| 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] (00:00:00)
[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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:55)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/635cf67e24ec561/tmp/folded.pdb (00:05:55)
[INFO] Main: Simulation completed successfully. (00:10:36)
|
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 | -1.7282 | |
| 3 | F | A | -0.9291 | |
| 4 | P | A | -1.5425 | |
| 5 | K | A | -2.3592 | |
| 6 | N | A | -2.0919 | |
| 7 | F | A | -1.0085 | |
| 8 | M | A | -0.4445 | |
| 9 | F | A | 0.0270 | |
| 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 | 0.0000 | |
| 22 | L | A | -0.4808 | |
| 23 | P | A | -0.8681 | |
| 24 | G | A | -0.9961 | |
| 25 | S | A | 0.0000 | |
| 26 | E | A | -2.0198 | |
| 27 | V | A | 0.0000 | |
| 28 | E | A | -1.8267 | |
| 29 | S | A | 0.0000 | |
| 30 | D | A | 0.0000 | |
| 31 | W | A | 0.0000 | |
| 32 | W | A | -0.2085 | |
| 33 | V | A | 0.5924 | |
| 34 | W | A | 0.0000 | |
| 35 | V | A | 0.0000 | |
| 36 | H | A | -0.6739 | |
| 37 | D | A | -1.3273 | |
| 38 | K | A | -2.6904 | |
| 39 | E | A | -2.6619 | |
| 40 | N | A | -1.3820 | |
| 41 | I | A | -1.0035 | |
| 42 | A | A | -1.0352 | |
| 43 | S | A | -0.9661 | |
| 44 | G | A | -0.6483 | |
| 45 | L | A | 0.0554 | |
| 46 | V | A | 0.0000 | |
| 47 | S | A | -0.7095 | |
| 48 | G | A | -0.9678 | |
| 49 | D | A | -1.6143 | |
| 50 | L | A | -0.7311 | |
| 51 | P | A | 0.0000 | |
| 52 | E | A | -2.1934 | |
| 53 | N | A | -1.5922 | |
| 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 | -0.7057 | |
| 60 | L | A | -0.4257 | |
| 61 | Y | A | 0.0000 | |
| 62 | K | A | -1.6892 | |
| 63 | Q | A | -1.8735 | |
| 64 | D | A | 0.0000 | |
| 65 | H | A | 0.0000 | |
| 66 | D | A | -2.3948 | |
| 67 | I | A | 0.0000 | |
| 68 | A | A | 0.0000 | |
| 69 | E | A | -2.7764 | |
| 70 | K | A | -2.4962 | |
| 71 | L | A | 0.0000 | |
| 72 | G | A | -1.6227 | |
| 73 | M | A | 0.0000 | |
| 74 | D | A | -0.8038 | |
| 75 | C | A | 0.0000 | |
| 76 | I | A | 0.0000 | |
| 77 | R | A | 0.0000 | |
| 78 | G | A | 0.0000 | |
| 79 | G | A | -0.0602 | |
| 80 | I | A | 0.0000 | |
| 81 | E | A | 0.0000 | |
| 82 | W | A | 0.0000 | |
| 83 | A | A | -0.6565 | |
| 84 | R | A | -0.9625 | |
| 85 | I | A | 0.0000 | |
| 86 | F | A | 0.0000 | |
| 87 | P | A | -1.3310 | |
| 88 | K | A | -1.9225 | |
| 89 | P | A | -0.9703 | |
| 90 | T | A | 0.0000 | |
| 91 | F | A | -0.9549 | |
| 92 | D | A | -1.9407 | |
| 93 | V | A | 0.0000 | |
| 94 | K | A | -2.5011 | |
| 95 | V | A | -1.9110 | |
| 96 | D | A | -3.0323 | |
| 97 | V | A | -2.2244 | |
| 98 | E | A | -3.1435 | |
| 99 | K | A | -3.6561 | |
| 100 | D | A | -3.6326 | |
| 101 | E | A | -3.6896 | |
| 102 | E | A | -3.4253 | |
| 103 | G | A | -2.7733 | |
| 104 | N | A | -1.9822 | |
| 105 | I | A | 0.0000 | |
| 106 | I | A | -0.4607 | |
| 107 | S | A | -1.3382 | |
| 108 | V | A | -1.6901 | |
