Chain sequence(s) |
A: MVKLSNLLVATFGVLLVLNGCLARQSLGVPPQLQNECNLDNLDVLQATETIKSEAGQIEYWDHNHPQLRCVGVSVARYVIEQGGLYLPTFFTSPKISYVVQGTGISGRVVPGCAETFMDSQPMQGQQQGQPWQGRQGQQGQPWEGQGQQGQQGRQGQPWEGQGQQGQQGRQGQQGQPWEGQGQQGQQGFRDMHQKVEHVRRGDVFANTPGSAHWIYNSGEQPLVIIALLDIANYQNQLDRNPRVFHLAGNNQQGGFGGSQQQQEQKNLWSGFDAQVIAQALKIDVQLAQQLQNQQDSRGNIVRVKGPFQVVRPPLRQPYESEEWRHPRSPQGNGLEETICSMRSHENIDDPARADVYKPSLGRVTSVNSYTLPILEYVRLSATRGVLQGNAMVLPKYNMNANEILYCTGGQGRIQVVNDNGQNVLDQQVQKGQLVVIPQGFAYVVQSHGNKFEWISFKTNENAMISTLAGRTSLLRALPLEVISNGFQISPEEARKIKFNTLETTLTRAAGRQQQQLIEEIVEA
input PDB |
Selected Chain(s) | A |
Distance of aggregation | 10 Å |
FoldX usage | Yes |
pH calculations | Yes |
alphaCutter usage |
A: MVKLSNLLVATFGVLLVLNGCLARQSLGVPPQLQNECNLDNLDVLQATETIKSEAGQIEYWDHNHPQLRCVGVSVARYVIEQGGLYLPTFFTSPKISYVVQGTGISGRVVPGCAETFMDS QPMQGQQQGQPWQGRQGQQGQPWEGQGQQGQQGRQGQPWEGQGQQGQQGRQGQQGQPWEGQGQQGQ QGFRDMHQKVEHVRRGDVFANTPGSAHWIYNSGEQPLVIIALLDIANYQNQLDRNPRVFHLAGNNQQGGFGGSQQQQEQKNLWSGFDAQVIAQALKIDVQLAQQLQNQQDSRGNIVRVKGPFQVVRPPLRQPYESEEWRHPRSPQGNGLEETICSMRSHENIDDPARADVYKPSLGRVTSVNSYTLPILEYVRLSATRGVLQGNAMVLPKYNMNANEILYCTGGQGRIQVVNDNGQNVLDQQVQKGQLVVIPQGFAYVVQSHGNKFEWISFKTNENAMISTLAGRTSLLRALPLEVISNGFQISPEEARKIKFNTLETTLTRAAGRQQQQLIEEIVEA(Red indicates removed residues) |
Dynamic mode | No |
Automated mutations | No |
Downloads | Download all the data |
Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:02) [WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow to prevent this behavior) (00:00:02) [INFO] runJob: Starting aggrescan3d job on: input.pdb with A chain(s) selected (00:00:02) [INFO] runJob: Creating pdb object from: input.pdb (00:00:02) [INFO] PDB: Running AlphaCutter (00:00:02) [INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:21) [INFO] FoldX: Starting FoldX energy minimization (00:00:21) [INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:55) [INFO] agg3D: Running pKa-ANI on /STORAGE/DATA/lcbio/aggreskan/d7fabcd9023df1b/tmp/folded.pdb (00:11:55) [INFO] Main: Simulation completed successfully. (00:18:18) |
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 |
---|---|---|---|---|
1 | M | A | 1.4759 | |
2 | V | A | 1.5811 | |
3 | K | A | -0.1045 | |
4 | L | A | 1.4246 | |
5 | S | A | 1.1662 | |
6 | N | A | 0.7208 | |
7 | L | A | 2.1521 | |
8 | L | A | 2.5253 | |
9 | V | A | 3.1360 | |
10 | A | A | 2.3988 | |
11 | T | A | 2.9369 | |
12 | F | A | 4.2155 | |
13 | G | A | 3.2791 | |
14 | V | A | 3.5855 | |
15 | L | A | 3.7561 | |
16 | L | A | 3.7999 | |
17 | V | A | 3.8833 | |
18 | L | A | 3.2451 | |
19 | N | A | 1.1975 | |
20 | G | A | 1.1673 | |
21 | C | A | 1.0953 | |
22 | L | A | 1.0762 | |
23 | A | A | -0.1154 | |
24 | R | A | -1.7223 | |
25 | Q | A | -1.1753 | |
