| Chain sequence(s) |
A: RGESLNKSLPILHEWKFFDYDFGSDERRQDAILSGEYDYKNNYPSDIDQWHDKIFVTMLRYNGVPSSLNVISKKVGDGGPLLQPYPDWSFAKYDDCSGIVSASKLAIDKCDRLWVLDSGLVNNTQPMCSPKLLTFDLTTSQLLKQVEIPHDVAVNATTGKGRLSSLAVQSLDCNDTMVYIADEKGEGLIVYHNSDDSFHRLTSNTFDYDPKFTKMTIDGESYTAQDGISGMALSPMTNNLYYSPVASTSLYYVNTEQFRTSDYQDIHYEGVQNILDTQSSAKVVSKSGVLFFGLVGDSALGCWNEHRTLERHNIRTVAQSDETLQMIASMKIKEALPHVPIFDRYINREYILVLSNKMQKMVNNDFNFDDVNFRIMNANVNELILNTRCENPDNDRTPFKISIHL
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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:08:13)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/838248f0f43ab4e/tmp/folded.pdb (00:08:13)
[INFO] Main: Simulation completed successfully. (00:13:33)
|
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 |
|---|---|---|---|---|
| 23 | R | A | -2.5656 | |
| 24 | G | A | -2.2783 | |
| 25 | E | A | -2.7082 | |
| 26 | S | A | 0.0000 | |
| 27 | L | A | -1.6707 | |
| 28 | N | A | -2.3674 | |
| 29 | K | A | -1.4860 | |
| 30 | S | A | -1.1045 | |
| 31 | L | A | 0.0000 | |
| 32 | P | A | 0.4812 | |
| 33 | I | A | 1.3661 | |
| 34 | L | A | 1.0919 | |
| 35 | H | A | 0.1147 | |
| 36 | E | A | -0.5316 | |
| 37 | W | A | 0.0000 | |
| 38 | K | A | -1.9968 | |
| 39 | F | A | -1.1732 | |
| 40 | F | A | 0.0000 | |
| 41 | D | A | -0.6040 | |
| 42 | Y | A | 0.0000 | |
| 43 | D | A | -1.6824 | |
| 44 | F | A | 0.0000 | |
| 45 | G | A | -1.5599 | |
| 46 | S | A | -2.5217 | |
| 47 | D | A | -3.7036 | |
| 48 | E | A | -3.7197 | |
| 49 | R | A | -2.9099 | |
| 50 | R | A | -2.5913 | |
| 51 | Q | A | -2.3073 | |
| 52 | D | A | -2.4484 | |
| 53 | A | A | 0.0000 | |
| 54 | I | A | 0.4415 | |
| 55 | L | A | 0.8442 | |
| 56 | S | A | -0.0617 | |
| 57 | G | A | -0.4175 | |
| 58 | E | A | -0.9053 | |
| 59 | Y | A | 0.0000 | |
| 60 | D | A | -0.7085 | |
| 61 | Y | A | -0.3299 | |
| 62 | K | A | -1.9263 | |
| 63 | N | A | -1.2530 | |
| 64 | N | A | 0.0000 | |
| 65 | Y | A | 0.0000 | |
| 66 | P | A | 0.0000 | |
| 67 | S | A | -0.0977 | |
| 68 | D | A | 0.0000 | |
| 69 | I | A | 0.0000 | |
| 70 | D | A | 0.0000 | |
| 71 | Q | A | -0.4510 | |
| 72 | W | A | -0.9756 | |
| 73 | H | A | -1.6191 | |
| 74 | D | A | -2.2941 | |
| 75 | K | A | -1.1030 | |
| 76 | I | A | -0.1238 | |
| 77 | F | A | 0.0000 | |
| 78 | V | A | 0.0000 | |
| 79 | T | A | 0.0000 | |
| 80 | M | A | 0.0000 | |
| 81 | L | A | 0.0000 | |
| 82 | R | A | 0.0000 | |
| 83 | Y | A | -0.9748 | |
| 84 | N | A | -1.7043 | |
| 85 | G | A | 0.0000 | |
| 86 | V | A | 0.0000 | |
