Chain sequence(s) |
A: MMRARFPLLLLGLVFLASVSVSFGIAYWEKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEGEIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDSELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY
input PDB |
Selected Chain(s) | A |
Distance of aggregation | 5 Å |
FoldX usage | Yes |
pH calculations | Yes |
alphaCutter usage |
A: MMRARFPLLLLGLVFLASVSVSFGIAYW EKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEGEIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDS ELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY(Red indicates removed residues) |
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 A chain(s) selected (00:00:00) [INFO] runJob: Creating pdb object from: input.pdb (00:00:00) [INFO] PDB: Running AlphaCutter (00:00:01) [INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:12) [INFO] FoldX: Starting FoldX energy minimization (00:00:12) [INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:27) [INFO] agg3D: Running pKa-ANI on /STORAGE/DATA/lcbio/aggreskan/97b9229d7136a9c/tmp/folded.pdb (00:10:27) [INFO] Main: Simulation completed successfully. (00:14:15) |
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 |
---|---|---|---|---|
29 | E | A | -2.1226 | |
30 | K | A | -2.3572 | |
31 | E | A | -2.1674 | |
32 | N | A | -0.5756 | |
33 | P | A | -0.5324 | |
34 | K | A | -1.3974 | |
35 | H | A | 0.0000 | |
36 | N | A | -1.0816 | |
37 | K | A | -1.7863 | |
38 | C | A | -0.1242 | |
39 | L | A | 0.2053 | |
40 | Q | A | -1.1434 | |
41 | S | A | -0.3164 | |
42 | C | A | 0.0000 | |
43 | N | A | -1.3110 | |
44 | S | A | -0.5506 | |
45 | E | A | -0.9862 | |
46 | R | A | -2.0440 | |
47 | D | A | -0.8615 | |
48 | S | A | -0.0629 | |
49 | Y | A | 1.2081 | |
50 | R | A | -0.2006 | |
51 | N | A | -0.6096 | |
52 | Q | A | -1.2550 | |
53 | A | A | -0.2168 | |
54 | C | A | 0.0775 | |
55 | H | A | -0.2820 | |
56 | A | A | -0.1266 | |
57 | R | A | -0.5744 | |
58 | C | A | 0.0000 | |
59 | N | A | -0.3755 | |
60 | L | A | 1.4816 | |
61 | L | A | 0.3435 | |
62 | K | A | -1.0051 | |
63 | V | A | 0.1072 | |
64 | E | A | -2.0091 | |
65 | K | A | -2.3496 | |
66 | E | A | -2.4482 | |
67 | E | A | -2.0137 | |
68 | C | A | 0.0851 | |
69 | E | A | -2.0088 | |
70 | E | A | -2.2206 | |
71 | G | A | -1.1086 | |
72 | E | A | -1.9025 | |
187 | L | A | 0.8446 | |
188 | R | A | -1.9620 | |
189 | R | A | -2.1720 | |
190 | H | A | 0.0000 | |
191 | K | A | -1.8577 | |
192 | N | A | -1.8631 | |
193 | K | A | -1.9240 | |
194 | N | A | 0.0000 | |
195 | P | A | -0.0312 | |
196 | F | A | 0.0000 | |
197 | L | A | 0.0000 | |
198 | F | A | 0.0000 | |
199 | G | A | -0.1439 | |
200 | S | A | -0.3352 | |
201 | N | A | -1.4418 | |
202 | R | A | -1.0534 | |