26 | S | A | 0.0321 | |
27 | L | A | 0.7901 | |
28 | G | A | 0.5430 | |
29 | V | A | 1.0871 | |
30 | P | A | -0.0155 | |
31 | P | A | -0.9421 | |
32 | Q | A | -1.5483 | |
33 | L | A | -1.1233 | |
34 | Q | A | -2.0059 | |
35 | N | A | -2.3524 | |
36 | E | A | -2.0295 | |
37 | C | A | -1.6092 | |
38 | N | A | -2.8321 | |
39 | L | A | 0.0000 | |
40 | D | A | -3.3168 | |
41 | N | A | -3.0061 | |
42 | L | A | 0.0000 | |
43 | D | A | -2.4544 | |
44 | V | A | 0.0000 | |
45 | L | A | 0.0000 | |
46 | Q | A | -1.8238 | |
47 | A | A | -1.3649 | |
48 | T | A | -1.4410 | |
49 | E | A | -2.1484 | |
50 | T | A | -1.4996 | |
51 | I | A | 0.0000 | |
52 | K | A | -2.6099 | |
53 | S | A | -2.0771 | |
54 | E | A | -1.9396 | |
55 | A | A | 0.0000 | |
56 | G | A | -1.2306 | |
57 | Q | A | -1.1590 | |
58 | I | A | 0.0000 | |
59 | E | A | -1.2103 | |
60 | Y | A | 0.0000 | |
61 | W | A | 0.0000 | |
62 | D | A | -1.7280 | |
63 | H | A | 0.0000 | |
64 | N | A | -1.5383 | |
65 | H | A | -1.1541 | |
66 | P | A | -1.1214 | |
67 | Q | A | 0.0000 | |
68 | L | A | 0.0000 | |
69 | R | A | -1.5292 | |
70 | C | A | 0.0000 | |
71 | V | A | 0.0000 | |
72 | G | A | 0.0000 | |
73 | V | A | 0.0000 | |
74 | S | A | 0.0000 | |
75 | V | A | 0.0000 | |
76 | A | A | 0.0000 | |
77 | R | A | -0.2153 | |
78 | Y | A | 0.0000 | |
79 | V | A | -0.2547 | |
80 | I | A | 0.0000 | |
81 | E | A | -1.6601 | |
82 | Q | A | -2.2082 | |
83 | G | A | -1.4517 | |
84 | G | A | 0.0000 | |
85 | L | A | -0.0946 | |
86 | Y | A | 0.0000 | |
87 | L | A | 0.0000 | |
88 | P | A | 0.4279 | |
89 | T | A | 0.0000 | |
90 | F | A | 0.5197 | |
91 | F | A | 0.0000 | |
92 | T | A | -0.2528 | |
93 | S | A | 0.0000 | |
94 | P | A | 0.0000 | |
95 | K | A | 0.0000 | |
96 | I | A | 0.0000 | |
97 | S | A | 0.0000 | |
98 | Y | A | 0.0000 | |
99 | V | A | 0.0000 | |
100 | V | A | -0.7153 | |
101 | Q | A | -1.3453 | |
102 | G | A | -1.8712 | |
103 | T | A | -1.6515 | |
104 | G | A | 0.0000 | |
105 | I | A | 0.0000 | |
106 | S | A | 0.0000 | |
107 | G | A | 0.0000 | |
108 | R | A | 0.2598 | |
109 | V | A | 0.7460 | |
110 | V | A | 0.8269 | |
111 | P | A | 0.0135 | |
112 | G | A | -0.4454 | |
113 | C | A | -0.4095 | |
114 | A | A | -0.8446 | |
115 | E | A | -1.5413 | |
116 | T | A | -0.9348 | |
117 | F | A | -0.3920 | |
118 | M | A | -0.1103 | |
119 | D | A | -0.7380 | |
120 | S | A | -0.9000 | |
121 | Q | A | -1.6900 | |
188 | G | A | -0.7655 | |
189 | F | A | -0.3426 | |
190 | R | A | -2.0518 | |
191 | D | A | -1.6056 | |
192 | M | A | -0.2605 | |
193 | H | A | -0.6348 | |
194 | Q | A | -0.8638 | |
195 | K | A | -1.1684 | |
196 | V | A | 0.0000 | |
197 | E | A | 0.0000 | |
198 | H | A | -0.3815 | |
199 | V | A | 0.0000 | |
