| Chain sequence(s) |
A: QPSFRPKALLLPVTKDPSTLQYTTVINQRTPLVPASVVFDLGGREFWVDCDQGYVSTTYRSPRCNSAVCSRAGSIACGTCFSPPRPGCSNNTCGAFPDNSITGWATSGEFALDVVSIQSTNGSNPGRFVKIPNLIFSCGSTSLLKGLAKGAVGMAGMGRHNIGLPLQFAAAFSFNRKFAVCLTSGRGVAFFGNGPYVFLPGIQISRLQKTPLLINPGTTVFEFSKGEKSPEYFIGVTAIKIVEKTLPIDPTLLKINASTGIGGTKISSVNPYTVLESSIYKAFTSEFIRQAAARSIKRVASVKPFGACFSTKNVGVTRLGYAVPEIQLVLHSKDVVWRIFGANSMVSVSDDVICLGFVDGGVNPGASVVIGGFQLEDNLIEFDLASNKFGFSSTLLGRQTNCANFNFTSTA
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. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:07:03)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3ffc4448234f31a/tmp/folded.pdb (00:07:03)
[INFO] Main: Simulation completed successfully. (00:12:28)
|
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 |
|---|---|---|---|---|
| 24 | Q | A | -1.1917 | |
| 25 | P | A | -0.8523 | |
| 26 | S | A | -0.5748 | |
| 27 | F | A | -0.5042 | |
| 28 | R | A | -1.7424 | |
| 29 | P | A | 0.0000 | |
| 30 | K | A | -2.4616 | |
| 31 | A | A | 0.0000 | |
| 32 | L | A | 0.0000 | |
| 33 | L | A | 0.0000 | |
| 34 | L | A | 0.0000 | |
| 35 | P | A | 0.0000 | |
| 36 | V | A | 0.0000 | |
| 37 | T | A | -0.7455 | |
| 38 | K | A | -0.7612 | |
| 39 | D | A | -0.9029 | |
| 40 | P | A | -0.4934 | |
| 41 | S | A | -0.5713 | |
| 42 | T | A | -0.4363 | |
| 43 | L | A | 0.1116 | |
| 44 | Q | A | 0.0000 | |
| 45 | Y | A | 0.0000 | |
| 46 | T | A | -0.1216 | |
| 47 | T | A | 0.0000 | |
| 48 | V | A | 0.4520 | |
| 49 | I | A | 0.0000 | |
| 50 | N | A | 0.0979 | |
| 51 | Q | A | 0.0000 | |
| 52 | R | A | 0.3926 | |
| 53 | T | A | 0.3355 | |
| 54 | P | A | 0.3519 | |
| 55 | L | A | 0.6488 | |
| 56 | V | A | 0.8966 | |
| 57 | P | A | 0.2359 | |
| 58 | A | A | 0.0000 | |
| 59 | S | A | -0.1051 | |
| 60 | V | A | 0.0000 | |
| 61 | V | A | 0.0000 | |
| 62 | F | A | 0.0000 | |
| 63 | D | A | 0.0000 | |
| 64 | L | A | 0.0000 | |
| 65 | G | A | -0.2162 | |
| 66 | G | A | -0.1826 | |
| 67 | R | A | 0.0000 | |
| 68 | E | A | 0.0000 | |
| 69 | F | A | 0.0000 | |
| 70 | W | A | 0.0000 | |
| 71 | V | A | 0.0000 | |
| 72 | D | A | 0.0000 | |
| 73 | C | A | 0.0000 | |
| 74 | D | A | -2.6192 | |
| 75 | Q | A | -2.0206 | |
| 76 | G | A | -0.9833 | |
| 77 | Y | A | 0.0000 | |
| 78 | V | A | 1.3553 | |
| 79 | S | A | 0.5979 | |
| 80 | T | A | -0.0105 | |
| 81 | T | A | -0.5182 | |
| 82 | Y | A | -0.8150 | |
| 83 | R | A | -2.2141 | |
| 84 | S | A | -1.8381 | |
| 85 | P | A | 0.0000 | |
| 86 | R | A | -2.8325 | |
| 87 | C | A | 0.0000 | |
| 88 | N | A | -1.5824 | |
| 89 | S | A | -1.2124 | |