203 | F | A | -0.2880 | |
204 | E | A | -1.7925 | |
205 | T | A | -0.2562 | |
206 | L | A | 0.7728 | |
207 | F | A | 0.1915 | |
208 | K | A | -1.7456 | |
209 | N | A | -0.7398 | |
210 | Q | A | -1.1942 | |
211 | Y | A | 0.0135 | |
212 | G | A | -0.0977 | |
213 | R | A | -0.7571 | |
214 | I | A | 0.0000 | |
215 | R | A | 0.0000 | |
216 | V | A | 0.0000 | |
217 | L | A | 0.0000 | |
218 | Q | A | -0.4742 | |
219 | R | A | -0.5131 | |
220 | F | A | 0.0000 | |
221 | N | A | -0.5570 | |
222 | Q | A | -1.3084 | |
223 | R | A | -0.6097 | |
224 | S | A | 0.0000 | |
225 | P | A | -0.3863 | |
226 | Q | A | -0.7799 | |
227 | L | A | 0.0000 | |
228 | Q | A | -1.2947 | |
229 | N | A | -1.4591 | |
230 | L | A | 0.0000 | |
231 | R | A | -1.2376 | |
232 | D | A | -0.8205 | |
233 | Y | A | -0.0040 | |
234 | R | A | -0.1619 | |
235 | I | A | 0.0000 | |
236 | L | A | 0.0000 | |
237 | E | A | 0.0000 | |
238 | F | A | 0.0000 | |
239 | N | A | -0.1793 | |
240 | S | A | 0.0000 | |
241 | K | A | -1.1522 | |
242 | P | A | -0.2680 | |
243 | N | A | -0.1964 | |
244 | T | A | 0.0000 | |
245 | L | A | 0.1630 | |
246 | L | A | 0.0000 | |
247 | L | A | 0.0000 | |
248 | P | A | -0.0726 | |
249 | N | A | 0.0000 | |
250 | H | A | -0.1624 | |
251 | A | A | 0.0000 | |
252 | D | A | -0.2238 | |
253 | A | A | 0.0000 | |
254 | D | A | 0.0000 | |
255 | Y | A | 0.0000 | |
256 | L | A | 0.0000 | |
257 | I | A | 0.0000 | |
258 | V | A | 0.0000 | |
259 | I | A | 0.0000 | |
260 | L | A | 0.0000 | |
261 | N | A | -0.3445 | |
262 | G | A | -0.1279 | |
263 | T | A | -0.1185 | |
264 | A | A | 0.0000 | |
265 | I | A | 0.0000 | |
266 | L | A | 0.0000 | |
267 | S | A | 0.0000 | |
268 | L | A | 0.0000 | |
269 | V | A | 0.3064 | |
270 | N | A | -0.9349 | |
271 | N | A | -1.7397 | |
272 | D | A | -2.3418 | |
273 | D | A | -2.2378 | |
274 | R | A | -1.0692 | |
275 | D | A | -0.8558 | |
276 | S | A | 0.0000 | |
277 | Y | A | 0.0000 | |
278 | R | A | -0.8291 | |
279 | L | A | 0.0000 | |
280 | Q | A | -0.7403 | |
281 | S | A | -0.2139 | |
282 | G | A | 0.0000 | |
283 | D | A | 0.0000 | |
284 | A | A | 0.0000 | |
285 | L | A | 0.0000 | |
286 | R | A | -0.3088 | |
287 | V | A | 0.0000 | |
288 | P | A | -0.0552 | |
289 | S | A | -0.0581 | |
290 | G | A | -0.1591 | |
291 | T | A | 0.0000 | |
292 | T | A | -0.0342 | |
293 | Y | A | 0.0000 | |
294 | Y | A | 0.0000 | |
295 | V | A | 0.0000 | |
296 | V | A | 0.0000 | |
297 | N | A | 0.0000 | |
298 | P | A | -0.1018 | |
299 | D | A | -0.6591 | |
300 | N | A | -1.5793 | |
301 | N | A | -1.6722 | |
302 | E | A | -1.2781 | |
303 | N | A | -0.8939 | |
304 | L | A | 0.0000 | |
305 | R | A | -0.2640 | |
306 | L | A | 0.0000 | |
307 | I | A | 0.0000 | |
308 | T | A | 0.0000 | |