| 109 | D | A | -2.6484 | |
| 110 | V | A | 0.0000 | |
| 111 | P | A | -2.1145 | |
| 112 | E | A | -2.4744 | |
| 113 | S | A | -1.9780 | |
| 114 | T | A | -1.9900 | |
| 115 | I | A | 0.0000 | |
| 116 | K | A | -2.8095 | |
| 117 | E | A | -3.3391 | |
| 118 | L | A | 0.0000 | |
| 119 | E | A | -1.9320 | |
| 120 | K | A | -2.6667 | |
| 121 | I | A | -1.6662 | |
| 122 | A | A | -1.5421 | |
| 123 | N | A | -1.5010 | |
| 124 | M | A | -1.3932 | |
| 125 | E | A | -2.4083 | |
| 126 | A | A | 0.0000 | |
| 127 | L | A | 0.0000 | |
| 128 | E | A | -2.8791 | |
| 129 | H | A | -2.1358 | |
| 130 | Y | A | 0.0000 | |
| 131 | R | A | -2.1207 | |
| 132 | K | A | -1.9266 | |
| 133 | I | A | 0.0000 | |
| 134 | Y | A | 0.0000 | |
| 135 | S | A | -1.8043 | |
| 136 | D | A | -1.7108 | |
| 137 | W | A | 0.0000 | |
| 138 | K | A | -2.1566 | |
| 139 | E | A | -2.5725 | |
| 140 | R | A | -2.1833 | |
| 141 | G | A | -1.9297 | |
| 142 | K | A | -1.8018 | |
| 143 | T | A | -0.7160 | |
| 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 | 0.0000 | |
| 151 | W | A | 0.0000 | |
| 152 | P | A | 0.0000 | |
| 153 | L | A | 0.0000 | |
| 154 | P | A | 0.0000 | |
| 155 | L | A | 0.1205 | |
| 156 | W | A | -0.0002 | |
| 157 | I | A | 0.0000 | |
| 158 | H | A | 0.0000 | |
| 159 | D | A | -0.5119 | |
| 160 | P | A | 0.0000 | |
| 161 | I | A | -0.5442 | |
| 162 | A | A | -0.9050 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | -1.7911 | |
| 165 | K | A | -1.5913 | |
| 166 | L | A | 0.0161 | |
| 167 | G | A | -0.5480 | |
| 168 | P | A | -1.1613 | |
| 169 | D | A | -1.5498 | |
| 170 | A | A | -0.7036 | |
| 171 | A | A | -0.7553 | |
| 172 | P | A | -0.5544 | |
| 173 | A | A | 0.0000 | |
| 174 | G | A | 0.0000 | |
| 175 | W | A | 0.0000 | |
| 176 | L | A | 0.0000 | |
| 177 | D | A | -1.9717 | |
| 178 | E | A | -2.8248 | |
| 179 | K | A | -2.3193 | |
| 180 | T | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | V | A | -0.7878 | |
| 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 | -0.3289 | |
| 194 | H | A | -0.6252 | |
| 195 | L | A | 0.0000 | |
| 196 | D | A | -1.7185 | |
| 197 | D | A | -2.2014 | |
| 198 | L | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | D | A | -1.0920 | |
| 201 | M | A | -0.6640 | |
| 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 | -0.1106 | |
| 208 | P | A | 0.0000 | |
| 209 | N | A | -0.4518 | |
| 210 | V | A | -0.1209 | |
| 211 | V | A | -0.0768 | |
| 212 | Y | A | 0.0000 | |
| 213 | N | A | -0.6734 | |
| 214 | Q | A | -0.3032 | |
| 215 | G | A | 0.0000 | |
| 216 | Y | A | 0.0000 | |
| 217 | I | A | 1.2906 | |
| 218 | N | A | 0.8636 | |
| 219 | L | A | 1.7556 | |
| 220 | A | A | 0.8620 | |
| 221 | S | A | 0.2971 | |
| 222 | G | A | 0.2597 | |
| 223 | F | A | 0.0997 | |
| 224 | P | A | 0.0000 | |
| 225 | P | A | 0.0000 | |
| 226 | G | A | 0.2365 | |
| 227 | F | A | 0.9682 | |
| 228 | L | A | 1.5946 | |
