| Chain sequence(s) |
A: GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
B: GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLS 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 (00:09:27)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3e05ae4ff436252/tmp/folded.pdb (00:09:27)
[INFO] Main: Simulation completed successfully. (00:13:13)
|
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 |
|---|---|---|---|---|
| 236 | G | A | -0.9724 | |
| 237 | G | A | -1.0903 | |
| 238 | P | A | -1.0700 | |
| 239 | S | A | -0.4269 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 0.9145 | |
| 242 | L | A | 0.0000 | |
| 243 | F | A | 1.1778 | |
| 244 | P | A | -0.0860 | |
| 245 | P | A | 0.0000 | |
| 246 | K | A | -2.1819 | |
| 247 | P | A | -1.4639 | |
| 248 | K | A | -1.4207 | |
| 249 | D | A | -1.1350 | |
| 250 | T | A | 0.0000 | |
| 251 | L | A | -0.0671 | |
| 252 | M | A | 0.8628 | |
| 253 | I | A | 2.0120 | |
| 254 | S | A | 0.5521 | |
| 255 | R | A | -0.4747 | |
| 256 | T | A | -0.3401 | |
| 257 | P | A | 0.0000 | |
| 258 | E | A | -0.9149 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | 0.2414 | |
| 261 | C | A | 0.0000 | |
| 262 | V | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | -0.8096 | |
| 265 | D | A | -2.2751 | |
| 266 | V | A | 0.0000 | |
| 267 | S | A | -2.3793 | |
| 268 | H | A | -2.8370 | |
| 269 | E | A | -2.9403 | |
| 270 | D | A | -2.9234 | |
| 271 | P | A | -2.7416 | |
| 272 | E | A | -3.1235 | |
| 273 | V | A | -1.9823 | |
| 274 | K | A | -2.1638 | |
| 275 | F | A | -0.9341 | |
| 276 | N | A | -1.0454 | |
| 277 | W | A | 0.0000 | |
| 278 | Y | A | -0.5240 | |
| 279 | V | A | -0.6995 | |
| 280 | D | A | -1.5216 | |
| 281 | G | A | -0.6071 | |
| 282 | V | A | 0.9515 | |
| 283 | E | A | -0.2535 | |
| 284 | V | A | -0.4264 | |
| 285 | H | A | -1.7060 | |
| 286 | N | A | -1.9586 | |
| 287 | A | A | -1.7121 | |
| 288 | K | A | -2.1213 | |
| 289 | T | A | -1.7938 | |
| 290 | K | A | -2.6752 | |
| 291 | P | A | -2.4896 | |
| 292 | R | A | -3.7571 | |
| 293 | E | A | -3.9226 | |
| 294 | E | A | -3.6253 | |
| 295 | Q | A | -2.3153 | |
| 296 | Y | A | -0.2411 | |
| 297 | N | A | -1.4036 | |
| 298 | S | A | -1.7709 | |
| 299 | T | A | -2.4243 | |
| 300 | Y | A | -2.8681 | |
| 301 | R | A | -2.7625 | |
| 302 | V | A | 0.0000 | |
| 303 | V | A | 0.0000 | |
| 304 | S | A | 0.0000 | |
| 305 | V | A | 0.0000 | |
| 306 | L | A | 0.0000 | |
| 307 | T | A | -0.4997 | |
| 308 | V | A | 0.0000 | |
| 309 | L | A | 0.8835 | |
| 310 | H | A | 0.0088 | |
| 311 | Q | A | -1.2766 | |
| 312 | D | A | -1.1811 | |
| 313 | W | A | 0.0000 | |
| 314 | L | A | -0.8891 | |
| 315 | N | A | -2.0410 | |
| 316 | G | A | -1.9800 | |
| 317 | K | A | -2.1703 | |
| 318 | E | A | -2.5858 | |
| 319 | Y | A | 0.0000 | |
| 320 | K | A | -1.7820 | |
| 321 | C | A | 0.0000 | |
| 322 | K | A | -1.4520 | |
| 323 | V | A | 0.0000 | |
| 324 | S | A | -1.4215 | |
| 325 | N | A | -1.7707 | |
| 326 | K | A | -2.4010 | |
| 327 | A | A | -1.5011 | |
