| Chain sequence(s) |
A: GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
B: GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL 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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:40)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/1cd2d6b106d8719/tmp/folded.pdb (00:05:40)
[INFO] Main: Simulation completed successfully. (00:08:49)
|
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 |
|---|---|---|---|---|
| 237 | G | A | -0.9232 | |
| 238 | P | A | 0.0000 | |
| 239 | S | A | -0.1490 | |
| 240 | V | A | 0.0000 | |
| 241 | F | A | 1.2143 | |
| 242 | L | A | 0.0000 | |
| 243 | F | A | 1.3036 | |
| 244 | P | A | -0.0493 | |
| 245 | P | A | 0.0000 | |
| 246 | K | A | -2.1041 | |
| 247 | P | A | -1.4470 | |
| 248 | K | A | -1.3435 | |
| 249 | D | A | -1.4592 | |
| 250 | T | A | 0.0000 | |
| 251 | L | A | 0.0000 | |
| 252 | M | A | 0.2129 | |
| 253 | I | A | 1.2059 | |
| 254 | S | A | -0.1410 | |
| 255 | R | A | -1.5215 | |
| 256 | T | A | -0.9254 | |
| 257 | P | A | 0.0000 | |
| 258 | E | A | -1.1185 | |
| 259 | V | A | 0.0000 | |
| 260 | T | A | 0.2673 | |
| 261 | C | A | 0.0000 | |
| 262 | V | A | 0.0000 | |
| 263 | V | A | 0.0000 | |
| 264 | V | A | -0.4940 | |
| 265 | D | A | -1.7579 | |
| 266 | V | A | 0.0000 | |
| 267 | S | A | -2.1199 | |
| 268 | H | A | -2.4322 | |
| 269 | E | A | -2.9411 | |
| 270 | D | A | -2.5996 | |
| 271 | P | A | -2.6547 | |
| 272 | E | A | -2.8622 | |
| 273 | V | A | -1.7402 | |
| 274 | K | A | -2.1577 | |
| 275 | F | A | -1.1309 | |
| 276 | N | A | -1.1309 | |
| 277 | W | A | 0.0000 | |
| 278 | Y | A | -0.5200 | |
| 279 | V | A | -0.6790 | |
| 280 | D | A | -1.4223 | |
| 281 | G | A | -0.5586 | |
| 282 | V | A | 0.9070 | |
| 283 | E | A | -0.5530 | |
| 284 | V | A | -0.4905 | |
| 285 | H | A | -1.8491 | |
| 286 | N | A | -2.1648 | |
| 287 | A | A | -1.8947 | |
| 288 | K | A | -2.4504 | |
| 289 | T | A | -1.7830 | |
| 290 | K | A | -2.5347 | |
| 291 | P | A | -2.4421 | |
| 292 | R | A | -3.4766 | |
| 293 | E | A | -3.3509 | |
| 294 | E | A | -2.1374 | |
| 295 | Q | A | -1.5310 | |
| 296 | Y | A | -0.0050 | |
| 297 | N | A | -1.1389 | |
| 298 | S | A | -0.9897 | |
| 299 | T | A | 0.0000 | |
| 300 | Y | A | -1.9839 | |
| 301 | R | A | -2.2261 | |
| 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 | -0.6545 | |
| 308 | V | A | 0.0000 | |
| 309 | L | A | 0.8108 | |
| 310 | H | A | -0.1993 | |
| 311 | Q | A | -1.1725 | |
| 312 | D | A | -1.2784 | |
| 313 | W | A | 0.0000 | |
| 314 | L | A | -1.0220 | |
| 315 | N | A | -2.1174 | |
| 316 | G | A | -2.0690 | |
| 317 | K | A | -2.2675 | |
| 318 | E | A | -2.2658 | |
| 319 | Y | A | 0.0000 | |
| 320 | K | A | -1.6594 | |
| 321 | C | A | 0.0000 | |
| 322 | K | A | -1.5878 | |
| 323 | V | A | 0.0000 | |
| 324 | S | A | -1.4323 | |
| 325 | N | A | 0.0000 | |
| 326 | K | A | -2.5334 | |
| 327 | A | A | -1.4089 | |
| 328 | L | A | -0.5985 | |
| 329 | P | A | -0.5135 | |
