| Chain sequence(s) |
A: PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPQVKFNWYVDGVQVHNAKTKPREQQYNSTYRVVSVLTVLHQNWLDGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
B: PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPQVKFNWYVDGVQVHNAKTKPREQQYNSTYRVVSVLTVLHQNWLDGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL input PDB |
| Selected Chain(s) | A,B |
| 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] (00:00:06)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:06)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:06)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:06)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:07)
[INFO] FoldX: Starting FoldX energy minimization (00:00:07)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:47)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/39cc3d94d2f66e3/tmp/folded.pdb (00:10:47)
[INFO] Main: Simulation completed successfully. (00:19:09)
|
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 |
|---|---|---|---|---|
| 238 | P | A | -0.8025 | |
| 239 | S | A | -0.2431 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 1.1860 | |
| 242 | L | A | 0.9320 | |
| 243 | F | A | 1.2098 | |
| 244 | P | A | -0.1257 | |
| 245 | P | A | -1.1215 | |
| 246 | K | A | -2.1089 | |
| 247 | P | A | -1.4773 | |
| 248 | K | A | -1.1801 | |
| 249 | D | A | 0.0000 | |
| 250 | T | A | 0.0000 | |
| 251 | L | A | 0.0000 | |
| 252 | M | A | 0.6663 | |
| 253 | I | A | 1.6661 | |
| 254 | S | A | 0.2725 | |
| 255 | R | A | -0.7468 | |
| 256 | T | A | -0.5892 | |
| 257 | P | A | 0.0000 | |
| 258 | E | A | -0.8892 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | 0.3117 | |
| 261 | C | A | 0.0000 | |
| 262 | V | A | 0.7883 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | -0.7316 | |
| 265 | D | A | -2.0546 | |
| 266 | V | A | 0.0000 | |
| 267 | S | A | -2.1451 | |
| 268 | H | A | -2.5284 | |
| 269 | E | A | -2.8366 | |
| 270 | D | A | -2.3506 | |
| 271 | P | A | -2.6256 | |
| 272 | Q | A | -2.5566 | |
| 273 | V | A | -1.9575 | |
| 274 | K | A | -2.0638 | |
| 275 | F | A | -1.1905 | |
| 276 | N | A | 0.0000 | |
| 277 | W | A | 0.0000 | |
| 278 | Y | A | -0.4223 | |
| 279 | V | A | 0.0000 | |
| 280 | D | A | -1.9198 | |
| 281 | G | A | -0.6365 | |
| 282 | V | A | 0.8216 | |
| 283 | Q | A | -0.1343 | |
| 284 | V | A | -0.5356 | |
| 285 | H | A | -1.4381 | |
| 286 | N | A | -2.4705 | |
| 287 | A | A | -1.8268 | |
| 288 | K | A | -2.6233 | |
| 289 | T | A | -2.2541 | |
| 290 | K | A | -2.6851 | |
| 291 | P | A | -2.2608 | |
| 292 | R | A | -3.3295 | |
| 293 | E | A | -3.5355 | |
