| 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] (00:00:01)
[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 all 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. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:14)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f4e234b887364b4/tmp/folded.pdb (00:06:14)
[INFO] Main: Simulation completed successfully. (00:08:08)
|
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 | -0.6612 | |
| 239 | S | A | -0.1775 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 1.2162 | |
| 242 | L | A | 0.8893 | |
| 243 | F | A | 1.1060 | |
| 244 | P | A | -0.2193 | |
| 245 | P | A | -1.1796 | |
| 246 | K | A | -1.9814 | |
| 247 | P | A | -1.2512 | |
| 248 | K | A | -1.0560 | |
| 249 | D | A | 0.0000 | |
| 250 | T | A | 0.0000 | |
| 251 | L | A | 0.0000 | |
| 252 | M | A | 0.3913 | |
| 253 | I | A | 1.4708 | |
| 254 | S | A | 0.0299 | |
| 255 | R | A | -1.2008 | |
| 256 | T | A | -0.7374 | |
| 257 | P | A | 0.0000 | |
| 258 | E | A | -1.1476 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | 0.6078 | |
| 261 | C | A | 0.0000 | |
| 262 | V | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | -0.3966 | |
| 265 | D | A | -2.0407 | |
| 266 | V | A | 0.0000 | |
| 267 | S | A | -2.0006 | |
| 268 | H | A | -2.3098 | |
| 269 | E | A | -2.7505 | |
| 270 | D | A | -2.3188 | |
| 271 | P | A | -2.4061 | |
| 272 | Q | A | -2.4951 | |
| 273 | V | A | -1.6686 | |
| 274 | K | A | -2.0804 | |
| 275 | F | A | -1.1976 | |
| 276 | N | A | -1.3283 | |
| 277 | W | A | 0.0000 | |
| 278 | Y | A | -0.6840 | |
| 279 | V | A | -0.8483 | |
| 280 | D | A | -1.7825 | |
| 281 | G | A | -0.6590 | |
| 282 | V | A | 0.6928 | |
| 283 | Q | A | -0.9398 | |
| 284 | V | A | -1.0324 | |
| 285 | H | A | -1.7971 | |
| 286 | N | A | -2.5815 | |
| 287 | A | A | -1.9664 | |
| 288 | K | A | -2.6590 | |
| 289 | T | A | -1.9725 | |
| 290 | K | A | -2.5317 | |
| 291 | P | A | -2.0485 | |
| 292 | R | A | -2.9962 | |
| 293 | E | A | -3.0517 | |
| 294 | Q | A | -2.3647 | |
| 295 | Q | A | -2.1998 | |
| 296 | Y | A | -0.9756 | |
| 297 | N | A | -1.5178 | |
| 298 | S | A | -1.1840 | |
| 299 | T | A | -1.4825 | |
| 300 | Y | A | -1.7738 | |
| 301 | R | A | -1.8488 | |
| 302 | V | A | 0.0000 | |
| 303 | V | A | -0.5533 | |
| 304 | S | A | 0.0000 | |
| 305 | V | A | -0.6198 | |
| 306 | L | A | 0.0000 | |
| 307 | T | A | -0.6719 | |
| 308 | V | A | 0.0000 | |
| 309 | L | A | 0.6605 | |
| 310 | H | A | -0.1823 | |
| 311 | Q | A | -1.4048 | |
| 312 | N | A | -1.4408 | |
| 313 | W | A | 0.0000 | |
| 314 | L | A | -1.2078 | |
| 315 | D | A | -2.5736 | |
| 316 | G | A | -2.5107 | |
| 317 | K | A | -2.2556 | |
| 318 | E | A | -2.1284 | |
| 319 | Y | A | 0.0000 | |
| 320 | K | A | -1.5015 | |
| 321 | C | A | 0.0000 | |
| 322 | K | A | -1.3623 | |
| 323 | V | A | 0.0000 | |
| 324 | S | A | -1.3642 | |
| 325 | N | A | -1.7191 | |
| 326 | K | A | -2.5013 | |
| 327 | A | A | -1.5156 | |
| 328 | L | A | -0.6053 | |