| 87 | P | A | 0.0000 | |
| 88 | S | A | 0.0000 | |
| 89 | S | A | 0.0000 | |
| 90 | L | A | 0.0000 | |
| 91 | N | A | 0.0000 | |
| 92 | V | A | -0.0115 | |
| 93 | I | A | -0.2670 | |
| 94 | S | A | -1.1681 | |
| 95 | K | A | -2.1010 | |
| 96 | K | A | -1.8352 | |
| 97 | V | A | -0.0584 | |
| 98 | G | A | -0.8503 | |
| 99 | D | A | -2.1594 | |
| 100 | G | A | 0.0000 | |
| 101 | G | A | -0.7349 | |
| 102 | P | A | -0.6332 | |
| 103 | L | A | 0.0000 | |
| 104 | L | A | 0.0000 | |
| 105 | Q | A | -1.3646 | |
| 106 | P | A | 0.0000 | |
| 107 | Y | A | 0.0000 | |
| 108 | P | A | -1.0448 | |
| 109 | D | A | -2.0212 | |
| 110 | W | A | -1.1192 | |
| 111 | S | A | -0.8813 | |
| 112 | F | A | -0.6516 | |
| 113 | A | A | 0.0000 | |
| 114 | K | A | -2.2046 | |
| 115 | Y | A | -1.5454 | |
| 116 | D | A | -2.6486 | |
| 117 | D | A | -2.6371 | |
| 118 | C | A | -1.2551 | |
| 119 | S | A | -1.1851 | |
| 120 | G | A | 0.0000 | |
| 121 | I | A | 0.0000 | |
| 122 | V | A | 0.0000 | |
| 123 | S | A | 0.0000 | |
| 124 | A | A | 0.0000 | |
| 125 | S | A | -0.2378 | |
| 126 | K | A | -0.2690 | |
| 127 | L | A | 0.0000 | |
| 128 | A | A | 0.1040 | |
| 129 | I | A | -0.1130 | |
| 130 | D | A | -0.6901 | |
| 131 | K | A | -1.7522 | |
| 132 | C | A | -1.1564 | |
| 133 | D | A | -1.0277 | |
| 134 | R | A | 0.0000 | |
| 135 | L | A | 0.0000 | |
| 136 | W | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | L | A | 0.0000 | |
| 139 | D | A | 0.0000 | |
| 140 | S | A | 0.0000 | |
| 141 | G | A | 0.0000 | |
| 142 | L | A | 0.0000 | |
| 143 | V | A | 0.0000 | |
| 144 | N | A | -1.2738 | |
| 145 | N | A | -1.1814 | |
| 146 | T | A | -1.0576 | |
| 147 | Q | A | -1.1882 | |
| 148 | P | A | -0.6597 | |
| 149 | M | A | -0.0553 | |
| 150 | C | A | 0.0000 | |
| 151 | S | A | -0.6061 | |
| 152 | P | A | -0.7219 | |
| 153 | K | A | -1.1665 | |
| 154 | L | A | 0.0000 | |
| 155 | L | A | 0.0000 | |
| 156 | T | A | 0.0000 | |
| 157 | F | A | 0.0000 | |
| 158 | D | A | -0.4375 | |
| 159 | L | A | 0.0000 | |
| 160 | T | A | -0.8410 | |
| 161 | T | A | -0.4111 | |
| 162 | S | A | -0.7240 | |
| 163 | Q | A | -0.9010 | |
| 164 | L | A | 0.4179 | |
| 165 | L | A | 1.0598 | |
| 166 | K | A | 0.0890 | |
| 167 | Q | A | -0.7490 | |
| 168 | V | A | -1.3545 | |
| 169 | E | A | -2.1150 | |
| 170 | I | A | 0.0000 | |
| 171 | P | A | -1.5900 | |
| 172 | H | A | -2.0604 | |
| 173 | D | A | -2.2177 | |
| 174 | V | A | -0.9439 | |
| 175 | A | A | 0.0000 | |
| 176 | V | A | -0.9911 | |
| 177 | N | A | -1.1773 | |