| 328 | L | A | -0.5921 | |
| 329 | P | A | -0.4336 | |
| 330 | A | A | -0.3689 | |
| 331 | P | A | -0.7865 | |
| 332 | I | A | -0.6443 | |
| 333 | E | A | -2.1324 | |
| 334 | K | A | -1.6065 | |
| 335 | T | A | -1.3229 | |
| 336 | I | A | -0.3606 | |
| 337 | S | A | -1.1252 | |
| 338 | K | A | 0.0000 | |
| 339 | A | A | -1.0149 | |
| 340 | K | A | -2.3106 | |
| 341 | G | A | -1.9645 | |
| 342 | Q | A | -2.1843 | |
| 343 | P | A | -1.8302 | |
| 344 | R | A | -2.0482 | |
| 345 | E | A | -2.7846 | |
| 346 | P | A | 0.0000 | |
| 347 | Q | A | -2.0648 | |
| 348 | V | A | 0.0000 | |
| 349 | Y | A | -1.1633 | |
| 350 | T | A | 0.0000 | |
| 351 | L | A | 0.0000 | |
| 352 | P | A | -0.1435 | |
| 353 | P | A | 0.0000 | |
| 354 | S | A | 0.0000 | |
| 355 | R | A | -2.5974 | |
| 356 | D | A | -2.8184 | |
| 357 | E | A | 0.0000 | |
| 358 | L | A | -2.0406 | |
| 359 | T | A | -1.9404 | |
| 360 | K | A | -2.9394 | |
| 361 | N | A | -2.8466 | |
| 362 | Q | A | -2.4241 | |
| 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 | -0.7505 | |
| 371 | G | A | -1.1748 | |
| 372 | F | A | 0.0000 | |
| 373 | Y | A | -1.1021 | |
| 374 | P | A | 0.0000 | |
| 375 | S | A | -0.1603 | |
| 376 | D | A | -1.0305 | |
| 377 | I | A | 0.0000 | |
| 378 | A | A | 0.0000 | |
| 379 | V | A | 0.0000 | |
| 380 | E | A | -2.2890 | |
| 381 | W | A | 0.0000 | |
| 382 | E | A | -2.0523 | |
| 383 | S | A | 0.0000 | |
| 384 | N | A | -1.7697 | |
| 385 | G | A | -1.8821 | |
| 386 | Q | A | -2.2948 | |
| 387 | P | A | -2.2703 | |
| 388 | E | A | -2.0370 | |
| 389 | N | A | -2.5815 | |
| 390 | N | A | -2.0343 | |
| 391 | Y | A | -1.4713 | |
| 392 | K | A | -0.9912 | |
| 393 | T | A | -0.3828 | |
| 394 | T | A | 0.0000 | |
| 395 | P | A | -0.1961 | |
| 396 | P | A | 0.1526 | |
| 397 | V | A | 0.6702 | |
| 398 | L | A | 0.9954 | |
| 399 | D | A | -0.3732 | |
| 400 | S | A | -1.1205 | |
| 401 | D | A | -1.8433 | |
| 402 | G | A | -0.8835 | |
| 403 | S | A | 0.0000 | |
| 404 | F | A | 0.1948 | |
| 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 | -0.9797 | |
| 412 | V | A | 0.0000 | |
| 413 | D | A | -2.6319 | |
| 414 | K | A | -2.6759 | |
| 415 | S | A | -2.1762 | |
| 416 | R | A | -1.9130 | |
| 417 | W | A | 0.0000 | |
| 418 | Q | A | -2.0900 | |
| 419 | Q | A | -1.7769 | |
| 420 | G | A | -0.4377 | |
| 421 | N | A | -0.3288 | |
| 422 | V | A | 0.8128 | |
| 423 | F | A | 0.0000 | |
| 424 | S | A | -1.1073 | |
| 425 | C | A | 0.0000 | |
| 426 | S | A | 0.0000 | |
| 427 | V | A | 0.0000 | |
| 428 | M | A | -0.5025 | |
| 429 | H | A | 0.0000 | |
| 430 | E | A | -1.2160 | |
| 431 | A | A | -1.6110 | |
| 432 | L | A | -1.6199 | |
| 433 | H | A | -1.8736 | |
| 434 | N | A | -1.8104 | |
| 435 | H | A | -1.3494 | |
| 436 | Y | A | -0.3629 | |
| 437 | T | A | -0.8311 | |
| 438 | Q | A | -1.3770 | |
| 439 | K | A | -1.7597 | |
| 440 | S | A | -0.7054 | |
| 441 | L | A | 0.0000 | |
| 442 | S | A | 0.6668 | |
| 443 | L | A | 1.2465 | |
| 236 | G | B | -1.3225 | |
| 237 | G | B | -1.3482 | |
