| Chain sequence(s) |
A: AKFPKNFMFGYSWSGFQFEMGLPGSEVESDWWVWVHDKENIASGLVSGDLPENGPAYWHLYKQDHDIAEKLGMDCIRGGIEWARIFPKPTFDVKVDVEKDEEGNIISVDVPESTIKELEKIANMEALEHYRKIYSDWKERGKTFILNLYHWPLPLWIHDPIAVRKLGPDRAPAGWLDEKTVVEFVKFAAFVAYHLDDLVDMWSTMNEPNVVYNQGYINLRSGFPPGYLSFEAAEKAKFNLIQAHIGAYDAIKEYSEKSVGVIYAFAWHDPLAEEYKDEVEEIRKKDYEFVTILHSKGKLDWIGVNYYSRLVYGAKDGHLVPLPGYGFMSERGGFAKSGRPASDFGWEMYPEGLENLLKYLNNAYELPMIITENGMADAADRYRPHYLVSHLKAVYNAMKEGADVRGYLHWSLTDNYEWAQGFRMRFGLVYVDFETKKRYLRPSALVFREIATQKEIPEELAHLADLKFVTR
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. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:43)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3065a6297e7257f/tmp/folded.pdb (00:11:43)
[INFO] Main: Simulation completed successfully. (00:15:37)
|
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 | A | A | -1.5875 | |
| 2 | K | A | -2.3890 | |
| 3 | F | A | 0.0000 | |
| 4 | P | A | -1.9609 | |
| 5 | K | A | -2.7721 | |
| 6 | N | A | -2.4008 | |
| 7 | F | A | 0.0000 | |
| 8 | M | A | -0.9971 | |
| 9 | F | A | 0.0000 | |
| 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 | 0.0000 | |
| 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 | -1.0347 | |
| 22 | L | A | -0.4765 | |
| 23 | P | A | -0.8713 | |
| 24 | G | A | -1.0759 | |
| 25 | S | A | 0.0000 | |
| 26 | E | A | -2.3483 | |
| 27 | V | A | -1.5367 | |
| 28 | E | A | -1.8725 | |
| 29 | S | A | 0.0000 | |
| 30 | D | A | 0.0000 | |
| 31 | W | A | 0.0000 | |
| 32 | W | A | -0.4863 | |
| 33 | V | A | -0.2943 | |
| 34 | W | A | 0.0000 | |
| 35 | V | A | 0.0000 | |
| 36 | H | A | -0.9608 | |
| 37 | D | A | -1.5871 | |
| 38 | K | A | -2.6674 | |
| 39 | E | A | -2.6592 | |
| 40 | N | A | 0.0000 | |
| 41 | I | A | -1.1902 | |
| 42 | A | A | -1.1065 | |
| 43 | S | A | -0.9007 | |
| 44 | G | A | -0.7565 | |
| 45 | L | A | -0.3960 | |
| 46 | V | A | 0.0000 | |
| 47 | S | A | -0.6829 | |
| 48 | G | A | -0.7245 | |
| 49 | D | A | -1.1051 | |
| 50 | L | A | -0.4433 | |
| 51 | P | A | 0.0000 | |
| 52 | E | A | -1.2387 | |
| 53 | N | A | -1.4581 | |
| 54 | G | A | 0.0000 | |
| 55 | P | A | 0.0000 | |
| 56 | A | A | 0.0000 | |
| 57 | Y | A | 0.0000 | |
| 58 | W | A | 0.0000 | |
| 59 | H | A | -0.8629 | |
| 60 | L | A | -0.8817 | |
| 61 | Y | A | 0.0000 | |
| 62 | K | A | -2.6736 | |
| 63 | Q | A | -2.3163 | |
| 64 | D | A | 0.0000 | |
| 65 | H | A | 0.0000 | |
| 66 | D | A | -2.3008 | |
| 67 | I | A | -1.2454 | |
| 68 | A | A | 0.0000 | |
| 69 | E | A | -2.3831 | |
| 70 | K | A | -2.5409 | |
| 71 | L | A | 0.0000 | |
| 72 | G | A | -1.7522 | |
| 73 | M | A | 0.0000 | |