| 178 | A | A | -0.7873 | |
| 179 | T | A | -0.3807 | |
| 180 | T | A | -0.7196 | |
| 181 | G | A | -1.3727 | |
| 182 | K | A | -1.6555 | |
| 183 | G | A | -1.2918 | |
| 184 | R | A | -0.9937 | |
| 185 | L | A | 0.0000 | |
| 186 | S | A | -0.3709 | |
| 187 | S | A | 0.0000 | |
| 188 | L | A | 0.0000 | |
| 189 | A | A | 0.0000 | |
| 190 | V | A | 0.0685 | |
| 191 | Q | A | 0.0000 | |
| 192 | S | A | -0.7720 | |
| 193 | L | A | -0.0079 | |
| 194 | D | A | -1.9428 | |
| 195 | C | A | -1.6068 | |
| 196 | N | A | -2.4442 | |
| 200 | D | A | -3.1726 | |
| 201 | T | A | 0.0000 | |
| 202 | M | A | 0.0000 | |
| 203 | V | A | 0.0000 | |
| 204 | Y | A | 0.0000 | |
| 205 | I | A | 0.0000 | |
| 206 | A | A | 0.0000 | |
| 207 | D | A | 0.0000 | |
| 208 | E | A | -1.3893 | |
| 209 | K | A | -1.9623 | |
| 210 | G | A | 0.0000 | |
| 211 | E | A | -1.9187 | |
| 212 | G | A | 0.0000 | |
| 213 | L | A | 0.0000 | |
| 214 | I | A | 0.0000 | |
| 215 | V | A | 0.0000 | |
| 216 | Y | A | 0.0000 | |
| 217 | H | A | -2.1298 | |
| 218 | N | A | -2.2183 | |
| 219 | S | A | -2.5379 | |
| 220 | D | A | -2.9858 | |
| 221 | D | A | -2.5512 | |
| 222 | S | A | -1.5518 | |
| 223 | F | A | -1.1010 | |
| 224 | H | A | -0.7521 | |
| 225 | R | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | T | A | -0.8184 | |
| 228 | S | A | -1.0144 | |
| 229 | N | A | -1.9616 | |
| 230 | T | A | -1.4865 | |
| 231 | F | A | 0.0000 | |
| 232 | D | A | -2.6072 | |
| 233 | Y | A | -1.6454 | |
| 234 | D | A | -1.2938 | |
| 235 | P | A | -1.3784 | |
| 236 | K | A | -1.8657 | |
| 237 | F | A | -1.0209 | |
| 238 | T | A | -1.2552 | |
| 239 | K | A | -1.7939 | |
| 240 | M | A | 0.0000 | |
| 241 | T | A | -1.6123 | |
| 242 | I | A | 0.0000 | |
| 243 | D | A | -3.1265 | |
| 244 | G | A | -2.4579 | |
| 245 | E | A | -2.7613 | |
| 246 | S | A | -1.7286 | |
| 247 | Y | A | -0.8307 | |
| 248 | T | A | -0.8595 | |
| 249 | A | A | -0.8401 | |
| 250 | Q | A | -1.8677 | |
| 251 | D | A | -1.4809 | |
| 252 | G | A | 0.0000 | |
| 253 | I | A | 0.0000 | |
| 254 | S | A | 0.0000 | |
| 255 | G | A | 0.0000 | |
| 256 | M | A | 0.0000 | |
| 257 | A | A | 0.0000 | |
| 258 | L | A | 0.1537 | |
| 259 | S | A | 0.0000 | |
| 260 | P | A | -0.5646 | |
| 261 | M | A | -0.4024 | |
| 262 | T | A | -0.4164 | |
| 263 | N | A | -0.4454 | |
| 264 | N | A | -0.5615 | |
| 265 | L | A | 0.0000 | |
| 266 | Y | A | 0.0000 | |
| 267 | Y | A | 0.0000 | |
| 268 | S | A | 0.0000 | |
| 269 | P | A | 0.0000 | |
| 270 | V | A | -0.2690 | |