| 238 | P | B | -1.0177 | |
| 239 | S | B | -0.3803 | |
| 240 | V | B | 0.0000 | |
| 241 | F | B | 0.9172 | |
| 242 | L | B | 0.0000 | |
| 243 | F | B | 1.4242 | |
| 244 | P | B | 0.0489 | |
| 245 | P | B | 0.0000 | |
| 246 | K | B | -1.7882 | |
| 247 | P | B | -1.2211 | |
| 248 | K | B | -1.1723 | |
| 249 | D | B | -0.8957 | |
| 250 | T | B | 0.0000 | |
| 251 | L | B | -0.2336 | |
| 252 | M | B | 0.6045 | |
| 253 | I | B | 1.8857 | |
| 254 | S | B | 0.3735 | |
| 255 | R | B | -0.7084 | |
| 256 | T | B | -0.3677 | |
| 257 | P | B | 0.0000 | |
| 258 | E | B | -0.5809 | |
| 259 | V | B | 0.0000 | |
| 260 | T | B | 0.4366 | |
| 261 | C | B | 0.0000 | |
| 262 | V | B | 0.0000 | |
| 263 | V | B | 0.0000 | |
| 264 | V | B | -0.7821 | |
| 265 | D | B | -2.1430 | |
| 266 | V | B | 0.0000 | |
| 267 | S | B | -2.0330 | |
| 268 | H | B | -2.4635 | |
| 269 | E | B | -2.6678 | |
| 270 | D | B | 0.0000 | |
| 271 | P | B | -2.2446 | |
| 272 | E | B | -2.7989 | |
| 273 | V | B | -1.6508 | |
| 274 | K | B | -2.1323 | |
| 275 | F | B | -0.9012 | |
| 276 | N | B | -1.1864 | |
| 277 | W | B | 0.0000 | |
| 278 | Y | B | -0.8128 | |
| 279 | V | B | -0.7562 | |
| 280 | D | B | -1.4467 | |
| 281 | G | B | -0.6812 | |
| 282 | V | B | 0.5122 | |
| 283 | E | B | -1.1451 | |
| 284 | V | B | -0.7599 | |
| 285 | H | B | -1.8470 | |
| 286 | N | B | -1.9292 | |
| 287 | A | B | -1.6735 | |
| 288 | K | B | -2.1446 | |
| 289 | T | B | -1.7366 | |
| 290 | K | B | -2.5553 | |
| 291 | P | B | -2.0908 | |
| 292 | R | B | -2.9223 | |
| 293 | E | B | -2.6858 | |
| 294 | E | B | -1.9546 | |
| 295 | Q | B | -1.4325 | |
| 296 | Y | B | -0.2822 | |
| 297 | N | B | -1.2361 | |
| 298 | S | B | -1.3681 | |
| 299 | T | B | -1.7449 | |
| 300 | Y | B | -1.8592 | |
| 301 | R | B | -2.0571 | |
| 302 | V | B | 0.0000 | |
| 303 | V | B | -0.8805 | |
| 304 | S | B | 0.0000 | |
| 305 | V | B | 0.0000 | |
| 306 | L | B | 0.0000 | |
| 307 | T | B | -0.3990 | |
| 308 | V | B | 0.0000 | |
| 309 | L | B | 0.9537 | |
| 310 | H | B | 0.0452 | |
| 311 | Q | B | -1.2208 | |
| 312 | D | B | -1.0444 | |
| 313 | W | B | 0.0000 | |
| 314 | L | B | -0.9382 | |
| 315 | N | B | -1.9377 | |
| 316 | G | B | 0.0000 | |
| 317 | K | B | -1.9341 | |
| 318 | E | B | -2.0080 | |
| 319 | Y | B | 0.0000 | |
| 320 | K | B | -1.7614 | |
| 321 | C | B | 0.0000 | |
| 322 | K | B | -1.5136 | |
| 323 | V | B | 0.0000 | |
| 324 | S | B | -1.4205 | |
| 325 | N | B | -1.6446 | |
| 326 | K | B | -2.3763 | |
| 327 | A | B | -1.4753 | |
| 328 | L | B | -0.7468 | |
| 329 | P | B | -0.5662 | |
| 330 | A | B | -0.5254 | |
| 331 | P | B | -0.8317 | |
| 332 | I | B | -0.7896 | |
| 333 | E | B | -2.1725 | |
| 334 | K | B | -1.5930 | |
| 335 | T | B | -1.0274 | |
| 336 | I | B | -0.2342 | |
| 337 | S | B | -0.8588 | |
| 338 | K | B | -1.2106 | |
| 339 | A | B | -1.4038 | |
| 340 | K | B | -2.3761 | |
| 341 | G | B | -1.9661 | |
| 342 | Q | B | -2.1329 | |
| 343 | P | B | -1.7555 | |
| 344 | R | B | -1.9738 | |
| 345 | E | B | -2.7904 | |