309 | L | A | 0.0000 | |
310 | A | A | 0.0000 | |
311 | I | A | 0.2023 | |
312 | P | A | 0.0000 | |
313 | V | A | 0.2660 | |
314 | N | A | -1.4877 | |
315 | K | A | -1.9469 | |
316 | P | A | -0.4865 | |
317 | G | A | 0.0000 | |
318 | R | A | -1.7921 | |
319 | F | A | -0.3833 | |
320 | E | A | -1.7791 | |
321 | S | A | -0.3183 | |
322 | F | A | 0.4039 | |
323 | F | A | 0.0000 | |
324 | L | A | 0.5999 | |
325 | S | A | 0.0724 | |
326 | S | A | -0.0265 | |
327 | T | A | 0.0000 | |
328 | E | A | -1.8094 | |
329 | A | A | -0.2880 | |
330 | Q | A | -0.3250 | |
331 | Q | A | -1.2196 | |
332 | S | A | 0.0000 | |
333 | Y | A | 0.6498 | |
334 | L | A | 0.1982 | |
335 | Q | A | -0.4623 | |
336 | G | A | -0.2999 | |
337 | F | A | 1.2320 | |
338 | S | A | -0.2039 | |
339 | R | A | -1.9690 | |
340 | N | A | -1.2239 | |
341 | I | A | 1.7744 | |
342 | L | A | 0.0000 | |
343 | E | A | -0.7056 | |
344 | A | A | -0.1093 | |
345 | S | A | -0.0864 | |
346 | Y | A | 0.2870 | |
347 | D | A | -1.6794 | |
348 | T | A | -0.6582 | |
349 | K | A | -1.6611 | |
350 | F | A | -0.3983 | |
351 | E | A | -1.9440 | |
352 | E | A | -1.2563 | |
353 | I | A | 0.0000 | |
354 | N | A | -0.4629 | |
355 | K | A | -1.4181 | |
356 | V | A | 1.5684 | |
357 | L | A | 0.8873 | |
358 | F | A | 0.0000 | |
359 | S | A | -0.4072 | |
360 | R | A | -1.0073 | |
361 | E | A | -2.2691 | |
362 | E | A | -2.2318 | |
363 | G | A | -1.0064 | |
364 | Q | A | -1.5016 | |
365 | Q | A | -1.6343 | |
366 | Q | A | -1.4985 | |
367 | G | A | -1.0259 | |
368 | E | A | -2.1192 | |
369 | Q | A | -1.8520 | |
370 | R | A | -2.0301 | |
371 | L | A | -0.3027 | |
372 | Q | A | -0.9683 | |
373 | E | A | -1.9316 | |
374 | S | A | 0.0000 | |
375 | V | A | 0.0000 | |
376 | I | A | 0.0000 | |
377 | V | A | -0.1567 | |
378 | E | A | -1.7876 | |
379 | I | A | 0.0000 | |
380 | S | A | -0.3534 | |
381 | K | A | -1.8353 | |
382 | E | A | -2.2873 | |
383 | Q | A | -1.4303 | |
384 | I | A | 0.0000 | |
385 | R | A | -1.8353 | |
386 | A | A | -0.2369 | |
387 | L | A | 0.2704 | |
388 | S | A | -0.2858 | |
389 | K | A | -2.0343 | |
390 | R | A | -2.1455 | |
391 | A | A | -0.6284 | |
392 | K | A | -1.7364 | |
393 | S | A | -0.6097 | |
394 | S | A | -0.0735 | |
395 | S | A | -0.4150 | |
396 | R | A | -2.1611 | |
397 | K | A | -2.0285 | |
398 | T | A | 0.0000 | |
399 | I | A | 0.0000 | |
400 | S | A | -0.2169 | |
401 | S | A | -0.3919 | |
402 | E | A | -2.1452 | |
403 | D | A | -2.2668 | |
404 | K | A | -1.1704 | |
405 | P | A | 0.0000 | |
406 | F | A | 0.0000 | |
407 | N | A | -0.1442 | |
408 | L | A | 0.0000 | |
409 | R | A | -0.8657 | |
410 | S | A | -0.4859 | |
411 | R | A | -2.0761 | |
412 | D | A | -2.1202 | |
413 | P | A | -0.1644 | |
414 | I | A | 1.1681 | |
