Chain sequence(s) |
A: MMRARFPLLLLGLVFLASVSVSFGIAYWEKENPKHNKCLQSCNSERDSYRNQACHARCNLLKVEKEECEEGEIPRPRPRPQHPEREPQQPGEKEEDEDEQPRPIPFPRPQPRQEEEHEQREEQEWPRKEEKRGEKGSEEEDEDEDEEQDERQFPFPRPPHQKEERKQEEDEDEEQQRESEESEDSELRRHKNKNPFLFGSNRFETLFKNQYGRIRVLQRFNQRSPQLQNLRDYRILEFNSKPNTLLLPNHADADYLIVILNGTAILSLVNNDDRDSYRLQSGDALRVPSGTTYYVVNPDNNENLRLITLAIPVNKPGRFESFFLSSTEAQQSYLQGFSRNILEASYDTKFEEINKVLFSREEGQQQGEQRLQESVIVEISKEQIRALSKRAKSSSRKTISSEDKPFNLRSRDPIYSNKLGKFFEITPEKNPQLRDLDIFLSIVDMNEGALLLPHFNSKAIVILVINEGDANIELVGLKEQQQEQQQEEQPLEVRKYRAELSEQDIFVIPAGYPVVVNATSNLNFFAIGINAENNQRNFLAGSQDNVISQIPSQVQELAFPGSAQAVEKLLKNQRESYFVDAQPKKKEEGNKGRKGPLSSILRAFY
input PDB |
Selected Chain(s) | A |
Distance of aggregation | 10 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] (00:00:01) [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 A chain(s) selected (00:00:01) [INFO] runJob: Creating pdb object from: input.pdb (00:00:01) [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 (00:09:35) [INFO] agg3D: Running pKa-ANI on /STORAGE/DATA/lcbio/aggreskan/6c17ea014918dac/tmp/folded.pdb (00:09:35) [INFO] Main: Simulation completed successfully. (00:13:01) |
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 | -3.2114 | |
30 | K | A | -3.6460 | |
31 | E | A | -3.8456 | |
32 | N | A | -3.1227 | |
33 | P | A | -2.5209 | |
34 | K | A | -2.7439 | |
35 | H | A | 0.0000 | |
36 | N | A | -2.9367 | |
37 | K | A | -2.8875 | |
38 | C | A | -2.1708 | |
39 | L | A | -1.7279 | |
40 | Q | A | -2.4964 | |
41 | S | A | -1.9677 | |
42 | C | A | 0.0000 | |
43 | N | A | -2.2738 | |
44 | S | A | -1.8959 | |
45 | E | A | -2.4863 | |
46 | R | A | -2.6704 | |
47 | D | A | -1.6804 | |
48 | S | A | -0.9357 | |
49 | Y | A | 0.0083 | |
50 | R | A | -1.0172 | |
51 | N | A | -1.8204 | |
52 | Q | A | -1.3522 | |
53 | A | A | -0.8331 | |
54 | C | A | -0.8590 | |
55 | H | A | -0.9827 | |
56 | A | A | -0.6177 | |
57 | R | A | -0.5841 | |
58 | C | A | 0.0000 | |
59 | N | A | -0.4600 | |
60 | L | A | 0.3534 | |
61 | L | A | -1.0956 | |
62 | K | A | -2.5179 | |
63 | V | A | -1.8190 | |
64 | E | A | -3.4352 | |
65 | K | A | -4.3332 | |
66 | E | A | -4.8883 | |
67 | E | A | -4.6400 | |
68 | C | A | -3.3866 | |
69 | E | A | -4.6307 | |
70 | E | A | -4.4672 | |
71 | G | A | -3.1417 | |
72 | E | A | -2.8780 | |
187 | L | A | -1.3487 | |
188 | R | A | -3.0858 | |
189 | R | A | -3.5419 | |
190 | H | A | 0.0000 | |
191 | K | A | -3.9039 | |
192 | N | A | -3.5742 | |
193 | K | A | -3.4185 | |
194 | N | A | 0.0000 | |
195 | P | A | -1.2809 | |
196 | F | A | 0.0000 | |
197 | L | A | 0.0000 | |