| 294 | Q | A | -2.7749 | |
| 295 | Q | A | -2.2111 | |
| 296 | Y | A | -1.3124 | |
| 297 | N | A | -1.6327 | |
| 298 | S | A | -1.2228 | |
| 299 | T | A | -1.8116 | |
| 300 | Y | A | -2.3243 | |
| 301 | R | A | -2.1340 | |
| 302 | V | A | 0.0000 | |
| 303 | V | A | -0.9985 | |
| 304 | S | A | 0.0000 | |
| 305 | V | A | -0.9476 | |
| 306 | L | A | 0.0000 | |
| 307 | T | A | -0.7059 | |
| 308 | V | A | 0.0000 | |
| 309 | L | A | 0.9919 | |
| 310 | H | A | -0.0782 | |
| 311 | Q | A | -1.2038 | |
| 312 | N | A | -1.5094 | |
| 313 | W | A | 0.0000 | |
| 314 | L | A | -1.1582 | |
| 315 | D | A | -2.5880 | |
| 316 | G | A | -2.1915 | |
| 317 | K | A | -2.1748 | |
| 318 | E | A | -2.0749 | |
| 319 | Y | A | 0.0000 | |
| 320 | K | A | -1.2841 | |
| 321 | C | A | 0.0000 | |
| 322 | K | A | -1.3152 | |
| 323 | V | A | 0.0000 | |
| 324 | S | A | -1.3653 | |
| 325 | N | A | 0.0000 | |
| 326 | K | A | -2.4205 | |
| 327 | A | A | -1.3597 | |
| 328 | L | A | -0.5003 | |
| 329 | P | A | -0.5328 | |
| 330 | A | A | -0.4216 | |
| 331 | P | A | -0.8740 | |
| 332 | I | A | -0.5771 | |
| 333 | E | A | -1.6754 | |
| 334 | K | A | -1.0859 | |
| 335 | T | A | -0.9773 | |
| 336 | I | A | -0.3998 | |
| 337 | S | A | -1.2817 | |
| 338 | K | A | -1.3098 | |
| 339 | A | A | -1.3050 | |
| 340 | K | A | -2.3923 | |
| 341 | G | A | -2.0142 | |
| 342 | Q | A | -1.9836 | |
| 343 | P | A | -1.8371 | |
| 344 | R | A | -2.2372 | |
| 345 | E | A | -2.6093 | |
| 346 | P | A | 0.0000 | |
| 347 | Q | A | -1.3629 | |
| 348 | V | A | 0.0000 | |
| 349 | Y | A | 0.0000 | |
| 350 | T | A | -0.8162 | |
| 351 | L | A | 0.0000 | |
| 352 | P | A | -0.2218 | |
| 353 | P | A | -0.7635 | |
| 354 | S | A | -1.4104 | |
| 355 | R | A | -2.6259 | |
| 356 | E | A | -2.4587 | |
| 357 | E | A | 0.0000 | |
| 358 | M | A | -1.8060 | |
| 359 | T | A | -1.6658 | |
| 360 | K | A | -2.4363 | |
| 361 | N | A | -2.6110 | |
| 362 | Q | A | -2.5247 | |
| 363 | V | A | 0.0000 | |
| 364 | S | A | 0.0000 | |
| 365 | L | A | 0.0000 | |
| 366 | T | A | 0.0000 | |
| 367 | C | A | 0.0000 | |
| 368 | L | A | 0.0000 | |
| 369 | V | A | 0.0000 | |
| 370 | K | A | -0.4849 | |
| 371 | G | A | 0.0000 | |
| 372 | F | A | 0.0000 | |
| 373 | Y | A | -1.1656 | |
| 374 | P | A | 0.0000 | |
| 375 | S | A | -0.4398 | |
| 376 | D | A | -1.4197 | |
| 377 | I | A | -0.7196 | |
| 378 | A | A | -0.5319 | |
| 379 | V | A | -0.2843 | |
| 380 | E | A | -1.1316 | |
| 381 | W | A | 0.0000 | |
| 382 | E | A | -1.7857 | |
| 383 | S | A | -1.2706 | |
| 384 | N | A | -2.0588 | |
| 385 | G | A | -1.8756 | |
| 386 | Q | A | -2.4152 | |
| 387 | P | A | -2.0004 | |