415 | Y | A | 0.3120 | |
416 | S | A | -0.3138 | |
417 | N | A | -0.5930 | |
418 | K | A | -1.7150 | |
419 | L | A | -0.1348 | |
420 | G | A | -0.1793 | |
421 | K | A | -0.9362 | |
422 | F | A | 0.0000 | |
423 | F | A | 0.0000 | |
424 | E | A | -0.2312 | |
425 | I | A | 0.0000 | |
426 | T | A | -0.0095 | |
427 | P | A | 0.0000 | |
428 | E | A | -1.7289 | |
429 | K | A | -1.5499 | |
430 | N | A | 0.0000 | |
431 | P | A | -0.2245 | |
432 | Q | A | 0.0000 | |
433 | L | A | 0.0000 | |
434 | R | A | -2.0315 | |
435 | D | A | -2.0940 | |
436 | L | A | 0.0000 | |
437 | D | A | -0.4671 | |
438 | I | A | 0.0000 | |
439 | F | A | 0.0000 | |
440 | L | A | 0.0000 | |
441 | S | A | 0.0000 | |
442 | I | A | 0.0000 | |
443 | V | A | 0.0000 | |
444 | D | A | -0.5032 | |
445 | M | A | 0.0000 | |
446 | N | A | -1.4783 | |
447 | E | A | -2.2019 | |
448 | G | A | -0.4515 | |
449 | A | A | 0.0000 | |
450 | L | A | 0.2392 | |
451 | L | A | 0.0000 | |
452 | L | A | 0.0000 | |
453 | P | A | -0.0533 | |
454 | H | A | 0.0000 | |
455 | F | A | 0.3922 | |
456 | N | A | 0.0000 | |
457 | S | A | -0.2209 | |
458 | K | A | -0.5062 | |
459 | A | A | 0.0000 | |
460 | I | A | 0.2199 | |
461 | V | A | 0.0000 | |
462 | I | A | 0.0000 | |
463 | L | A | 0.0000 | |
464 | V | A | 0.0000 | |
465 | I | A | 0.0000 | |
466 | N | A | 0.0000 | |
467 | E | A | -1.1410 | |
468 | G | A | -0.4582 | |
469 | D | A | -0.8213 | |
470 | A | A | 0.0000 | |
471 | N | A | -0.4730 | |
472 | I | A | 0.0000 | |
473 | E | A | -1.1222 | |
474 | L | A | 0.0000 | |
475 | V | A | 0.3419 | |
476 | G | A | 0.0000 | |
477 | L | A | 0.6948 | |
478 | K | A | -1.2533 | |
479 | E | A | -2.2165 | |
480 | Q | A | -1.6779 | |
481 | Q | A | -1.6192 | |
482 | Q | A | -1.7372 | |
483 | E | A | -2.2624 | |
484 | Q | A | -1.7576 | |
485 | Q | A | -1.6246 | |
486 | Q | A | -1.7382 | |
487 | E | A | -2.3626 | |
488 | E | A | -2.3664 | |
489 | Q | A | -1.5753 | |
490 | P | A | -0.1887 | |
491 | L | A | 1.1705 | |
492 | E | A | -1.2145 | |
493 | V | A | 1.4143 | |
494 | R | A | -0.4518 | |
495 | K | A | -1.2094 | |
496 | Y | A | 0.0000 | |
497 | R | A | -1.3082 | |
498 | A | A | 0.0000 | |
499 | E | A | -1.1504 | |
500 | L | A | 0.0000 | |
501 | S | A | -0.4303 | |
502 | E | A | -1.2091 | |
503 | Q | A | -0.4409 | |
504 | D | A | -0.2540 | |
505 | I | A | 0.0000 | |
506 | F | A | 0.0000 | |
507 | V | A | 0.0000 | |
508 | I | A | 0.0000 | |
509 | P | A | 0.0026 | |
510 | A | A | -0.0637 | |
511 | G | A | -0.2589 | |
512 | Y | A | 0.1761 | |
513 | P | A | 0.0328 | |
514 | V | A | 0.0000 | |
515 | V | A | 0.1908 | |
516 | V | A | 0.0000 | |
517 | N | A | -0.2483 | |
518 | A | A | 0.0000 | |
519 | T | A | -0.0820 | |
520 | S | A | -0.5574 | |