| 329 | P | A | -0.5341 | |
| 330 | A | A | -0.4157 | |
| 331 | P | A | -0.8935 | |
| 332 | I | A | -0.5569 | |
| 333 | E | A | -1.6388 | |
| 334 | K | A | -1.2105 | |
| 335 | T | A | -0.7377 | |
| 336 | I | A | -0.3341 | |
| 337 | S | A | -1.3786 | |
| 338 | K | A | -1.6913 | |
| 339 | A | A | -1.4758 | |
| 340 | K | A | -2.5697 | |
| 341 | G | A | -2.0657 | |
| 342 | Q | A | -2.1357 | |
| 343 | P | A | -1.8093 | |
| 344 | R | A | -2.0336 | |
| 345 | E | A | -2.6286 | |
| 346 | P | A | 0.0000 | |
| 347 | Q | A | -1.2083 | |
| 348 | V | A | 0.0000 | |
| 349 | Y | A | 0.0000 | |
| 350 | T | A | -0.7295 | |
| 351 | L | A | 0.0000 | |
| 352 | P | A | -0.2133 | |
| 353 | P | A | -0.6912 | |
| 354 | S | A | -1.2146 | |
| 355 | R | A | -2.2381 | |
| 356 | E | A | -1.7004 | |
| 357 | E | A | 0.0000 | |
| 358 | M | A | -1.4872 | |
| 359 | T | A | -1.2481 | |
| 360 | K | A | -1.8737 | |
| 361 | N | A | -2.2615 | |
| 362 | Q | A | -2.2540 | |
| 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 | -0.6449 | |
| 371 | G | A | -1.1561 | |
| 372 | F | A | 0.0000 | |
| 373 | Y | A | -1.1394 | |
| 374 | P | A | 0.0000 | |
| 375 | S | A | -0.0053 | |
| 376 | D | A | -0.8017 | |
| 377 | I | A | -0.3443 | |
| 378 | A | A | -0.3330 | |
| 379 | V | A | -0.3191 | |
| 380 | E | A | -1.1433 | |
| 381 | W | A | 0.0000 | |
| 382 | E | A | -1.8400 | |
| 383 | S | A | -1.1274 | |
| 384 | N | A | -1.9161 | |
| 385 | G | A | -1.8921 | |
| 386 | Q | A | -2.2629 | |
| 387 | P | A | -2.2422 | |
| 388 | E | A | -2.6355 | |
| 389 | N | A | -2.4649 | |
| 390 | N | A | -2.1759 | |
| 391 | Y | A | -1.2744 | |
| 392 | K | A | -0.8482 | |
| 393 | T | A | -0.2444 | |
| 394 | T | A | 0.0000 | |
| 395 | P | A | -0.2013 | |
| 396 | P | A | 0.1676 | |
| 397 | V | A | 0.5107 | |
| 398 | L | A | 0.6410 | |
| 399 | D | A | -0.8160 | |
| 400 | S | A | -1.3372 | |
| 401 | D | A | -1.9511 | |
| 402 | G | A | -0.9785 | |
| 403 | S | A | 0.0000 | |
| 404 | F | A | -0.0235 | |
| 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 | -1.0820 | |
| 412 | V | A | 0.0000 | |
| 413 | D | A | -2.6998 | |
| 414 | K | A | -2.9297 | |
| 415 | S | A | -2.7757 | |
| 416 | R | A | -3.1337 | |
| 417 | W | A | 0.0000 | |
| 418 | Q | A | -2.4961 | |
| 419 | Q | A | -2.4536 | |
| 420 | G | A | -0.9673 | |
| 421 | N | A | -0.8768 | |
| 422 | V | A | 0.9386 | |
| 423 | F | A | 0.0000 | |
| 424 | S | A | -0.8001 | |
| 425 | C | A | 0.0000 | |
| 426 | S | A | 0.0000 | |
| 427 | V | A | 0.0000 | |
| 428 | M | A | -0.4207 | |
| 429 | H | A | 0.0000 | |
| 430 | E | A | -1.1195 | |
| 431 | A | A | -1.4829 | |
| 432 | L | A | -1.3763 | |
| 433 | H | A | -1.8037 | |
| 434 | N | A | -1.7100 | |
| 435 | H | A | -0.9485 | |
| 436 | Y | A | -0.4987 | |
| 437 | T | A | -0.9360 | |
| 438 | Q | A | -1.5107 | |
| 439 | K | A | -1.2638 | |
| 440 | S | A | -0.2951 | |
| 441 | L | A | 0.5733 | |
| 442 | S | A | 0.7923 | |
| 443 | L | A | 0.9186 | |
| 238 | P | B | -0.7974 | |
| 239 | S | B | -0.4257 | |
| 240 | V | B | 0.0000 | |
