0.9387 | 3.3198 | View | CSV | PDB |
| 8.0 | -0.8971 | 3.3174 | View | CSV | PDB |
| 8.5 | -0.8447 | 3.3167 | View | CSV | PDB |
| 9.0 | -0.7827 | 3.3164 | 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