| 229 | S | A | 0.9426 | |
| 230 | F | A | 0.7258 | |
| 231 | E | A | -1.8127 | |
| 232 | A | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | E | A | -2.7115 | |
| 235 | K | A | -2.6543 | |
| 236 | A | A | 0.0000 | |
| 237 | K | A | -1.5551 | |
| 238 | F | A | -0.7542 | |
| 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 | -0.4771 | |
| 249 | D | A | -0.9111 | |
| 250 | A | A | 0.0000 | |
| 251 | I | A | 0.0000 | |
| 252 | K | A | -1.7854 | |
| 253 | E | A | -1.9323 | |
| 254 | Y | A | -1.0027 | |
| 255 | S | A | -1.7086 | |
| 256 | E | A | -2.4839 | |
| 257 | K | A | -1.8423 | |
| 258 | S | A | -1.0651 | |
| 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 | -0.0648 | |
| 265 | F | A | 0.0000 | |
| 266 | A | A | 0.1185 | |
| 267 | W | A | 0.0000 | |
| 268 | H | A | 0.0000 | |
| 269 | D | A | -0.4071 | |
| 270 | P | A | -1.2410 | |
| 271 | L | A | 0.1571 | |
| 272 | A | A | -1.2342 | |
| 273 | E | A | -3.1579 | |
| 274 | E | A | -3.3864 | |
| 275 | Y | A | -2.8369 | |
| 276 | K | A | -3.9031 | |
| 277 | D | A | -4.4320 | |
| 278 | E | A | -4.3337 | |
| 279 | V | A | 0.0000 | |
| 280 | E | A | -3.7581 | |
| 281 | E | A | -4.4414 | |
| 282 | I | A | -3.1212 | |
| 283 | R | A | 0.0000 | |
| 284 | K | A | -3.9776 | |
| 285 | K | A | -3.6843 | |
| 286 | D | A | -2.5360 | |
| 287 | Y | A | 0.0000 | |
| 288 | E | A | -1.9757 | |
| 289 | F | A | 0.0000 | |
| 290 | V | A | 0.0000 | |
| 291 | T | A | -0.8556 | |
| 292 | I | A | 0.0361 | |
| 293 | L | A | 0.0000 | |
| 294 | H | A | -1.1447 | |
| 295 | S | A | -0.8073 | |
| 296 | K | A | -1.4162 | |
| 297 | G | A | -1.3005 | |
| 298 | K | A | -1.0038 | |
| 299 | L | A | 0.0000 | |
| 300 | D | A | -0.7225 | |
| 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 | 0.3710 | |
| 308 | S | A | 0.0000 | |
| 309 | R | A | 0.0000 | |
| 310 | L | A | 0.6804 | |
| 311 | V | A | 0.0000 | |
| 312 | Y | A | 0.1077 | |
| 313 | G | A | 0.0000 | |
| 314 | A | A | -1.3120 | |
| 315 | K | A | -2.7699 | |
| 316 | D | A | -3.0244 | |
| 317 | G | A | -2.2557 | |
| 318 | H | A | -2.2690 | |
| 319 | L | A | -1.0379 | |
| 320 | V | A | -0.2655 | |
| 321 | P | A | 0.4957 | |
| 322 | L | A | 0.3942 | |
| 323 | P | A | -0.2177 | |
| 324 | G | A | -0.3282 | |
| 325 | Y | A | 0.1207 | |
| 326 | G | A | 0.0000 | |
| 327 | F | A | 1.0472 | |
| 328 | M | A | 0.2325 | |
| 329 | S | A | -0.6515 | |
| 330 | E | A | -2.2500 | |
| 331 | R | A | -2.6145 | |
| 332 | G | A | -1.6045 | |
| 333 | G | A | -0.7068 | |
| 334 | F | A | 0.6182 | |
| 335 | A | A | 0.0000 | |
| 336 | K | A | -1.4622 | |
| 337 | S | A | -0.8471 | |
| 338 | G | A | -0.7133 | |
| 339 | R | A | -0.3340 | |
| 340 | P | A | -0.2337 | |
| 341 | A | A | 0.0000 | |
| 342 | S | A | 0.0000 | |
| 343 | D | A | -1.6512 | |
| 344 | F | A | -0.7581 | |
| 345 | G | A | -1.1490 | |
| 346 | W | A | 0.0000 | |
| 347 | E | A | 0.0000 | |
| 348 | M | A | 0.3465 | |