| 241 | F | B | 1.2993 | |
| 242 | L | B | 0.8004 | |
| 243 | F | B | 1.0579 | |
| 244 | P | B | -0.2573 | |
| 245 | P | B | -1.2100 | |
| 246 | K | B | -2.1794 | |
| 247 | P | B | -1.4774 | |
| 248 | K | B | -1.4989 | |
| 249 | D | B | -1.5126 | |
| 250 | T | B | 0.0000 | |
| 251 | L | B | -0.2849 | |
| 252 | M | B | 0.4552 | |
| 253 | I | B | 1.4185 | |
| 254 | S | B | -0.1332 | |
| 255 | R | B | -1.5797 | |
| 256 | T | B | -0.9796 | |
| 257 | P | B | 0.0000 | |
| 258 | E | B | -1.1929 | |
| 259 | V | B | 0.0000 | |
| 260 | T | B | 0.5541 | |
| 261 | C | B | 0.0000 | |
| 262 | V | B | 0.0000 | |
| 263 | V | B | 0.0000 | |
| 264 | V | B | -0.6179 | |
| 265 | D | B | -1.9402 | |
| 266 | V | B | 0.0000 | |
| 267 | S | B | -2.2269 | |
| 268 | H | B | -2.6357 | |
| 269 | E | B | -2.9656 | |
| 270 | D | B | -2.5452 | |
| 271 | P | B | -2.7382 | |
| 272 | Q | B | -2.6921 | |
| 273 | V | B | -1.7734 | |
| 274 | K | B | -2.1294 | |
| 275 | F | B | -1.2698 | |
| 276 | N | B | -1.4042 | |
| 277 | W | B | 0.0000 | |
| 278 | Y | B | -0.7287 | |
| 279 | V | B | -1.0244 | |
| 280 | D | B | -2.3416 | |
| 281 | G | B | -0.8650 | |
| 282 | V | B | 0.7945 | |
| 283 | Q | B | -0.6238 | |
| 284 | V | B | -0.9376 | |
| 285 | H | B | -1.6888 | |
| 286 | N | B | -2.5466 | |
| 287 | A | B | -1.9180 | |
| 288 | K | B | -2.6886 | |
| 289 | T | B | -2.0520 | |
| 290 | K | B | -2.5593 | |
| 291 | P | B | -2.3509 | |
| 292 | R | B | -3.1031 | |
| 293 | E | B | -3.6017 | |
| 294 | Q | B | -2.6939 | |
| 295 | Q | B | -1.9814 | |
| 296 | Y | B | -0.4751 | |
| 297 | N | B | -1.2192 | |
| 298 | S | B | -1.0490 | |
| 299 | T | B | -1.6086 | |
| 300 | Y | B | -1.8293 | |
| 301 | R | B | -1.9370 | |
| 302 | V | B | 0.0000 | |
| 303 | V | B | -0.8249 | |
| 304 | S | B | 0.0000 | |
| 305 | V | B | -0.7808 | |
| 306 | L | B | 0.0000 | |
| 307 | T | B | -0.6817 | |
| 308 | V | B | 0.0000 | |
| 309 | L | B | 0.7561 | |
| 310 | H | B | -0.2277 | |
| 311 | Q | B | -1.4027 | |
| 312 | N | B | -1.5523 | |
| 313 | W | B | 0.0000 | |
| 314 | L | B | -1.1122 | |
| 315 | D | B | -2.6636 | |
| 316 | G | B | 0.0000 | |
| 317 | K | B | -2.5074 | |
| 318 | E | B | -2.6553 | |
| 319 | Y | B | 0.0000 | |
| 320 | K | B | -2.0132 | |
| 321 | C | B | 0.0000 | |
| 322 | K | B | -1.6832 | |
| 323 | V | B | 0.0000 | |
| 324 | S | B | -1.4525 | |
| 325 | N | B | -1.7778 | |
| 326 | K | B | -2.5458 | |
| 327 | A | B | -1.5921 | |
| 328 | L | B | -0.6408 | |
| 329 | P | B | -0.5271 | |
| 330 | A | B | -0.4700 | |
| 331 | P | B | -1.0271 | |
| 332 | I | B | -0.9460 | |
| 333 | E | B | -2.2228 | |
| 334 | K | B | -1.6485 | |
| 335 | T | B | -1.1568 | |
| 336 | I | B | -0.4252 | |
| 337 | S | B | -1.3232 | |
| 338 | K | B | -1.3964 | |
| 339 | A | B | -1.2329 | |
| 340 | K | B | -2.3923 | |
| 341 | G | B | -1.8413 | |
| 342 | Q | B | -2.1003 | |
| 343 | P | B | -1.9097 | |
| 344 | R | B | -2.2514 | |
| 345 | E | B | -2.7125 | |
| 346 | P | B | 0.0000 | |
| 347 | Q | B | -1.0682 | |