| 388 | E | A | -2.1336 | |
| 389 | N | A | -2.3059 | |
| 390 | N | A | -1.8222 | |
| 391 | Y | A | -1.1890 | |
| 392 | K | A | -0.8631 | |
| 393 | T | A | -0.2608 | |
| 394 | T | A | 0.0000 | |
| 395 | P | A | -0.1003 | |
| 396 | P | A | 0.0780 | |
| 397 | V | A | 0.4984 | |
| 398 | L | A | 0.6971 | |
| 399 | D | A | -0.5054 | |
| 400 | S | A | -1.2164 | |
| 401 | D | A | -1.8526 | |
| 402 | G | A | -0.8758 | |
| 403 | S | A | 0.0000 | |
| 404 | F | A | 0.0575 | |
| 405 | F | A | 0.0000 | |
| 406 | L | A | 0.0000 | |
| 407 | Y | A | 0.0000 | |
| 408 | S | A | 0.0000 | |
| 409 | K | A | 0.0000 | |
| 410 | L | A | 0.0000 | |
| 411 | T | A | -1.1331 | |
| 412 | V | A | 0.0000 | |
| 413 | D | A | -2.7933 | |
| 414 | K | A | -2.8364 | |
| 415 | S | A | -2.3121 | |
| 416 | R | A | -1.9837 | |
| 417 | W | A | 0.0000 | |
| 418 | Q | A | -1.9670 | |
| 419 | Q | A | -1.9521 | |
| 420 | G | A | -0.9241 | |
| 421 | N | A | -0.6247 | |
| 422 | V | A | 0.4839 | |
| 423 | F | A | 0.0000 | |
| 424 | S | A | -0.8559 | |
| 425 | C | A | 0.0000 | |
| 426 | S | A | 0.0000 | |
| 427 | V | A | 0.0000 | |
| 428 | M | A | 0.0000 | |
| 429 | H | A | 0.0000 | |
| 430 | E | A | -1.1962 | |
| 431 | A | A | -1.5788 | |
| 432 | L | A | 0.0000 | |
| 433 | H | A | -1.8194 | |
| 434 | N | A | -1.6144 | |
| 435 | H | A | -1.0631 | |
| 436 | Y | A | -0.2117 | |
| 437 | T | A | -0.6613 | |
| 438 | Q | A | -1.0244 | |
| 439 | K | A | -1.2562 | |
| 440 | S | A | -0.5704 | |
| 441 | L | A | 0.0000 | |
| 442 | S | A | 0.3889 | |
| 443 | L | A | 0.8799 | |
| 238 | P | B | -0.9457 | |
| 239 | S | B | -0.2679 | |
| 240 | V | B | 0.0000 | |
| 241 | F | B | 1.3986 | |
| 242 | L | B | 1.0526 | |
| 243 | F | B | 1.0999 | |
| 244 | P | B | -0.1912 | |
| 245 | P | B | 0.0000 | |
| 246 | K | B | -2.1519 | |
| 247 | P | B | -1.4983 | |
| 248 | K | B | -1.3474 | |
| 249 | D | B | -1.2660 | |
| 250 | T | B | 0.0000 | |
| 251 | L | B | 0.0000 | |
| 252 | M | B | 0.3828 | |
| 253 | I | B | 1.5020 | |
| 254 | S | B | 0.1672 | |
| 255 | R | B | -0.9046 | |
| 256 | T | B | -0.5768 | |
| 257 | P | B | 0.0000 | |
| 258 | E | B | -0.9034 | |
| 259 | V | B | 0.0000 | |
| 260 | T | B | 0.3649 | |
| 261 | C | B | 0.0000 | |
| 262 | V | B | 0.0000 | |
| 263 | V | B | 0.0000 | |
| 264 | V | B | -0.4727 | |
| 265 | D | B | -2.0650 | |
| 266 | V | B | 0.0000 | |
| 267 | S | B | -1.9576 | |
| 268 | H | B | -2.4736 | |
| 269 | E | B | -2.8654 | |
| 270 | D | B | -2.3965 | |
| 271 | P | B | -2.4651 | |
| 272 | Q | B | -2.5732 | |
| 273 | V | B | -1.9499 | |
| 274 | K | B | -2.1273 | |
| 275 | F | B | -1.2731 | |
| 276 | N | B | -1.2458 | |