198 | F | A | 0.0000 | |
199 | G | A | -1.5637 | |
200 | S | A | -1.4914 | |
201 | N | A | -2.0878 | |
202 | R | A | -2.0588 | |
203 | F | A | -1.6343 | |
204 | E | A | -2.0324 | |
205 | T | A | -0.9893 | |
206 | L | A | -0.0235 | |
207 | F | A | -0.5571 | |
208 | K | A | -1.9350 | |
209 | N | A | -1.8565 | |
210 | Q | A | -2.1532 | |
211 | Y | A | -1.6220 | |
212 | G | A | -1.6047 | |
213 | R | A | -1.4143 | |
214 | I | A | 0.0000 | |
215 | R | A | 0.0000 | |
216 | V | A | 0.0000 | |
217 | L | A | 0.0000 | |
218 | Q | A | -1.6872 | |
219 | R | A | -1.9805 | |
220 | F | A | 0.0000 | |
221 | N | A | -2.4009 | |
222 | Q | A | -2.1692 | |
223 | R | A | -1.4836 | |
224 | S | A | 0.0000 | |
225 | P | A | -1.6567 | |
226 | Q | A | -1.8437 | |
227 | L | A | 0.0000 | |
228 | Q | A | -2.7872 | |
229 | N | A | -2.3946 | |
230 | L | A | 0.0000 | |
231 | R | A | -2.9368 | |
232 | D | A | -2.1274 | |
233 | Y | A | -1.0776 | |
234 | R | A | -0.8581 | |
235 | I | A | 0.0000 | |
236 | L | A | 0.0000 | |
237 | E | A | 0.0000 | |
238 | F | A | 0.0000 | |
239 | N | A | -0.9665 | |
240 | S | A | 0.0000 | |
241 | K | A | -2.4792 | |
242 | P | A | -2.3490 | |
243 | N | A | -2.1968 | |
244 | T | A | 0.0000 | |
245 | L | A | -0.4058 | |
246 | L | A | 0.0000 | |
247 | L | A | 0.0000 | |
248 | P | A | 0.2063 | |
249 | N | A | 0.0000 | |
250 | H | A | -0.2733 | |
251 | A | A | 0.0000 | |
252 | D | A | -1.2320 | |
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 | -0.9875 | |
262 | G | A | -1.2842 | |
263 | T | A | -0.9775 | |
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 | -1.3440 | |
270 | N | A | -2.6099 | |
271 | N | A | -3.0052 | |
272 | D | A | -3.5542 | |
273 | D | A | -3.6234 | |
274 | R | A | -2.6854 | |
275 | D | A | -2.3340 | |
276 | S | A | 0.0000 | |
277 | Y | A | 0.0000 | |
278 | R | A | -1.8046 | |
279 | L | A | 0.0000 | |
280 | Q | A | -1.0832 | |
281 | S | A | -0.7247 | |
282 | G | A | 0.0000 | |
283 | D | A | 0.0000 | |
284 | A | A | 0.0000 | |
285 | L | A | 0.0000 | |
286 | R | A | -1.2392 | |
287 | V | A | 0.0000 | |
288 | P | A | -0.4566 | |
289 | S | A | -0.1927 | |
290 | G | A | -0.2002 | |
291 | T | A | 0.0000 | |
292 | T | A | -0.2358 | |
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 | -1.7573 | |
299 | D | A | -2.2166 | |
300 | N | A | -2.8464 | |
301 | N | A | -2.8236 | |
302 | E | A | -2.6599 | |
303 | N | A | -2.2072 | |
304 | L | A | 0.0000 | |
305 | R | A | -0.8582 | |
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 | -0.5828 | |
312 | P | A | 0.0000 | |
313 | V | A | -1.0090 | |