| 348 | V | B | 0.0000 | |
| 349 | Y | B | 0.0000 | |
| 350 | T | B | 0.0000 | |
| 351 | L | B | 0.0000 | |
| 352 | P | B | -0.2442 | |
| 353 | P | B | -0.8937 | |
| 354 | S | B | -1.6453 | |
| 355 | R | B | -2.7185 | |
| 356 | E | B | -2.7605 | |
| 357 | E | B | 0.0000 | |
| 358 | M | B | -1.9195 | |
| 359 | T | B | -1.6152 | |
| 360 | K | B | -1.9702 | |
| 361 | N | B | -2.3992 | |
| 362 | Q | B | -2.4525 | |
| 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 | -0.6955 | |
| 371 | G | B | -1.0681 | |
| 372 | F | B | 0.0000 | |
| 373 | Y | B | -1.1220 | |
| 374 | P | B | -0.9872 | |
| 375 | S | B | -0.0958 | |
| 376 | D | B | -1.1903 | |
| 377 | I | B | -0.5556 | |
| 378 | A | B | -0.2110 | |
| 379 | V | B | -0.2514 | |
| 380 | E | B | -0.9939 | |
| 381 | W | B | 0.0000 | |
| 382 | E | B | -1.7932 | |
| 383 | S | B | -1.3005 | |
| 384 | N | B | -2.0308 | |
| 385 | G | B | -1.9031 | |
| 386 | Q | B | -2.2790 | |
| 387 | P | B | -2.1276 | |
| 388 | E | B | -2.4740 | |
| 389 | N | B | -2.4369 | |
| 390 | N | B | -2.2771 | |
| 391 | Y | B | -1.3777 | |
| 392 | K | B | -1.0131 | |
| 393 | T | B | -0.3694 | |
| 394 | T | B | 0.0000 | |
| 395 | P | B | -0.2798 | |
| 396 | P | B | 0.1936 | |
| 397 | V | B | 0.6969 | |
| 398 | L | B | 0.9865 | |
| 399 | D | B | -0.4368 | |
| 400 | S | B | -1.1581 | |
| 401 | D | B | -1.8191 | |
| 402 | G | B | -0.9400 | |
| 403 | S | B | 0.0000 | |
| 404 | F | B | 0.0368 | |
| 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 | -1.0999 | |
| 412 | V | B | 0.0000 | |
| 413 | D | B | -2.7062 | |
| 414 | K | B | -2.9033 | |
| 415 | S | B | -2.6395 | |
| 416 | R | B | -2.8847 | |
| 417 | W | B | 0.0000 | |
| 418 | Q | B | -2.4215 | |
| 419 | Q | B | -2.4011 | |
| 420 | G | B | -1.1495 | |
| 421 | N | B | -1.1432 | |
| 422 | V | B | 0.3230 | |
| 423 | F | B | 0.0000 | |
| 424 | S | B | -0.7975 | |
| 425 | C | B | 0.0000 | |
| 426 | S | B | 0.0000 | |
| 427 | V | B | 0.0000 | |
| 428 | M | B | -0.4001 | |
| 429 | H | B | 0.0000 | |
| 430 | E | B | -1.3519 | |
| 431 | A | B | -1.5336 | |
| 432 | L | B | -1.5069 | |
| 433 | H | B | -1.9002 | |
| 434 | N | B | -1.8449 | |
| 435 | H | B | -1.1691 | |
| 436 | Y | B | -0.4206 | |
| 437 | T | B | -0.7083 | |
| 438 | Q | B | -1.0295 | |
| 439 | K | B | -0.9849 | |
| 440 | S | B | -0.3941 | |
| 441 | L | B | 0.0000 | |
| 442 | S | B | 0.4378 | |
| 443 | L | B | 0.7672 |
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 | -0.8865 | 3.4318 | View | CSV | PDB |
| 4.5 | -0.9453 | 3.4177 | View | CSV | PDB |
| 5.0 | -1.0141 | 3.4033 | View | CSV | PDB |
| 5.5 | -1.0761 | 3.3998 | View | CSV | PDB |
| 6.0 | -1.1143 | 3.4146 | View | CSV | PDB |
| 6.5 | -1.1196 | 3.4471 | View | CSV | PDB |
| 7.0 | -1.0964 | 3.4938 | View | CSV | PDB |
| 7.5 | -1.0569 | 3.5498 | View | CSV | PDB |
| 8.0 | -1.0089 | 3.61 | View | CSV | PDB |
| 8.5 | -0.9544 | 3.6712 | View | CSV | PDB |
| 9.0 | -0.8924 | 3.7306 | 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