| 74 | D | A | -1.2484 | |
| 75 | C | A | 0.0000 | |
| 76 | I | A | 0.0000 | |
| 77 | R | A | 0.0000 | |
| 78 | G | A | 0.0000 | |
| 79 | G | A | 0.0000 | |
| 80 | I | A | 0.0000 | |
| 81 | E | A | 0.0000 | |
| 82 | W | A | 0.0000 | |
| 83 | A | A | 0.0000 | |
| 84 | R | A | 0.0000 | |
| 85 | I | A | 0.0000 | |
| 86 | F | A | 0.0000 | |
| 87 | P | A | -1.3346 | |
| 88 | K | A | -1.6824 | |
| 89 | P | A | -0.8854 | |
| 90 | T | A | 0.0000 | |
| 91 | F | A | -0.5482 | |
| 92 | D | A | -1.8398 | |
| 93 | V | A | 0.0000 | |
| 94 | K | A | -2.5707 | |
| 95 | V | A | 0.0000 | |
| 96 | D | A | -3.1083 | |
| 97 | V | A | -1.9468 | |
| 98 | E | A | -2.4849 | |
| 99 | K | A | -2.7008 | |
| 100 | D | A | -2.7465 | |
| 101 | E | A | -3.1629 | |
| 102 | E | A | -3.2553 | |
| 103 | G | A | -2.3813 | |
| 104 | N | A | -1.5225 | |
| 105 | I | A | 0.0000 | |
| 106 | I | A | 0.4849 | |
| 107 | S | A | -0.6265 | |
| 108 | V | A | 0.0000 | |
| 109 | D | A | -2.9025 | |
| 110 | V | A | 0.0000 | |
| 111 | P | A | -2.2071 | |
| 112 | E | A | -2.6592 | |
| 113 | S | A | -2.0487 | |
| 114 | T | A | 0.0000 | |
| 115 | I | A | 0.0000 | |
| 116 | K | A | -3.2251 | |
| 117 | E | A | -3.1215 | |
| 118 | L | A | 0.0000 | |
| 119 | E | A | -2.0799 | |
| 120 | K | A | -2.4887 | |
| 121 | I | A | -1.6687 | |
| 122 | A | A | -1.6070 | |
| 123 | N | A | -1.6997 | |
| 124 | M | A | -1.6867 | |
| 125 | E | A | -2.5742 | |
| 126 | A | A | 0.0000 | |
| 127 | L | A | 0.0000 | |
| 128 | E | A | -3.1490 | |
| 129 | H | A | -2.3517 | |
| 130 | Y | A | 0.0000 | |
| 131 | R | A | -2.4652 | |
| 132 | K | A | -2.7287 | |
| 133 | I | A | 0.0000 | |
| 134 | Y | A | 0.0000 | |
| 135 | S | A | -1.8760 | |
| 136 | D | A | -2.0527 | |
| 137 | W | A | 0.0000 | |
| 138 | K | A | -2.1984 | |
| 139 | E | A | -2.4442 | |
| 140 | R | A | -1.9882 | |
| 141 | G | A | -1.5986 | |
| 142 | K | A | -1.5054 | |
| 143 | T | A | -0.8482 | |
| 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 | -0.0696 | |
| 151 | W | A | 0.0000 | |
| 152 | P | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | P | A | 0.0000 | |
| 155 | L | A | -0.3529 | |
| 156 | W | A | -0.3127 | |
| 157 | I | A | 0.0000 | |
| 158 | H | A | 0.0000 | |
| 159 | D | A | -0.4610 | |
| 160 | P | A | 0.0000 | |
| 161 | I | A | -0.5731 | |
| 162 | A | A | -1.1209 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | -1.0163 | |
| 165 | K | A | -1.7101 | |
| 166 | L | A | -0.9660 | |
| 167 | G | A | -1.3200 | |
| 168 | P | A | -1.7970 | |
| 169 | D | A | -2.6775 | |
| 170 | R | A | -2.7752 | |
| 171 | A | A | -1.6618 | |
| 172 | P | A | -1.1857 | |