| 346 | P | B | 0.0000 | |
| 347 | Q | B | -1.8779 | |
| 348 | V | B | 0.0000 | |
| 349 | Y | B | -1.1328 | |
| 350 | T | B | 0.0000 | |
| 351 | L | B | 0.0000 | |
| 352 | P | B | -0.3394 | |
| 353 | P | B | 0.0000 | |
| 354 | S | B | 0.0000 | |
| 355 | R | B | -2.5770 | |
| 356 | D | B | -2.9174 | |
| 357 | E | B | 0.0000 | |
| 358 | L | B | -1.9335 | |
| 359 | T | B | -1.9223 | |
| 360 | K | B | -2.9434 | |
| 361 | N | B | -2.8734 | |
| 362 | Q | B | -2.4956 | |
| 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 | -0.7177 | |
| 371 | G | B | -1.1423 | |
| 372 | F | B | 0.0000 | |
| 373 | Y | B | -1.0656 | |
| 374 | P | B | 0.0000 | |
| 375 | S | B | -0.1733 | |
| 376 | D | B | -0.9527 | |
| 377 | I | B | 0.0000 | |
| 378 | A | B | 0.0000 | |
| 379 | V | B | 0.0000 | |
| 380 | E | B | -1.0091 | |
| 381 | W | B | 0.0000 | |
| 382 | E | B | -1.6649 | |
| 383 | S | B | -1.1850 | |
| 384 | N | B | -1.7617 | |
| 385 | G | B | -1.8544 | |
| 386 | Q | B | -2.2635 | |
| 387 | P | B | -1.9453 | |
| 388 | E | B | 0.0000 | |
| 389 | N | B | -2.2352 | |
| 390 | N | B | -1.8935 | |
| 391 | Y | B | -1.2101 | |
| 392 | K | B | -0.8609 | |
| 393 | T | B | -0.2247 | |
| 394 | T | B | 0.0000 | |
| 395 | P | B | -0.1969 | |
| 396 | P | B | 0.1655 | |
| 397 | V | B | 0.7230 | |
| 398 | L | B | 1.0836 | |
| 399 | D | B | -0.3057 | |
| 400 | S | B | -1.0861 | |
| 401 | D | B | -1.8173 | |
| 402 | G | B | -0.9226 | |
| 403 | S | B | 0.0000 | |
| 404 | F | B | 0.2640 | |
| 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 | -0.9602 | |
| 412 | V | B | 0.0000 | |
| 413 | D | B | -2.6193 | |
| 414 | K | B | -2.6075 | |
| 415 | S | B | -2.1643 | |
| 416 | R | B | -1.9435 | |
| 417 | W | B | -1.6095 | |
| 418 | Q | B | -2.2680 | |
| 419 | Q | B | -2.1055 | |
| 420 | G | B | -1.2361 | |
| 421 | N | B | -0.8730 | |
| 422 | V | B | 0.6583 | |
| 423 | F | B | 0.0000 | |
| 424 | S | B | -0.9649 | |
| 425 | C | B | 0.0000 | |
| 426 | S | B | 0.0000 | |
| 427 | V | B | 0.0000 | |
| 428 | M | B | -0.4371 | |
| 429 | H | B | 0.0000 | |
| 430 | E | B | -1.3763 | |
| 431 | A | B | -1.6908 | |
| 432 | L | B | 0.0000 | |
| 433 | H | B | -1.9260 | |
| 434 | N | B | -1.7717 | |
| 435 | H | B | -1.4119 | |
| 436 | Y | B | -0.4219 | |
| 437 | T | B | -0.8415 | |
| 438 | Q | B | -1.1874 | |
| 439 | K | B | -1.7028 | |
| 440 | S | B | -0.6040 | |
| 441 | L | B | 0.0000 | |
| 442 | S | B | -0.1955 |
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 | -0.7846 | 4.1435 | View | CSV | PDB |
| 4.5 | -0.8517 | 4.1413 | View | CSV | PDB |
| 5.0 | -0.9317 | 4.1455 | View | CSV | PDB |
| 5.5 | -1.0069 | 4.1638 | View | CSV | PDB |
| 6.0 | -1.0599 | 4.1966 | View | CSV | PDB |
| 6.5 | -1.0792 | 4.24 | View | CSV | PDB |
| 7.0 | -1.067 | 4.2913 | View | CSV | PDB |
| 7.5 | -1.035 | 4.3483 | View | CSV | PDB |
| 8.0 | -0.9929 | 4.4078 | View | CSV | PDB |
| 8.5 | -0.9434 | 4.467 | View | CSV | PDB |
| 9.0 | -0.8865 | 4.5226 | 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