| 330 | A | A | -0.4361 | |
| 331 | P | A | -0.9158 | |
| 332 | I | A | -0.8058 | |
| 333 | E | A | -2.1272 | |
| 334 | K | A | -1.2383 | |
| 335 | T | A | -0.9903 | |
| 336 | I | A | -0.1259 | |
| 337 | S | A | -0.9929 | |
| 338 | K | A | -1.3659 | |
| 339 | A | A | -1.2016 | |
| 340 | K | A | -2.3262 | |
| 341 | G | A | -2.0317 | |
| 342 | Q | A | -2.0339 | |
| 343 | P | A | -1.9317 | |
| 344 | R | A | -2.4044 | |
| 345 | E | A | -2.6309 | |
| 346 | P | A | 0.0000 | |
| 347 | Q | A | -0.9201 | |
| 348 | V | A | 0.0000 | |
| 349 | Y | A | 0.0000 | |
| 350 | T | A | -0.5254 | |
| 351 | L | A | 0.0000 | |
| 352 | P | A | -0.1119 | |
| 353 | P | A | 0.0000 | |
| 354 | S | A | -1.3051 | |
| 355 | R | A | -2.3546 | |
| 356 | E | A | -2.0670 | |
| 357 | E | A | 0.0000 | |
| 358 | M | A | -1.5644 | |
| 359 | T | A | -1.2315 | |
| 360 | K | A | -1.7604 | |
| 361 | N | A | -2.3016 | |
| 362 | Q | A | -2.1711 | |
| 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 | -0.3770 | |
| 371 | G | A | 0.0000 | |
| 372 | F | A | 0.0000 | |
| 373 | Y | A | -1.2279 | |
| 374 | P | A | 0.0000 | |
| 375 | S | A | -0.2784 | |
| 376 | D | A | -1.2442 | |
| 377 | I | A | -0.6283 | |
| 378 | A | A | 0.0000 | |
| 379 | V | A | 0.0000 | |
| 380 | E | A | -1.4508 | |
| 381 | W | A | 0.0000 | |
| 382 | E | A | -1.6883 | |
| 383 | S | A | 0.0000 | |
| 384 | N | A | -1.7841 | |
| 385 | G | A | -1.8389 | |
| 386 | Q | A | -2.2312 | |
| 387 | P | A | -1.9053 | |
| 388 | E | A | 0.0000 | |
| 389 | N | A | -2.1097 | |
| 390 | N | A | -1.6729 | |
| 391 | Y | A | -1.0234 | |
| 392 | K | A | -0.8297 | |
| 393 | T | A | -0.3108 | |
| 394 | T | A | 0.0000 | |
| 395 | P | A | -0.0578 | |
| 396 | P | A | 0.1899 | |
| 397 | V | A | 0.7449 | |
| 398 | L | A | 1.0817 | |
| 399 | D | A | -0.2844 | |
| 400 | S | A | -1.1287 | |
| 401 | D | A | -1.9112 | |
| 402 | G | A | -1.0527 | |
| 403 | S | A | 0.0000 | |
| 404 | F | A | 0.1997 | |
| 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 | -0.8983 | |
| 412 | V | A | 0.0000 | |
| 413 | D | A | -2.4813 | |
| 414 | K | A | -2.5094 | |
| 415 | S | A | -2.1776 | |
| 416 | R | A | -2.0108 | |
| 417 | W | A | 0.0000 | |
| 418 | Q | A | -2.0705 | |
| 419 | Q | A | -1.8961 | |
| 420 | G | A | -0.6908 | |
| 421 | N | A | -0.3998 | |
| 422 | V | A | 0.8230 | |
| 423 | F | A | 0.0000 | |
| 424 | S | A | -0.6215 | |
| 425 | C | A | 0.0000 | |
| 426 | S | A | 0.0000 | |
| 427 | V | A | 0.0000 | |
| 428 | M | A | -0.4764 | |
| 429 | H | A | 0.0000 | |
| 430 | E | A | -1.1829 | |
| 431 | A | A | -1.7157 | |
| 432 | L | A | 0.0000 | |
| 433 | H | A | -1.8383 | |
| 434 | N | A | -1.4975 | |
| 435 | H | A | -0.9617 | |
| 436 | Y | A | -0.4260 | |
| 437 | T | A | -0.6023 | |
| 438 | Q | A | -0.8697 | |
| 439 | K | A | -0.8101 | |
| 440 | S | A | -0.2999 | |
| 441 | L | A | 0.0000 | |
| 442 | S | A | 0.6650 | |
| 443 | L | A | 1.1075 | |
| 237 | G | B | -0.8665 | |
| 238 | P | B | 0.0000 | |
| 239 | S | B | -0.0572 | |
| 240 | V | B | 0.0000 | |