| 271 | A | A | 0.0000 | |
| 272 | S | A | 0.0000 | |
| 273 | T | A | 0.0000 | |
| 274 | S | A | 0.0000 | |
| 275 | L | A | 0.0000 | |
| 276 | Y | A | 0.0000 | |
| 277 | Y | A | -0.4307 | |
| 278 | V | A | 0.0000 | |
| 279 | N | A | -0.9517 | |
| 280 | T | A | 0.0000 | |
| 281 | E | A | -1.2396 | |
| 282 | Q | A | -1.7998 | |
| 283 | F | A | 0.0000 | |
| 284 | R | A | -2.4874 | |
| 285 | T | A | -1.6645 | |
| 286 | S | A | -1.6836 | |
| 287 | D | A | -2.6282 | |
| 288 | Y | A | -1.9687 | |
| 289 | Q | A | -2.7780 | |
| 292 | D | A | -2.8331 | |
| 293 | I | A | -1.7507 | |
| 294 | H | A | -1.7414 | |
| 295 | Y | A | -1.0105 | |
| 296 | E | A | -1.5020 | |
| 297 | G | A | -0.7279 | |
| 298 | V | A | -0.5969 | |
| 299 | Q | A | -1.2563 | |
| 300 | N | A | -1.0464 | |
| 301 | I | A | -1.0559 | |
| 302 | L | A | -1.4427 | |
| 303 | D | A | -2.2550 | |
| 304 | T | A | 0.0000 | |
| 305 | Q | A | 0.0000 | |
| 306 | S | A | 0.0000 | |
| 307 | S | A | -0.0040 | |
| 308 | A | A | 0.0000 | |
| 309 | K | A | 0.0000 | |
| 310 | V | A | 0.2271 | |
| 311 | V | A | 0.0000 | |
| 312 | S | A | 0.0000 | |
| 313 | K | A | -1.7003 | |
| 314 | S | A | -1.2332 | |
| 315 | G | A | 0.0000 | |
| 316 | V | A | 0.0000 | |
| 317 | L | A | 0.0000 | |
| 318 | F | A | 0.0000 | |
| 319 | F | A | 0.0000 | |
| 320 | G | A | 0.0000 | |
| 321 | L | A | 0.0000 | |
| 322 | V | A | 0.0000 | |
| 323 | G | A | -1.7162 | |
| 324 | D | A | -2.0087 | |
| 325 | S | A | -1.8213 | |
| 326 | A | A | 0.0000 | |
| 327 | L | A | 0.0000 | |
| 328 | G | A | 0.0000 | |
| 329 | C | A | 0.0000 | |
| 330 | W | A | 0.0000 | |
| 331 | N | A | 0.0000 | |
| 332 | E | A | -0.9042 | |
| 333 | H | A | -1.4769 | |
| 334 | R | A | -1.7009 | |
| 335 | T | A | -1.1174 | |
| 336 | L | A | -0.9289 | |
| 337 | E | A | -1.8863 | |
| 338 | R | A | -3.0514 | |
| 339 | H | A | -2.6875 | |
| 340 | N | A | 0.0000 | |
| 341 | I | A | 0.0000 | |
| 342 | R | A | -2.3966 | |
| 343 | T | A | -1.5884 | |
| 344 | V | A | 0.0000 | |
| 345 | A | A | 0.0000 | |
| 346 | Q | A | 0.0000 | |
| 347 | S | A | 0.0000 | |
| 348 | D | A | -3.2737 | |
| 349 | E | A | -2.9240 | |
| 350 | T | A | -1.5915 | |
| 351 | L | A | 0.0000 | |
| 352 | Q | A | -1.9446 | |
| 353 | M | A | 0.0000 | |
| 354 | I | A | 0.0000 | |
| 355 | A | A | -0.0406 | |
| 356 | S | A | 0.0000 | |
| 357 | M | A | 0.0000 | |
| 358 | K | A | -0.1185 | |
| 359 | I | A | -0.4324 | |
| 360 | K | A | -0.7289 | |
| 361 | E | A | -0.7183 | |
| 362 | A | A | 0.1029 | |
| 363 | L | A | 1.0971 | |