| 90 | A | A | -0.6151 | |
| 91 | V | A | -0.6054 | |
| 92 | C | A | 0.0000 | |
| 93 | S | A | -0.6491 | |
| 94 | R | A | -1.2063 | |
| 95 | A | A | 0.0000 | |
| 96 | G | A | -0.1920 | |
| 97 | S | A | 0.7033 | |
| 98 | I | A | 1.7685 | |
| 99 | A | A | 0.9518 | |
| 100 | C | A | 0.0277 | |
| 101 | G | A | -0.6181 | |
| 102 | T | A | -0.3587 | |
| 103 | C | A | 0.0666 | |
| 104 | F | A | 1.6105 | |
| 105 | S | A | 0.3814 | |
| 106 | P | A | -0.3388 | |
| 107 | P | A | -0.7777 | |
| 108 | R | A | -1.3942 | |
| 109 | P | A | -1.0186 | |
| 110 | G | A | -0.8979 | |
| 111 | C | A | -0.7893 | |
| 112 | S | A | -1.4158 | |
| 113 | N | A | -1.9743 | |
| 114 | N | A | -2.4707 | |
| 115 | T | A | 0.0000 | |
| 116 | C | A | 0.0000 | |
| 117 | G | A | 0.1378 | |
| 118 | A | A | 0.0000 | |
| 119 | F | A | 0.2265 | |
| 120 | P | A | 0.0000 | |
| 121 | D | A | 0.2657 | |
| 122 | N | A | 0.0000 | |
| 123 | S | A | 0.1241 | |
| 124 | I | A | 0.1922 | |
| 125 | T | A | -0.1653 | |
| 126 | G | A | 0.1987 | |
| 127 | W | A | 0.5636 | |
| 128 | A | A | 0.3467 | |
| 129 | T | A | 0.2457 | |
| 130 | S | A | -0.3933 | |
| 131 | G | A | -0.2202 | |
| 132 | E | A | 0.0000 | |
| 133 | F | A | 0.0000 | |
| 134 | A | A | 0.0000 | |
| 135 | L | A | 0.0000 | |
| 136 | D | A | 0.0000 | |
| 137 | V | A | 0.0000 | |
| 138 | V | A | 0.0000 | |
| 139 | S | A | 0.0000 | |
| 140 | I | A | 0.0000 | |
| 141 | Q | A | -0.4795 | |
| 142 | S | A | 0.0000 | |
| 143 | T | A | 0.0000 | |
| 144 | N | A | -1.7362 | |
| 145 | G | A | 0.0000 | |
| 146 | S | A | -0.5873 | |
| 147 | N | A | -0.6327 | |
| 148 | P | A | 0.0000 | |
| 149 | G | A | -1.0425 | |
| 150 | R | A | -1.1321 | |
| 151 | F | A | -0.1655 | |
| 152 | V | A | 0.0000 | |
| 153 | K | A | -1.7191 | |
| 154 | I | A | 0.0000 | |
| 155 | P | A | -1.3569 | |
| 156 | N | A | -1.8042 | |
| 157 | L | A | 0.0000 | |
| 158 | I | A | 0.0000 | |
| 159 | F | A | 0.0000 | |
| 160 | S | A | 0.0000 | |
| 161 | C | A | 0.0000 | |
| 162 | G | A | 0.0000 | |
| 163 | S | A | -0.7936 | |
| 164 | T | A | -0.9454 | |
| 165 | S | A | -0.5995 | |
| 166 | L | A | 0.0000 | |
| 167 | L | A | -0.6836 | |
| 168 | K | A | -1.7635 | |
| 169 | G | A | -1.3527 | |
| 170 | L | A | 0.0000 | |
| 171 | A | A | 0.0000 | |
| 172 | K | A | -2.1656 | |
| 173 | G | A | -1.1501 | |
| 174 | A | A | 0.0000 | |
| 175 | V | A | -0.1480 | |
| 176 | G | A | 0.0000 | |
| 177 | M | A | 0.0000 | |
| 178 | A | A | 0.0000 | |
| 179 | G | A | 0.0000 | |
| 180 | M | A | 0.0000 | |
| 181 | G | A | 0.0000 | |