| 241 | F | B | 1.4498 | |
| 242 | L | B | 1.0725 | |
| 243 | F | B | 1.4507 | |
| 244 | P | B | 0.0369 | |
| 245 | P | B | 0.0000 | |
| 246 | K | B | -2.0209 | |
| 247 | P | B | -1.3374 | |
| 248 | K | B | -1.0482 | |
| 249 | D | B | -1.1165 | |
| 250 | T | B | 0.0000 | |
| 251 | L | B | 0.0000 | |
| 252 | M | B | 0.5146 | |
| 253 | I | B | 1.6083 | |
| 254 | S | B | 0.2869 | |
| 255 | R | B | -0.6428 | |
| 256 | T | B | -0.5086 | |
| 257 | P | B | 0.0000 | |
| 258 | E | B | -0.9221 | |
| 259 | V | B | 0.0000 | |
| 260 | T | B | 0.3867 | |
| 261 | C | B | 0.0000 | |
| 262 | V | B | 0.0000 | |
| 263 | V | B | 0.0000 | |
| 264 | V | B | -0.3084 | |
| 265 | D | B | -1.5072 | |
| 266 | V | B | 0.0000 | |
| 267 | S | B | -1.8764 | |
| 268 | H | B | -1.9963 | |
| 269 | E | B | -2.7272 | |
| 270 | D | B | -2.4361 | |
| 271 | P | B | -2.5395 | |
| 272 | E | B | -2.8527 | |
| 273 | V | B | -1.7444 | |
| 274 | K | B | -2.1771 | |
| 275 | F | B | -1.1127 | |
| 276 | N | B | -1.2570 | |
| 277 | W | B | 0.0000 | |
| 278 | Y | B | -0.8645 | |
| 279 | V | B | -0.8809 | |
| 280 | D | B | -1.5694 | |
| 281 | G | B | -0.7683 | |
| 282 | V | B | 0.5352 | |
| 283 | E | B | -1.3337 | |
| 284 | V | B | -0.8052 | |
| 285 | H | B | -1.9954 | |
| 286 | N | B | -2.2245 | |
| 287 | A | B | -1.8500 | |
| 288 | K | B | -2.4218 | |
| 289 | T | B | -1.7297 | |
| 290 | K | B | -2.4371 | |
| 291 | P | B | -2.4032 | |
| 292 | R | B | -3.4472 | |
| 293 | E | B | -3.3207 | |
| 294 | E | B | -2.0659 | |
| 295 | Q | B | -1.4152 | |
| 296 | Y | B | 0.0418 | |
| 297 | N | B | -1.0917 | |
| 298 | S | B | -0.8722 | |
| 299 | T | B | -1.4536 | |
| 300 | Y | B | -1.8712 | |
| 301 | R | B | -2.1386 | |
| 302 | V | B | 0.0000 | |
| 303 | V | B | 0.0000 | |
| 304 | S | B | 0.0000 | |
| 305 | V | B | 0.0000 | |
| 306 | L | B | 0.0000 | |
| 307 | T | B | -0.6218 | |
| 308 | V | B | 0.0000 | |
| 309 | L | B | 0.5945 | |
| 310 | H | B | -0.1834 | |
| 311 | Q | B | -1.1980 | |
| 312 | D | B | -1.3439 | |
| 313 | W | B | 0.0000 | |
| 314 | L | B | -1.0268 | |
| 315 | N | B | -2.1352 | |
| 316 | G | B | -2.0721 | |
| 317 | K | B | -2.2276 | |
| 318 | E | B | -2.3684 | |
| 319 | Y | B | 0.0000 | |
| 320 | K | B | -1.6579 | |
| 321 | C | B | 0.0000 | |
| 322 | K | B | -1.4884 | |
| 323 | V | B | 0.0000 | |
| 324 | S | B | -1.4261 | |
| 325 | N | B | 0.0000 | |
| 326 | K | B | -2.5334 | |
| 327 | A | B | -1.3952 | |
| 328 | L | B | -0.5648 | |
| 329 | P | B | -0.5197 | |
| 330 | A | B | -0.4244 | |
| 331 | P | B | -0.8931 | |
| 332 | I | B | -0.7352 | |
| 333 | E | B | -1.9525 | |
| 334 | K | B | -1.0853 | |
| 335 | T | B | -0.9057 | |
| 336 | I | B | -0.1044 | |
| 337 | S | B | -1.0114 | |
| 338 | K | B | -1.3508 | |
| 339 | A | B | -1.1881 | |
| 340 | K | B | -2.3234 | |
| 341 | G | B | -2.0279 | |
| 342 | Q | B | -2.0423 | |
| 343 | P | B | -1.9506 | |
| 344 | R | B | -2.4292 | |
| 345 | E | B | -2.6046 | |
| 346 | P | B | 0.0000 | |
| 347 | Q | B | -0.9479 | |