| 349 | Y | A | -0.1623 | |
| 350 | P | A | -0.6796 | |
| 351 | E | A | -1.6651 | |
| 352 | G | A | 0.0000 | |
| 353 | L | A | 0.0000 | |
| 354 | E | A | -1.7642 | |
| 355 | N | A | -1.7576 | |
| 356 | L | A | 0.0000 | |
| 357 | L | A | 0.0000 | |
| 358 | K | A | -2.0180 | |
| 359 | Y | A | -1.0964 | |
| 360 | L | A | 0.0000 | |
| 361 | N | A | -2.3055 | |
| 362 | N | A | -1.9903 | |
| 363 | A | A | -1.1820 | |
| 364 | Y | A | 0.0000 | |
| 365 | E | A | -2.5003 | |
| 366 | L | A | -1.3466 | |
| 367 | P | A | -1.0434 | |
| 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 | -0.7495 | |
| 379 | A | A | -0.6643 | |
| 380 | D | A | 0.0000 | |
| 381 | R | A | -1.8954 | |
| 382 | Y | A | -0.9116 | |
| 383 | R | A | 0.0000 | |
| 384 | P | A | -0.1265 | |
| 385 | H | A | -0.7825 | |
| 386 | Y | A | 0.0000 | |
| 387 | L | A | 0.0000 | |
| 388 | V | A | 0.3505 | |
| 389 | S | A | -0.4810 | |
| 390 | H | A | 0.0000 | |
| 391 | L | A | -0.1586 | |
| 392 | K | A | -1.3369 | |
| 393 | A | A | 0.0000 | |
| 394 | V | A | 0.0000 | |
| 395 | Y | A | -1.6616 | |
| 396 | N | A | -2.4766 | |
| 397 | A | A | 0.0000 | |
| 398 | M | A | -2.2543 | |
| 399 | K | A | -2.9680 | |
| 400 | E | A | -3.2509 | |
| 401 | G | A | -2.7248 | |
| 402 | A | A | 0.0000 | |
| 403 | D | A | -2.1325 | |
| 404 | V | A | 0.0000 | |
| 405 | R | A | -1.1604 | |
| 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 | -0.7540 | |
| 418 | W | A | -0.1348 | |
| 419 | A | A | -0.2316 | |
| 420 | Q | A | -0.9797 | |
| 421 | G | A | 0.0000 | |
| 422 | F | A | -1.1466 | |
| 423 | R | A | -2.1717 | |
| 424 | M | A | 0.0000 | |
| 425 | R | A | -1.0969 | |
| 426 | F | A | 0.0000 | |
| 427 | G | A | 0.0000 | |
| 428 | L | A | 0.0000 | |
| 429 | V | A | 0.0000 | |
| 430 | Y | A | 0.8827 | |
| 431 | V | A | 0.0000 | |
| 432 | D | A | -1.3280 | |
| 433 | F | A | -1.3030 | |
| 434 | E | A | -2.2284 | |
| 435 | T | A | -1.6358 | |
| 436 | K | A | -1.4535 | |
| 437 | K | A | -1.9922 | |
| 438 | R | A | -0.5417 | |
| 439 | Y | A | 0.8710 | |
| 440 | L | A | 1.4469 | |
| 441 | R | A | 0.0000 | |
| 442 | P | A | 0.5592 | |
| 443 | S | A | 0.0000 | |
| 444 | A | A | 0.0000 | |
| 445 | L | A | 2.2722 | |
| 446 | V | A | 2.3918 | |
| 447 | S | A | 1.4092 | |
| 448 | V | A | 0.6095 | |
| 449 | K | A | -1.0308 |
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 | -0.5215 | 3.7244 | View | CSV | PDB |
| 4.5 | -0.5982 | 3.5224 | View | CSV | PDB |
| 5.0 | -0.6951 | 3.2394 | View | CSV | PDB |
| 5.5 | -0.7934 | 2.9238 | View | CSV | PDB |
| 6.0 | -0.8722 | 2.7436 | View | CSV | PDB |
| 6.5 | -0.9148 | 2.752 | View | CSV | PDB |
| 7.0 | -0.9183 | 2.8527 | View | CSV | PDB |
| 7.5 | -0.8938 | 2.9669 | View | CSV | PDB |
| 8.0 | -0.8537 | 3.0863 | View | CSV | PDB |
| 8.5 | -0.8034 | 3.2071 | View | CSV | PDB |
| 9.0 | -0.7444 | 3.3275 | 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