| 173 | A | A | 0.0000 | |
| 174 | G | A | 0.0000 | |
| 175 | W | A | 0.0000 | |
| 176 | L | A | 0.0000 | |
| 177 | D | A | -2.6153 | |
| 178 | E | A | -3.0342 | |
| 179 | K | A | -2.5394 | |
| 180 | T | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | V | A | -0.9388 | |
| 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 | -0.2890 | |
| 194 | H | A | -0.5898 | |
| 195 | L | A | 0.0000 | |
| 196 | D | A | -1.5376 | |
| 197 | D | A | -2.1415 | |
| 198 | L | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | D | A | -1.3321 | |
| 201 | M | A | -0.6429 | |
| 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 | 0.0000 | |
| 208 | P | A | 0.0000 | |
| 209 | N | A | -0.7259 | |
| 210 | V | A | -0.2608 | |
| 211 | V | A | -0.1868 | |
| 212 | Y | A | 0.0000 | |
| 213 | N | A | -0.7743 | |
| 214 | Q | A | -0.5290 | |
| 215 | G | A | 0.0000 | |
| 216 | Y | A | 0.0000 | |
| 217 | I | A | 0.8362 | |
| 218 | N | A | -0.3617 | |
| 219 | L | A | 0.0307 | |
| 220 | R | A | -1.5841 | |
| 221 | S | A | -0.8723 | |
| 222 | G | A | 0.0000 | |
| 223 | F | A | 0.0000 | |
| 224 | P | A | 0.0000 | |
| 225 | P | A | 0.0000 | |
| 226 | G | A | 0.4200 | |
| 227 | Y | A | 1.1286 | |
| 228 | L | A | 1.9866 | |
| 229 | S | A | 0.8058 | |
| 230 | F | A | 0.7500 | |
| 231 | E | A | -1.6458 | |
| 232 | A | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | E | A | -2.6910 | |
| 235 | K | A | -2.6640 | |
| 236 | A | A | 0.0000 | |
| 237 | K | A | -1.4928 | |
| 238 | F | A | -0.7441 | |
| 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 | -0.4111 | |
| 249 | D | A | -0.6139 | |
| 250 | A | A | 0.0000 | |
| 251 | I | A | 0.0000 | |
| 252 | K | A | -1.4577 | |
| 253 | E | A | -1.4044 | |
| 254 | Y | A | -0.6619 | |
| 255 | S | A | -1.5809 | |
| 256 | E | A | -2.3580 | |
| 257 | K | A | -1.6378 | |
| 258 | S | A | -0.9620 | |
| 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 | -0.0792 | |
| 265 | F | A | 0.0000 | |
| 266 | A | A | -0.0862 | |
| 267 | W | A | 0.0000 | |
| 268 | H | A | 0.0000 | |
| 269 | D | A | -0.5353 | |
| 270 | P | A | -1.3797 | |
| 271 | L | A | 0.4118 | |
| 272 | A | A | -1.1336 | |
| 273 | E | A | -3.1913 | |
| 274 | E | A | -3.4773 | |
| 275 | Y | A | -3.1054 | |
| 276 | K | A | -4.5522 | |
| 277 | D | A | -4.8618 | |
| 278 | E | A | -4.2499 | |
| 279 | V | A | 0.0000 | |
| 280 | E | A | -4.6704 | |
| 281 | E | A | -4.5671 | |
| 282 | I | A | -3.2567 | |
| 283 | R | A | 0.0000 | |
| 284 | K | A | -4.1498 | |
| 285 | K | A | -4.1051 | |
| 286 | D | A | -3.2930 | |
| 287 | Y | A | 0.0000 | |
| 288 | E | A | -2.9227 | |