314 | N | A | -2.4517 | |
315 | K | A | -3.0136 | |
316 | P | A | -2.2022 | |
317 | G | A | 0.0000 | |
318 | R | A | -3.1634 | |
319 | F | A | -2.0668 | |
320 | E | A | -2.2192 | |
321 | S | A | -0.5866 | |
322 | F | A | -0.0007 | |
323 | F | A | 0.0000 | |
324 | L | A | 0.6564 | |
325 | S | A | 0.1747 | |
326 | S | A | -0.9092 | |
327 | T | A | 0.0000 | |
328 | E | A | -3.0838 | |
329 | A | A | -1.8276 | |
330 | Q | A | -1.2936 | |
331 | Q | A | -1.4177 | |
332 | S | A | 0.0000 | |
333 | Y | A | 0.5678 | |
334 | L | A | 0.5276 | |
335 | Q | A | -0.3374 | |
336 | G | A | -0.1622 | |
337 | F | A | 0.9068 | |
338 | S | A | -0.2840 | |
339 | R | A | -2.1514 | |
340 | N | A | -1.4208 | |
341 | I | A | 0.8075 | |
342 | L | A | 0.0000 | |
343 | E | A | -2.0675 | |
344 | A | A | -0.9233 | |
345 | S | A | -0.4404 | |
346 | Y | A | -0.5771 | |
347 | D | A | -1.8607 | |
348 | T | A | -2.1868 | |
349 | K | A | -3.3472 | |
350 | F | A | -2.6843 | |
351 | E | A | -3.8551 | |
352 | E | A | -2.5570 | |
353 | I | A | 0.0000 | |
354 | N | A | -2.3798 | |
355 | K | A | -2.6041 | |
356 | V | A | 0.3856 | |
357 | L | A | 0.6880 | |
358 | F | A | 0.0000 | |
359 | S | A | -1.9616 | |
360 | R | A | -3.0627 | |
361 | E | A | -4.4931 | |
362 | E | A | -3.9725 | |
363 | G | A | -2.9361 | |
364 | Q | A | -3.6809 | |
365 | Q | A | -3.2640 | |
366 | Q | A | -3.1704 | |
367 | G | A | -3.0893 | |
368 | E | A | -3.6139 | |
369 | Q | A | -3.7578 | |
370 | R | A | -3.8305 | |
371 | L | A | -2.6283 | |
372 | Q | A | -2.7212 | |
373 | E | A | -3.1523 | |
374 | S | A | 0.0000 | |
375 | V | A | 0.0000 | |
376 | I | A | 0.0000 | |
377 | V | A | -1.3748 | |
378 | E | A | -2.2362 | |
379 | I | A | 0.0000 | |
380 | S | A | -2.4691 | |
381 | K | A | -3.6767 | |
382 | E | A | -3.7006 | |
383 | Q | A | -3.0170 | |
384 | I | A | 0.0000 | |
385 | R | A | -3.7906 | |
386 | A | A | -2.6125 | |
387 | L | A | -1.9119 | |
388 | S | A | -2.6324 | |
389 | K | A | -3.1949 | |
390 | R | A | -3.5363 | |
391 | A | A | -2.5955 | |
392 | K | A | -2.9704 | |
393 | S | A | -1.7844 | |
394 | S | A | -1.6806 | |
395 | S | A | -1.9362 | |
396 | R | A | -3.1923 | |
397 | K | A | -2.7634 | |
398 | T | A | 0.0000 | |
399 | I | A | 0.0000 | |
400 | S | A | -2.1328 | |
401 | S | A | -2.2840 | |
402 | E | A | -3.4091 | |
403 | D | A | -3.2589 | |
404 | K | A | -2.7973 | |
405 | P | A | 0.0000 | |
406 | F | A | 0.0000 | |
407 | N | A | -1.2161 | |
408 | L | A | 0.0000 | |
409 | R | A | -2.1297 | |
410 | S | A | -2.5300 | |
411 | R | A | -3.1604 | |
412 | D | A | -2.7151 | |
413 | P | A | -1.2851 | |