| 182 | R | A | -0.8128 | |
| 183 | H | A | 0.0000 | |
| 184 | N | A | -1.4001 | |
| 185 | I | A | 0.0000 | |
| 186 | G | A | 0.0000 | |
| 187 | L | A | 0.0000 | |
| 188 | P | A | 0.0000 | |
| 189 | L | A | -0.8150 | |
| 190 | Q | A | 0.0000 | |
| 191 | F | A | 0.0000 | |
| 192 | A | A | 0.0000 | |
| 193 | A | A | -0.4331 | |
| 194 | A | A | -0.4553 | |
| 195 | F | A | -0.6215 | |
| 196 | S | A | -1.0146 | |
| 197 | F | A | -1.5680 | |
| 198 | N | A | -2.2285 | |
| 199 | R | A | -2.4675 | |
| 200 | K | A | -1.5772 | |
| 201 | F | A | 0.0000 | |
| 202 | A | A | 0.0000 | |
| 203 | V | A | 0.0000 | |
| 204 | C | A | 0.0000 | |
| 205 | L | A | 0.0000 | |
| 206 | T | A | 0.0000 | |
| 207 | S | A | -0.7094 | |
| 208 | G | A | -1.1512 | |
| 209 | R | A | -1.4888 | |
| 210 | G | A | 0.0000 | |
| 211 | V | A | 0.0000 | |
| 212 | A | A | 0.0000 | |
| 213 | F | A | 0.0000 | |
| 214 | F | A | 0.0000 | |
| 215 | G | A | 0.0000 | |
| 216 | N | A | -1.6138 | |
| 217 | G | A | -1.0244 | |
| 218 | P | A | -0.7790 | |
| 219 | Y | A | 0.0000 | |
| 220 | V | A | -0.4768 | |
| 221 | F | A | 0.0000 | |
| 222 | L | A | 0.2150 | |
| 223 | P | A | -0.1538 | |
| 224 | G | A | -0.3390 | |
| 225 | I | A | -0.4928 | |
| 226 | Q | A | -1.2446 | |
| 227 | I | A | 0.0000 | |
| 228 | S | A | -1.3610 | |
| 229 | R | A | -2.2053 | |
| 230 | L | A | -1.1874 | |
| 231 | Q | A | -1.4125 | |
| 232 | K | A | -1.5810 | |
| 233 | T | A | 0.0000 | |
| 234 | P | A | -0.6644 | |
| 235 | L | A | 0.0000 | |
| 236 | L | A | 0.3063 | |
| 237 | I | A | 0.3931 | |
| 238 | N | A | 0.0000 | |
| 239 | P | A | -0.7338 | |
| 240 | G | A | -0.7597 | |
| 241 | T | A | -0.6835 | |
| 242 | T | A | 0.0242 | |
| 243 | V | A | 0.8583 | |
| 244 | F | A | 1.4574 | |
| 245 | E | A | -0.4036 | |
| 246 | F | A | -0.3916 | |
| 247 | S | A | -0.9261 | |
| 248 | K | A | -2.4254 | |
| 249 | G | A | -1.8907 | |
| 250 | E | A | -1.8052 | |
| 251 | K | A | -2.0685 | |
| 252 | S | A | 0.0000 | |
| 253 | P | A | 0.0000 | |
| 254 | E | A | -0.3960 | |
| 255 | Y | A | 0.0000 | |
| 256 | F | A | 0.0000 | |
| 257 | I | A | 0.0000 | |
| 258 | G | A | -0.6830 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | -0.8688 | |
| 261 | A | A | -0.6353 | |
| 262 | I | A | 0.0000 | |
| 263 | K | A | -1.1751 | |
| 264 | I | A | 0.0000 | |
| 265 | V | A | -0.7817 | |
| 266 | E | A | -2.0714 | |
| 267 | K | A | -1.7628 | |
| 268 | T | A | -1.0066 | |
| 269 | L | A | 0.0000 | |
| 270 | P | A | -0.6644 | |
| 271 | I | A | -0.8386 | |
| 272 | D | A | -1.7021 | |