| 364 | P | A | 0.5434 | |
| 365 | H | A | 1.0504 | |
| 366 | V | A | 2.4146 | |
| 367 | P | A | 1.4888 | |
| 368 | I | A | 2.6703 | |
| 369 | F | A | 2.1745 | |
| 370 | D | A | 0.7896 | |
| 371 | R | A | -0.8267 | |
| 372 | Y | A | 0.9578 | |
| 373 | I | A | 1.1766 | |
| 374 | N | A | 0.0030 | |
| 375 | R | A | -0.1303 | |
| 376 | E | A | -0.9477 | |
| 377 | Y | A | 0.0000 | |
| 378 | I | A | 0.0000 | |
| 379 | L | A | 0.0000 | |
| 380 | V | A | 0.0000 | |
| 381 | L | A | 0.0000 | |
| 382 | S | A | 0.0000 | |
| 383 | N | A | 0.0000 | |
| 384 | K | A | -0.8322 | |
| 385 | M | A | 0.1473 | |
| 386 | Q | A | 0.0000 | |
| 387 | K | A | -1.7091 | |
| 388 | M | A | -0.5043 | |
| 389 | V | A | 0.5390 | |
| 390 | N | A | -1.6289 | |
| 391 | N | A | -2.6363 | |
| 392 | D | A | -3.0805 | |
| 393 | F | A | 0.0000 | |
| 394 | N | A | -3.0288 | |
| 395 | F | A | -2.4448 | |
| 396 | D | A | -3.1547 | |
| 397 | D | A | -3.1223 | |
| 398 | V | A | -1.4105 | |
| 399 | N | A | 0.0000 | |
| 400 | F | A | 0.0000 | |
| 401 | R | A | -0.1359 | |
| 402 | I | A | 0.0000 | |
| 403 | M | A | 0.0000 | |
| 404 | N | A | 0.0000 | |
| 405 | A | A | -0.0869 | |
| 406 | N | A | 0.0000 | |
| 407 | V | A | 0.0000 | |
| 408 | N | A | -0.9363 | |
| 409 | E | A | -1.4132 | |
| 410 | L | A | 0.0000 | |
| 411 | I | A | 0.0000 | |
| 412 | L | A | -0.7848 | |
| 413 | N | A | -1.6241 | |
| 414 | T | A | -1.8321 | |
| 415 | R | A | -2.6111 | |
| 416 | C | A | 0.0000 | |
| 417 | E | A | -1.8884 | |
| 418 | N | A | -1.8303 | |
| 419 | P | A | -2.0157 | |
| 420 | D | A | -2.6420 | |
| 421 | N | A | -2.8616 | |
| 422 | D | A | -3.4365 | |
| 423 | R | A | -3.2070 | |
| 424 | T | A | -1.6043 | |
| 425 | P | A | -0.6877 | |
| 426 | F | A | 1.0734 | |
| 427 | K | A | 1.0362 | |
| 428 | I | A | 2.1395 | |
| 429 | S | A | 0.7817 | |
| 430 | I | A | 0.5336 | |
| 431 | H | A | -0.5254 | |
| 432 | L | A | 0.9092 |
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 | -0.3975 | 4.8672 | View | CSV | PDB |
| 4.5 | -0.4822 | 4.8425 | View | CSV | PDB |
| 5.0 | -0.5812 | 4.8204 | View | CSV | PDB |
| 5.5 | -0.6803 | 4.8027 | View | CSV | PDB |
| 6.0 | -0.7679 | 4.7866 | View | CSV | PDB |
| 6.5 | -0.8372 | 4.7672 | View | CSV | PDB |
| 7.0 | -0.8892 | 4.7436 | View | CSV | PDB |
| 7.5 | -0.9307 | 4.7185 | View | CSV | PDB |
| 8.0 | -0.9651 | 4.696 | View | CSV | PDB |
| 8.5 | -0.9891 | 4.6796 | View | CSV | PDB |
| 9.0 | -0.9965 | 4.6704 | 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