414 | I | A | 0.2857 | |
415 | Y | A | 0.0281 | |
416 | S | A | -0.9551 | |
417 | N | A | -1.4102 | |
418 | K | A | -2.2120 | |
419 | L | A | -1.8085 | |
420 | G | A | -1.7134 | |
421 | K | A | -1.5616 | |
422 | F | A | 0.0000 | |
423 | F | A | 0.0000 | |
424 | E | A | -0.7431 | |
425 | I | A | 0.0000 | |
426 | T | A | -1.6836 | |
427 | P | A | 0.0000 | |
428 | E | A | -2.9753 | |
429 | K | A | -2.3684 | |
430 | N | A | 0.0000 | |
431 | P | A | -2.6912 | |
432 | Q | A | 0.0000 | |
433 | L | A | 0.0000 | |
434 | R | A | -3.6689 | |
435 | D | A | -2.9432 | |
436 | L | A | 0.0000 | |
437 | D | A | -2.2020 | |
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 | -1.6107 | |
445 | M | A | 0.0000 | |
446 | N | A | -2.9411 | |
447 | E | A | -3.1425 | |
448 | G | A | -1.7868 | |
449 | A | A | 0.0000 | |
450 | L | A | -0.4291 | |
451 | L | A | 0.0000 | |
452 | L | A | 0.0000 | |
453 | P | A | 0.1341 | |
454 | H | A | 0.0000 | |
455 | F | A | 0.0734 | |
456 | N | A | 0.0000 | |
457 | S | A | -1.0310 | |
458 | K | A | -1.2686 | |
459 | A | A | 0.0000 | |
460 | I | A | -0.2509 | |
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 | -2.1719 | |
468 | G | A | -2.2133 | |
469 | D | A | -2.2876 | |
470 | A | A | 0.0000 | |
471 | N | A | -1.4595 | |
472 | I | A | 0.0000 | |
473 | E | A | -1.8059 | |
474 | L | A | 0.0000 | |
475 | V | A | -0.0115 | |
476 | G | A | 0.0000 | |
477 | L | A | -0.1411 | |
478 | K | A | -2.0808 | |
479 | E | A | -3.1602 | |
480 | Q | A | -3.6041 | |
481 | Q | A | -3.6764 | |
482 | Q | A | -3.8415 | |
483 | E | A | -3.9696 | |
484 | Q | A | -3.6445 | |
485 | Q | A | -3.9480 | |
486 | Q | A | -3.8446 | |
487 | E | A | -4.1777 | |
488 | E | A | -3.5956 | |
489 | Q | A | -3.1127 | |
490 | P | A | -1.2913 | |
491 | L | A | -0.1593 | |
492 | E | A | -1.2256 | |
493 | V | A | 0.5954 | |
494 | R | A | -0.8238 | |
495 | K | A | -1.5724 | |
496 | Y | A | 0.0000 | |
497 | R | A | -2.3690 | |
498 | A | A | 0.0000 | |
499 | E | A | -1.9789 | |
500 | L | A | 0.0000 | |
501 | S | A | -1.6810 | |
502 | E | A | -1.9918 | |
503 | Q | A | -1.2667 | |
504 | D | A | -1.3722 | |
505 | I | A | 0.0000 | |
506 | F | A | 0.0000 | |
507 | V | A | 0.0000 | |
508 | I | A | 0.0000 | |
509 | P | A | -0.2353 | |
510 | A | A | -0.2138 | |
511 | G | A | -0.1985 | |
512 | Y | A | 0.3741 | |
513 | P | A | 0.0694 | |
514 | V | A | 0.0000 | |
515 | V | A | -0.2285 | |
516 | V | A | 0.0000 | |
517 | N | A | -1.0914 | |
518 | A | A | 0.0000 | |
519 | T | A | -1.6409 | |
520 | S | A | -2.2608 | |
521 | N | A | -2.9831 | |