| 289 | F | A | 0.0000 | |
| 290 | V | A | 0.0000 | |
| 291 | T | A | -1.3547 | |
| 292 | I | A | -0.5545 | |
| 293 | L | A | 0.0000 | |
| 294 | H | A | -1.2481 | |
| 295 | S | A | -0.8462 | |
| 296 | K | A | -1.0046 | |
| 297 | G | A | -1.1822 | |
| 298 | K | A | -0.9366 | |
| 299 | L | A | 0.0000 | |
| 300 | D | A | -0.6455 | |
| 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 | 0.2458 | |
| 308 | S | A | 0.0000 | |
| 309 | R | A | 0.0676 | |
| 310 | L | A | 0.4203 | |
| 311 | V | A | 0.0000 | |
| 312 | Y | A | 0.0000 | |
| 313 | G | A | 0.0000 | |
| 314 | A | A | -1.3309 | |
| 315 | K | A | -2.8311 | |
| 316 | D | A | -3.0482 | |
| 317 | G | A | -2.3177 | |
| 318 | H | A | -2.0849 | |
| 319 | L | A | -0.9824 | |
| 320 | V | A | -0.3372 | |
| 321 | P | A | 0.2240 | |
| 322 | L | A | 0.0000 | |
| 323 | P | A | -0.5381 | |
| 324 | G | A | -0.9667 | |
| 325 | Y | A | 0.0000 | |
| 326 | G | A | 0.0000 | |
| 327 | F | A | 0.3511 | |
| 328 | M | A | -0.0306 | |
| 329 | S | A | -1.2508 | |
| 330 | E | A | -2.5978 | |
| 331 | R | A | -2.3287 | |
| 332 | G | A | -1.5987 | |
| 333 | G | A | -1.2549 | |
| 334 | F | A | -1.1326 | |
| 335 | A | A | 0.0000 | |
| 336 | K | A | -2.2123 | |
| 337 | S | A | -1.2397 | |
| 338 | G | A | 0.0000 | |
| 339 | R | A | -0.8533 | |
| 340 | P | A | 0.0000 | |
| 341 | A | A | 0.0000 | |
| 342 | S | A | 0.0000 | |
| 343 | D | A | -1.3827 | |
| 344 | F | A | -0.8466 | |
| 345 | G | A | 0.0000 | |
| 346 | W | A | -0.0765 | |
| 347 | E | A | 0.0000 | |
| 348 | M | A | 0.0000 | |
| 349 | Y | A | -0.1494 | |
| 350 | P | A | 0.0000 | |
| 351 | E | A | -1.1511 | |
| 352 | G | A | 0.0000 | |
| 353 | L | A | 0.0000 | |
| 354 | E | A | -1.5719 | |
| 355 | N | A | -1.4754 | |
| 356 | L | A | 0.0000 | |
| 357 | L | A | 0.0000 | |
| 358 | K | A | -2.0048 | |
| 359 | Y | A | -0.9459 | |
| 360 | L | A | 0.0000 | |
| 361 | N | A | -2.0490 | |
| 362 | N | A | -1.9704 | |
| 363 | A | A | -1.2980 | |
| 364 | Y | A | 0.0000 | |
| 365 | E | A | -2.3986 | |
| 366 | L | A | -1.1803 | |
| 367 | P | A | -0.9439 | |
| 368 | M | A | 0.0000 | |
| 369 | I | A | 0.0000 | |
| 370 | I | A | 0.0000 | |
| 371 | T | A | 0.0000 | |
| 372 | E | A | 0.0000 | |
| 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 | -0.6967 | |
| 379 | A | A | -0.6550 | |
| 380 | D | A | -1.0346 | |
| 381 | R | A | -1.8823 | |
| 382 | Y | A | -0.7963 | |
| 383 | R | A | 0.0000 | |
| 384 | P | A | -0.2813 | |
| 385 | H | A | -0.2764 | |
| 386 | Y | A | 0.0000 | |
| 387 | L | A | 0.0000 | |
| 388 | V | A | 0.0000 | |
| 389 | S | A | 0.0000 | |