521 | N | A | -1.6475 | |
522 | L | A | 0.0000 | |
523 | N | A | -0.1814 | |
524 | F | A | 0.0000 | |
525 | F | A | 0.0000 | |
526 | A | A | 0.0000 | |
527 | I | A | 0.0000 | |
528 | G | A | 0.0000 | |
529 | I | A | 0.0000 | |
530 | N | A | -0.5618 | |
531 | A | A | 0.0000 | |
532 | E | A | -1.1231 | |
533 | N | A | -1.4647 | |
534 | N | A | -0.6228 | |
535 | Q | A | -1.2663 | |
536 | R | A | -0.4485 | |
537 | N | A | -0.2193 | |
538 | F | A | 0.0000 | |
539 | L | A | 0.3317 | |
540 | A | A | 0.0726 | |
541 | G | A | 0.0000 | |
542 | S | A | -0.3663 | |
543 | Q | A | -1.5195 | |
544 | D | A | -1.8602 | |
545 | N | A | 0.0000 | |
546 | V | A | 0.6069 | |
547 | I | A | 0.4606 | |
548 | S | A | -0.2663 | |
549 | Q | A | -1.1119 | |
550 | I | A | 0.3480 | |
551 | P | A | -0.1442 | |
552 | S | A | -0.3485 | |
553 | Q | A | -1.0221 | |
554 | V | A | 0.8534 | |
555 | Q | A | 0.0000 | |
556 | E | A | -1.5428 | |
557 | L | A | 1.2324 | |
558 | A | A | 0.4469 | |
559 | F | A | 0.5755 | |
560 | P | A | -0.1791 | |
561 | G | A | -0.2600 | |
562 | S | A | -0.1903 | |
563 | A | A | 0.0000 | |
564 | Q | A | -1.1906 | |
565 | A | A | -0.1736 | |
566 | V | A | 0.0000 | |
567 | E | A | -1.1391 | |
568 | K | A | -1.5709 | |
569 | L | A | 1.2756 | |
570 | L | A | 0.1679 | |
571 | K | A | -1.8927 | |
572 | N | A | -1.6480 | |
573 | Q | A | -0.9632 | |
574 | R | A | -2.0716 | |
575 | E | A | -1.1900 | |
576 | S | A | 0.0000 | |
577 | Y | A | 0.1697 | |
578 | F | A | 0.0000 | |
579 | V | A | 0.0000 | |
580 | D | A | -0.4757 | |
581 | A | A | -0.1935 | |
582 | Q | A | -0.7502 | |
583 | P | A | -0.6834 | |
584 | K | A | -2.0466 | |
585 | K | A | -2.3043 | |
586 | K | A | -2.3305 | |
587 | E | A | -2.4524 | |
588 | E | A | -2.2298 | |
589 | G | A | -1.0186 | |
590 | N | A | -1.6591 | |
591 | K | A | -2.0089 | |
592 | G | A | -1.0895 | |
593 | R | A | -2.2455 | |
594 | K | A | -2.1335 | |
595 | G | A | -0.8299 | |
596 | P | A | -0.0556 | |
597 | L | A | 1.4616 | |
598 | S | A | 0.0331 | |
599 | S | A | 0.1351 | |
600 | I | A | 2.2521 | |
601 | L | A | 1.5778 | |
602 | R | A | -1.5524 | |
603 | A | A | 0.0690 | |
604 | F | A | 2.1998 | |
605 | Y | A | 1.6814 |
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 | -0.5213 | 4.5872 | View | CSV | PDB |
4.5 | -0.5563 | 4.5872 | View | CSV | PDB |
5.0 | -0.6009 | 4.5872 | View | CSV | PDB |
5.5 | -0.6459 | 4.5872 | View | CSV | PDB |
6.0 | -0.6811 | 4.5872 | View | CSV | PDB |
6.5 | -0.6985 | 4.5872 | View | CSV | PDB |
7.0 | -0.6965 | 4.5872 | View | CSV | PDB |
7.5 | -0.6805 | 4.5872 | View | CSV | PDB |
8.0 | -0.657 | 4.5871 | View | CSV | PDB |
8.5 | -0.6297 | 4.5869 | View | CSV | PDB |
9.0 | -0.5997 | 4.5861 | View | CSV | PDB |