522 | L | A | 0.0000 | |
523 | N | A | -1.5112 | |
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 | -1.3484 | |
531 | A | A | 0.0000 | |
532 | E | A | -2.6296 | |
533 | N | A | -2.5478 | |
534 | N | A | -1.9746 | |
535 | Q | A | -1.9320 | |
536 | R | A | -1.2205 | |
537 | N | A | -0.8419 | |
538 | F | A | 0.0000 | |
539 | L | A | 0.1695 | |
540 | A | A | -0.8559 | |
541 | G | A | 0.0000 | |
542 | S | A | -2.4724 | |
543 | Q | A | -2.3427 | |
544 | D | A | -2.2425 | |
545 | N | A | 0.0000 | |
546 | V | A | -0.1578 | |
547 | I | A | 0.1511 | |
548 | S | A | -0.9512 | |
549 | Q | A | -0.9608 | |
550 | I | A | -0.0826 | |
551 | P | A | -0.5373 | |
552 | S | A | -1.0863 | |
553 | Q | A | -0.9527 | |
554 | V | A | 0.5885 | |
555 | Q | A | 0.0000 | |
556 | E | A | -1.2243 | |
557 | L | A | 0.8654 | |
558 | A | A | 0.6526 | |
559 | F | A | 0.4884 | |
560 | P | A | -0.1628 | |
561 | G | A | -0.6828 | |
562 | S | A | -1.3929 | |
563 | A | A | 0.0000 | |
564 | Q | A | -2.0390 | |
565 | A | A | -1.3995 | |
566 | V | A | 0.0000 | |
567 | E | A | -2.0786 | |
568 | K | A | -2.5552 | |
569 | L | A | -0.6304 | |
570 | L | A | -1.5035 | |
571 | K | A | -3.2593 | |
572 | N | A | -2.8592 | |
573 | Q | A | -2.6160 | |
574 | R | A | -3.4075 | |
575 | E | A | -2.6835 | |
576 | S | A | 0.0000 | |
577 | Y | A | -0.4516 | |
578 | F | A | 0.0000 | |
579 | V | A | 0.0000 | |
580 | D | A | -1.7153 | |
581 | A | A | -1.2499 | |
582 | Q | A | -2.2658 | |
583 | P | A | -3.0296 | |
584 | K | A | -4.4606 | |
585 | K | A | -4.9690 | |
586 | K | A | -5.4048 | |
587 | E | A | -5.6501 | |
588 | E | A | -5.5990 | |
589 | G | A | -4.6129 | |
590 | N | A | -4.9670 | |
591 | K | A | -4.8000 | |
592 | G | A | -3.8788 | |
593 | R | A | -4.2018 | |
594 | K | A | -3.3216 | |
595 | G | A | -1.6944 | |
596 | P | A | -0.4946 | |
597 | L | A | 1.1940 | |
598 | S | A | 0.9937 | |
599 | S | A | 1.1349 | |
600 | I | A | 2.3740 | |
601 | L | A | 1.8412 | |
602 | R | A | 0.1853 | |
603 | A | A | 1.1378 | |
604 | F | A | 2.3312 | |
605 | Y | A | 1.9627 |
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 | -1.306 | 4.3351 | View | CSV | PDB |
4.5 | -1.3913 | 4.3351 | View | CSV | PDB |
5.0 | -1.5003 | 4.3351 | View | CSV | PDB |
5.5 | -1.6102 | 4.3351 | View | CSV | PDB |
6.0 | -1.6956 | 4.3351 | View | CSV | PDB |
6.5 | -1.7368 | 4.3351 | View | CSV | PDB |
7.0 | -1.7297 | 4.3351 | View | CSV | PDB |
7.5 | -1.6876 | 4.335 | View | CSV | PDB |
8.0 | -1.6268 | 4.3348 | View | CSV | PDB |
8.5 | -1.5562 | 4.3342 | View | CSV | PDB |
9.0 | -1.4795 | 4.3322 | View | CSV | PDB |