| 390 | H | A | 0.0000 | |
| 391 | L | A | 0.0000 | |
| 392 | K | A | -1.0213 | |
| 393 | A | A | 0.0000 | |
| 394 | V | A | 0.0000 | |
| 395 | Y | A | -1.2429 | |
| 396 | N | A | -1.7857 | |
| 397 | A | A | 0.0000 | |
| 398 | M | A | -2.0665 | |
| 399 | K | A | -2.7729 | |
| 400 | E | A | -3.1530 | |
| 401 | G | A | -2.5239 | |
| 402 | A | A | 0.0000 | |
| 403 | D | A | -1.8485 | |
| 404 | V | A | 0.0000 | |
| 405 | R | A | -1.5478 | |
| 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 | 0.0000 | |
| 418 | W | A | 0.0000 | |
| 419 | A | A | -0.1748 | |
| 420 | Q | A | -0.8499 | |
| 421 | G | A | 0.0000 | |
| 422 | F | A | -1.0523 | |
| 423 | R | A | -2.0216 | |
| 424 | M | A | 0.0000 | |
| 425 | R | A | -0.6877 | |
| 426 | F | A | 0.0000 | |
| 427 | G | A | 0.0000 | |
| 428 | L | A | 0.0000 | |
| 429 | V | A | 0.0000 | |
| 430 | Y | A | 0.5137 | |
| 431 | V | A | 0.0000 | |
| 432 | D | A | -1.3398 | |
| 433 | F | A | -1.4565 | |
| 434 | E | A | -2.3709 | |
| 435 | T | A | -1.7052 | |
| 436 | K | A | -1.5861 | |
| 437 | K | A | -1.9900 | |
| 438 | R | A | -0.4423 | |
| 439 | Y | A | 1.0639 | |
| 440 | L | A | 1.5781 | |
| 441 | R | A | 0.0000 | |
| 442 | P | A | 0.0735 | |
| 443 | S | A | 0.0000 | |
| 444 | A | A | 0.0000 | |
| 445 | L | A | 0.3506 | |
| 446 | V | A | -0.1480 | |
| 447 | F | A | 0.0000 | |
| 448 | R | A | -1.9740 | |
| 449 | E | A | -1.8180 | |
| 450 | I | A | 0.0000 | |
| 451 | A | A | 0.0000 | |
| 452 | T | A | -1.6265 | |
| 453 | Q | A | -1.8588 | |
| 454 | K | A | -2.1207 | |
| 455 | E | A | -2.2729 | |
| 456 | I | A | 0.0000 | |
| 457 | P | A | 0.0000 | |
| 458 | E | A | -2.8467 | |
| 459 | E | A | -2.7552 | |
| 460 | L | A | -1.6794 | |
| 461 | A | A | -1.7534 | |
| 462 | H | A | -1.6799 | |
| 463 | L | A | -0.8593 | |
| 464 | A | A | -0.8845 | |
| 465 | D | A | -1.0783 | |
| 466 | L | A | 0.0000 | |
| 467 | K | A | -1.3018 | |
| 468 | F | A | 0.6511 | |
| 469 | V | A | -0.0776 | |
| 470 | T | A | -0.8801 | |
| 471 | R | A | -1.9537 |
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 | -0.6974 | 3.5445 | View | CSV | PDB |
| 4.5 | -0.776 | 3.2646 | View | CSV | PDB |
| 5.0 | -0.8727 | 2.934 | View | CSV | PDB |
| 5.5 | -0.9686 | 2.8179 | View | CSV | PDB |
| 6.0 | -1.0429 | 2.7734 | View | CSV | PDB |
| 6.5 | -1.0792 | 2.7458 | View | CSV | PDB |
| 7.0 | -1.0764 | 2.7331 | View | CSV | PDB |
| 7.5 | -1.0473 | 2.7284 | View | CSV | PDB |
| 8.0 | -1.0043 | 2.7268 | View | CSV | PDB |
| 8.5 | -0.9525 | 2.7262 | View | CSV | PDB |
| 9.0 | -0.8927 | 2.7259 | 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