| 277 | W | B | 0.0000 | |
| 278 | Y | B | -0.4056 | |
| 279 | V | B | -0.3068 | |
| 280 | D | B | -1.1579 | |
| 281 | G | B | -0.2528 | |
| 282 | V | B | 1.1332 | |
| 283 | Q | B | -0.1564 | |
| 284 | V | B | -0.4152 | |
| 285 | H | B | -1.4725 | |
| 286 | N | B | -2.4653 | |
| 287 | A | B | -1.7408 | |
| 288 | K | B | -2.5230 | |
| 289 | T | B | -2.1295 | |
| 290 | K | B | -2.5699 | |
| 291 | P | B | -2.1762 | |
| 292 | R | B | -3.2551 | |
| 293 | E | B | -3.4339 | |
| 294 | Q | B | -2.5596 | |
| 295 | Q | B | -2.0174 | |
| 296 | Y | B | -1.0715 | |
| 297 | N | B | -1.5541 | |
| 298 | S | B | -1.1735 | |
| 299 | T | B | -1.6620 | |
| 300 | Y | B | -1.8883 | |
| 301 | R | B | -2.0916 | |
| 302 | V | B | 0.0000 | |
| 303 | V | B | -0.8106 | |
| 304 | S | B | 0.0000 | |
| 305 | V | B | -0.6464 | |
| 306 | L | B | 0.0000 | |
| 307 | T | B | -0.6586 | |
| 308 | V | B | 0.0000 | |
| 309 | L | B | 0.9657 | |
| 310 | H | B | 0.0000 | |
| 311 | Q | B | -1.2332 | |
| 312 | N | B | -1.5459 | |
| 313 | W | B | 0.0000 | |
| 314 | L | B | -1.2125 | |
| 315 | D | B | -2.7558 | |
| 316 | G | B | -2.3935 | |
| 317 | K | B | -2.4476 | |
| 318 | E | B | -2.1868 | |
| 319 | Y | B | 0.0000 | |
| 320 | K | B | -1.2965 | |
| 321 | C | B | 0.0000 | |
| 322 | K | B | -1.6360 | |
| 323 | V | B | 0.0000 | |
| 324 | S | B | -1.5380 | |
| 325 | N | B | 0.0000 | |
| 326 | K | B | -2.4591 | |
| 327 | A | B | -1.3511 | |
| 328 | L | B | -0.5112 | |
| 329 | P | B | -0.5180 | |
| 330 | A | B | -0.4815 | |
| 331 | P | B | -1.1291 | |
| 332 | I | B | -1.0188 | |
| 333 | E | B | -2.2541 | |
| 334 | K | B | -1.5554 | |
| 335 | T | B | -0.9589 | |
| 336 | I | B | -0.3541 | |
| 337 | S | B | -1.2065 | |
| 338 | K | B | -1.3758 | |
| 339 | A | B | -1.2555 | |
| 340 | K | B | -2.3881 | |
| 341 | G | B | -1.9044 | |
| 342 | Q | B | -2.1338 | |
| 343 | P | B | -1.8563 | |
| 344 | R | B | -2.2114 | |
| 345 | E | B | -2.6725 | |
| 346 | P | B | 0.0000 | |
| 347 | Q | B | -1.0618 | |
| 348 | V | B | -0.6800 | |
| 349 | Y | B | 0.0000 | |
| 350 | T | B | 0.0000 | |
| 351 | L | B | 0.0000 | |
| 352 | P | B | -0.1559 | |
| 353 | P | B | 0.0000 | |
| 354 | S | B | -1.5709 | |
| 355 | R | B | -2.8293 | |
| 356 | E | B | -2.9007 | |
| 357 | E | B | 0.0000 | |
| 358 | M | B | -2.0349 | |
| 359 | T | B | -1.7637 | |
| 360 | K | B | -2.4667 | |
| 361 | N | B | -2.4761 | |
| 362 | Q | B | -2.1866 | |
| 363 | V | B | 0.0000 | |
| 364 | S | B | 0.0000 | |
| 365 | L | B | 0.0000 | |
| 366 | T | B | 0.0000 | |
| 367 | C | B | 0.0000 | |
| 368 | L | B | 0.0000 | |
| 369 | V | B | 0.0000 | |
| 370 | K | B | -0.4115 | |