| 273 | P | A | -1.2147 | |
| 274 | T | A | -1.0553 | |
| 275 | L | A | -0.8117 | |
| 276 | L | A | 0.0000 | |
| 277 | K | A | -1.7644 | |
| 278 | I | A | -0.6500 | |
| 279 | N | A | -0.9787 | |
| 280 | A | A | -0.4916 | |
| 281 | S | A | -0.3732 | |
| 282 | T | A | -0.2140 | |
| 283 | G | A | 0.0000 | |
| 284 | I | A | -0.0455 | |
| 285 | G | A | 0.0000 | |
| 286 | G | A | 0.0000 | |
| 287 | T | A | 0.0000 | |
| 288 | K | A | -0.2533 | |
| 289 | I | A | 0.0000 | |
| 290 | S | A | 0.0000 | |
| 291 | S | A | 0.0000 | |
| 292 | V | A | 0.2974 | |
| 293 | N | A | 0.0507 | |
| 294 | P | A | 0.1260 | |
| 295 | Y | A | 0.2806 | |
| 296 | T | A | 0.0000 | |
| 297 | V | A | -0.2818 | |
| 298 | L | A | 0.0000 | |
| 299 | E | A | 0.0000 | |
| 300 | S | A | -0.7810 | |
| 301 | S | A | -1.0005 | |
| 302 | I | A | 0.0000 | |
| 303 | Y | A | -1.2225 | |
| 304 | K | A | -1.9701 | |
| 305 | A | A | -0.8794 | |
| 306 | F | A | 0.0000 | |
| 307 | T | A | -0.9087 | |
| 308 | S | A | -0.8903 | |
| 309 | E | A | 0.0000 | |
| 310 | F | A | 0.0000 | |
| 311 | I | A | -1.1651 | |
| 312 | R | A | -1.7009 | |
| 313 | Q | A | -1.1993 | |
| 314 | A | A | 0.0000 | |
| 315 | A | A | -1.8085 | |
| 316 | A | A | -1.4380 | |
| 317 | R | A | -2.4476 | |
| 318 | S | A | -2.1448 | |
| 319 | I | A | 0.0000 | |
| 320 | K | A | -3.0866 | |
| 321 | R | A | -2.1501 | |
| 322 | V | A | -0.6025 | |
| 323 | A | A | -0.1355 | |
| 324 | S | A | -0.3932 | |
| 325 | V | A | 0.0402 | |
| 326 | K | A | -1.4114 | |
| 327 | P | A | -1.2414 | |
| 328 | F | A | 0.0000 | |
| 329 | G | A | -0.8475 | |
| 330 | A | A | 0.0000 | |
| 331 | C | A | 0.0000 | |
| 332 | F | A | 0.0000 | |
| 333 | S | A | -2.2710 | |
| 334 | T | A | -2.3467 | |
| 335 | K | A | -3.1545 | |
| 336 | N | A | -2.4827 | |
| 337 | V | A | 0.0000 | |
| 338 | G | A | -0.0571 | |
| 339 | V | A | 1.1789 | |
| 340 | T | A | 0.0044 | |
| 341 | R | A | -1.5410 | |
| 342 | L | A | -0.3151 | |
| 343 | G | A | 0.2017 | |
| 344 | Y | A | 0.7003 | |
| 345 | A | A | 0.0870 | |
| 346 | V | A | 0.2457 | |
| 347 | P | A | 0.0000 | |
| 348 | E | A | -0.5032 | |
| 349 | I | A | 0.0000 | |
| 350 | Q | A | -0.9476 | |
| 351 | L | A | 0.0000 | |
| 352 | V | A | 0.0000 | |
| 353 | L | A | 0.0000 | |
| 354 | H | A | -1.7096 | |
| 355 | S | A | -1.8421 | |
| 356 | K | A | -2.6841 | |
| 357 | D | A | -2.6303 | |
| 358 | V | A | -1.6747 | |
| 359 | V | A | -1.2223 | |
| 360 | W | A | 0.0000 | |
| 361 | R | A | -1.1482 | |
| 362 | I | A | 0.0000 | |
| 363 | F | A | -0.1862 | |
| 364 | G | A | 0.0000 | |