| 348 | V | B | 0.0000 | |
| 349 | Y | B | 0.0000 | |
| 350 | T | B | -0.5958 | |
| 351 | L | B | 0.0000 | |
| 352 | P | B | -0.2241 | |
| 353 | P | B | -0.7162 | |
| 354 | S | B | 0.0000 | |
| 355 | R | B | -2.0911 | |
| 356 | E | B | -1.5878 | |
| 357 | E | B | 0.0000 | |
| 358 | M | B | -1.3769 | |
| 359 | T | B | -1.2378 | |
| 360 | K | B | -1.9223 | |
| 361 | N | B | -2.4153 | |
| 362 | Q | B | -2.3791 | |
| 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 | -0.4106 | |
| 371 | G | B | 0.0000 | |
| 372 | F | B | 0.0000 | |
| 373 | Y | B | -1.2478 | |
| 374 | P | B | 0.0000 | |
| 375 | S | B | -0.2530 | |
| 376 | D | B | -1.0627 | |
| 377 | I | B | -0.4539 | |
| 378 | A | B | -0.3829 | |
| 379 | V | B | -0.3691 | |
| 380 | E | B | -1.4058 | |
| 381 | W | B | 0.0000 | |
| 382 | E | B | -1.8080 | |
| 383 | S | B | -1.2472 | |
| 384 | N | B | -1.8483 | |
| 385 | G | B | -1.7467 | |
| 386 | Q | B | -2.2814 | |
| 387 | P | B | -1.9974 | |
| 388 | E | B | -1.9470 | |
| 389 | N | B | -2.2423 | |
| 390 | N | B | -1.7984 | |
| 391 | Y | B | -1.1605 | |
| 392 | K | B | -0.8281 | |
| 393 | T | B | -0.2705 | |
| 394 | T | B | 0.0000 | |
| 395 | P | B | -0.1172 | |
| 396 | P | B | 0.1116 | |
| 397 | V | B | 0.5340 | |
| 398 | L | B | 0.6837 | |
| 399 | D | B | -0.4182 | |
| 400 | S | B | -1.1751 | |
| 401 | D | B | -1.9513 | |
| 402 | G | B | -1.1232 | |
| 403 | S | B | 0.0000 | |
| 404 | F | B | 0.0686 | |
| 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 | -0.9585 | |
| 412 | V | B | 0.0000 | |
| 413 | D | B | -2.8860 | |
| 414 | K | B | -2.9788 | |
| 415 | S | B | -2.7856 | |
| 416 | R | B | -3.1446 | |
| 417 | W | B | 0.0000 | |
| 418 | Q | B | -2.5730 | |
| 419 | Q | B | -2.3399 | |
| 420 | G | B | -0.9937 | |
| 421 | N | B | -0.9041 | |
| 422 | V | B | 0.3369 | |
| 423 | F | B | 0.0000 | |
| 424 | S | B | 0.0000 | |
| 425 | C | B | 0.0000 | |
| 426 | S | B | -0.6438 | |
| 427 | V | B | 0.0000 | |
| 428 | M | B | -0.3190 | |
| 429 | H | B | 0.0000 | |
| 430 | E | B | -1.1033 | |
| 431 | A | B | -1.6071 | |
| 432 | L | B | -1.4179 | |
| 433 | H | B | -1.7200 | |
| 434 | N | B | -1.5937 | |
| 435 | H | B | -1.0106 | |
| 436 | Y | B | -0.3041 | |
| 437 | T | B | -0.6057 | |
| 438 | Q | B | -1.0419 | |
| 439 | K | B | -0.8837 | |
| 440 | S | B | -0.4028 | |
| 441 | L | B | 0.0000 | |
| 442 | S | B | 0.3352 | |
| 443 | L | B | 1.1689 |
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 | -0.7367 | 4.0304 | View | CSV | PDB |
| 4.5 | -0.7997 | 4.0132 | View | CSV | PDB |
| 5.0 | -0.8752 | 3.9993 | View | CSV | PDB |
| 5.5 | -0.9465 | 4.0005 | View | CSV | PDB |
| 6.0 | -0.9962 | 4.0257 | View | CSV | PDB |
| 6.5 | -1.0124 | 4.0751 | View | CSV | PDB |
| 7.0 | -0.9977 | 4.1423 | View | CSV | PDB |
| 7.5 | -0.9649 | 4.2185 | View | CSV | PDB |
| 8.0 | -0.9238 | 4.2981 | View | CSV | PDB |
| 8.5 | -0.8773 | 4.3781 | View | CSV | PDB |
| 9.0 | -0.8253 | 4.4563 | 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