| 371 | G | B | -0.9659 | |
| 372 | F | B | 0.0000 | |
| 373 | Y | B | -1.1068 | |
| 374 | P | B | 0.0000 | |
| 375 | S | B | -0.2304 | |
| 376 | D | B | -1.1585 | |
| 377 | I | B | -0.6819 | |
| 378 | A | B | -0.6869 | |
| 379 | V | B | 0.0000 | |
| 380 | E | B | -1.4183 | |
| 381 | W | B | 0.0000 | |
| 382 | E | B | -1.6061 | |
| 383 | S | B | -1.0513 | |
| 384 | N | B | -1.8650 | |
| 385 | G | B | -1.8114 | |
| 386 | Q | B | -2.1681 | |
| 387 | P | B | -2.0297 | |
| 388 | E | B | -1.9759 | |
| 389 | N | B | -2.2365 | |
| 390 | N | B | -2.0562 | |
| 391 | Y | B | -1.3203 | |
| 392 | K | B | -0.9663 | |
| 393 | T | B | -0.3208 | |
| 394 | T | B | 0.0000 | |
| 395 | P | B | -0.0429 | |
| 396 | P | B | 0.1616 | |
| 397 | V | B | 0.6418 | |
| 398 | L | B | 1.0117 | |
| 399 | D | B | -0.3515 | |
| 400 | S | B | -1.1241 | |
| 401 | D | B | -1.8367 | |
| 402 | G | B | -0.8656 | |
| 403 | S | B | 0.0000 | |
| 404 | F | B | 0.0776 | |
| 405 | F | B | 0.0000 | |
| 406 | L | B | 0.0000 | |
| 407 | Y | B | 0.0000 | |
| 408 | S | B | 0.0000 | |
| 409 | K | B | 0.0000 | |
| 410 | L | B | 0.0000 | |
| 411 | T | B | -1.0384 | |
| 412 | V | B | 0.0000 | |
| 413 | D | B | -2.2020 | |
| 414 | K | B | -2.5971 | |
| 415 | S | B | -2.2098 | |
| 416 | R | B | -1.7729 | |
| 417 | W | B | 0.0000 | |
| 418 | Q | B | -1.9845 | |
| 419 | Q | B | -1.8987 | |
| 420 | G | B | -0.7335 | |
| 421 | N | B | -0.3578 | |
| 422 | V | B | 0.8900 | |
| 423 | F | B | 0.0000 | |
| 424 | S | B | -0.6524 | |
| 425 | C | B | 0.0000 | |
| 426 | S | B | 0.0000 | |
| 427 | V | B | 0.0000 | |
| 428 | M | B | 0.0000 | |
| 429 | H | B | 0.0000 | |
| 430 | E | B | -1.0971 | |
| 431 | A | B | -1.5218 | |
| 432 | L | B | 0.0000 | |
| 433 | H | B | -1.7666 | |
| 434 | N | B | -1.5942 | |
| 435 | H | B | -1.0391 | |
| 436 | Y | B | -0.1749 | |
| 437 | T | B | -0.6213 | |
| 438 | Q | B | -1.1096 | |
| 439 | K | B | -0.9298 | |
| 440 | S | B | -0.2735 | |
| 441 | L | B | 0.0000 | |
| 442 | S | B | 0.7471 | |
| 443 | L | B | 1.0373 |
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 | -0.7722 | 3.6835 | View | CSV | PDB |
| 4.5 | -0.8304 | 3.6657 | View | CSV | PDB |
| 5.0 | -0.8986 | 3.6481 | View | CSV | PDB |
| 5.5 | -0.9605 | 3.643 | View | CSV | PDB |
| 6.0 | -1.0003 | 3.6601 | View | CSV | PDB |
| 6.5 | -1.0096 | 3.7018 | View | CSV | PDB |
| 7.0 | -0.9918 | 3.7638 | View | CSV | PDB |
| 7.5 | -0.9575 | 3.8378 | View | CSV | PDB |
| 8.0 | -0.9145 | 3.9166 | View | CSV | PDB |
| 8.5 | -0.8646 | 3.9966 | View | CSV | PDB |
| 9.0 | -0.807 | 4.075 | 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