| 365 | A | A | 0.2185 | |
| 366 | N | A | 0.0000 | |
| 367 | S | A | 0.0000 | |
| 368 | M | A | 0.0000 | |
| 369 | V | A | 0.3967 | |
| 370 | S | A | -0.3678 | |
| 371 | V | A | -0.0071 | |
| 372 | S | A | -1.1781 | |
| 373 | D | A | -2.7266 | |
| 374 | D | A | -2.8782 | |
| 375 | V | A | -1.2309 | |
| 376 | I | A | 0.0000 | |
| 377 | C | A | 0.0000 | |
| 378 | L | A | 0.0000 | |
| 379 | G | A | 0.0000 | |
| 380 | F | A | 0.0000 | |
| 381 | V | A | -0.9637 | |
| 382 | D | A | -1.6902 | |
| 383 | G | A | -0.8172 | |
| 384 | G | A | -0.1976 | |
| 385 | V | A | 0.7118 | |
| 386 | N | A | -0.4290 | |
| 387 | P | A | -0.2144 | |
| 388 | G | A | -0.1780 | |
| 389 | A | A | 0.0000 | |
| 390 | S | A | 0.0000 | |
| 391 | V | A | 0.0000 | |
| 392 | V | A | 0.0000 | |
| 393 | I | A | 0.0000 | |
| 394 | G | A | 0.0000 | |
| 395 | G | A | 0.0000 | |
| 396 | F | A | 0.2320 | |
| 397 | Q | A | 0.0000 | |
| 398 | L | A | 0.0000 | |
| 399 | E | A | 0.0000 | |
| 400 | D | A | -0.3103 | |
| 401 | N | A | 0.0000 | |
| 402 | L | A | 0.0000 | |
| 403 | I | A | 0.0000 | |
| 404 | E | A | 0.0000 | |
| 405 | F | A | 0.0000 | |
| 406 | D | A | 0.0000 | |
| 407 | L | A | -0.9890 | |
| 408 | A | A | -1.0295 | |
| 409 | S | A | -0.8956 | |
| 410 | N | A | -0.7900 | |
| 411 | K | A | -1.0224 | |
| 412 | F | A | 0.0000 | |
| 413 | G | A | 0.0000 | |
| 414 | F | A | 0.0000 | |
| 415 | S | A | 0.0000 | |
| 416 | S | A | -0.3910 | |
| 417 | T | A | 0.0000 | |
| 418 | L | A | 0.0000 | |
| 419 | L | A | -0.9734 | |
| 420 | G | A | -1.1940 | |
| 421 | R | A | -1.4364 | |
| 422 | Q | A | -1.6720 | |
| 423 | T | A | 0.0000 | |
| 424 | N | A | -0.6044 | |
| 425 | C | A | 0.0000 | |
| 426 | A | A | -0.6682 | |
| 427 | N | A | -0.3780 | |
| 428 | F | A | 0.0000 | |
| 429 | N | A | -0.2208 | |
| 430 | F | A | -0.1518 | |
| 431 | T | A | -0.1817 | |
| 432 | S | A | -0.6205 | |
| 433 | T | A | -0.6685 | |
| 434 | A | A | -0.6036 |
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 | -0.4248 | 4.5665 | View | CSV | PDB |
| 4.5 | -0.4425 | 4.5665 | View | CSV | PDB |
| 5.0 | -0.4622 | 4.5665 | View | CSV | PDB |
| 5.5 | -0.4782 | 4.5665 | View | CSV | PDB |
| 6.0 | -0.4842 | 4.5665 | View | CSV | PDB |
| 6.5 | -0.4768 | 4.5665 | View | CSV | PDB |
| 7.0 | -0.4583 | 4.5665 | View | CSV | PDB |
| 7.5 | -0.4332 | 4.5665 | View | CSV | PDB |
| 8.0 | -0.4042 | 4.5665 | View | CSV | PDB |
| 8.5 | -0.3719 | 4.5665 | View | CSV | PDB |
| 9.0 | -0.3366 | 4.5665 | 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