200 | R | A | -1.9609 | |
201 | R | A | -2.4240 | |
202 | G | A | 0.0000 | |
203 | D | A | 0.0000 | |
204 | V | A | 0.0000 | |
205 | F | A | 0.0000 | |
206 | A | A | 0.0000 | |
207 | N | A | 0.0000 | |
208 | T | A | 0.0106 | |
209 | P | A | -0.2589 | |
210 | G | A | -0.0100 | |
211 | S | A | 0.0000 | |
212 | A | A | 0.0000 | |
213 | H | A | 0.0000 | |
214 | W | A | 0.3497 | |
215 | I | A | 0.0000 | |
216 | Y | A | -0.0049 | |
217 | N | A | 0.0000 | |
218 | S | A | -1.0372 | |
219 | G | A | -1.8676 | |
220 | E | A | -2.8503 | |
221 | Q | A | -2.5105 | |
222 | P | A | -1.4885 | |
223 | L | A | 0.0000 | |
224 | V | A | -0.4692 | |
225 | I | A | 0.0000 | |
226 | I | A | 0.0000 | |
227 | A | A | 0.0000 | |
228 | L | A | 0.0000 | |
229 | L | A | 0.0000 | |
230 | D | A | 0.0000 | |
231 | I | A | 0.0000 | |
232 | A | A | -0.2729 | |
233 | N | A | 0.0000 | |
234 | Y | A | 0.9837 | |
235 | Q | A | 0.2470 | |
236 | N | A | 0.0000 | |
237 | Q | A | -0.4421 | |
238 | L | A | 0.4723 | |
239 | D | A | -0.7149 | |
240 | R | A | -1.4329 | |
241 | N | A | -1.1605 | |
242 | P | A | 0.0000 | |
243 | R | A | -0.7474 | |
244 | V | A | 0.1094 | |
245 | F | A | 0.5656 | |
246 | H | A | 0.0000 | |
247 | L | A | 0.7589 | |
248 | A | A | 0.2757 | |
249 | G | A | 0.0000 | |
250 | N | A | 0.0000 | |
251 | N | A | 0.0000 | |
252 | Q | A | -3.5143 | |
253 | Q | A | -3.0300 | |
254 | G | A | 0.0000 | |
255 | G | A | -1.9666 | |
256 | F | A | -1.1358 | |
257 | G | A | -1.3502 | |
258 | G | A | -1.5570 | |
259 | S | A | -1.6276 | |
260 | Q | A | -3.0344 | |
261 | Q | A | -3.2931 | |
262 | Q | A | -3.6110 | |
263 | Q | A | -3.9676 | |
264 | E | A | -4.1198 | |
265 | Q | A | -2.5997 | |
266 | K | A | -1.9122 | |
267 | N | A | 0.0000 | |
268 | L | A | 0.7926 | |
269 | W | A | 0.2332 | |
270 | S | A | -0.4500 | |
271 | G | A | 0.0000 | |
272 | F | A | 0.9423 | |
273 | D | A | -0.6958 | |
274 | A | A | -0.7123 | |
275 | Q | A | -0.6405 | |
276 | V | A | 0.8191 | |
277 | I | A | 0.0000 | |
278 | A | A | 0.0000 | |
279 | Q | A | -1.0857 | |
280 | A | A | -0.1757 | |
281 | L | A | -0.1621 | |
282 | K | A | -1.4459 | |
283 | I | A | -0.8450 | |
284 | D | A | -1.4431 | |
285 | V | A | -0.8668 | |
286 | Q | A | -1.2794 | |
287 | L | A | -0.3093 | |
288 | A | A | 0.0000 | |
289 | Q | A | -1.5380 | |
290 | Q | A | -1.5734 | |
291 | L | A | -0.3153 | |
292 | Q | A | 0.0000 | |
293 | N | A | -1.8359 | |
294 | Q | A | -2.3178 | |
295 | Q | A | -2.3909 | |
296 | D | A | -2.0440 | |
297 | S | A | -1.8619 | |
298 | R | A | -2.1804 | |
299 | G | A | 0.0000 | |
300 | N | A | 0.0000 | |
301 | I | A | 0.0000 | |
302 | V | A | 0.0000 | |
303 | R | A | -1.4692 | |
304 | V | A | -0.9779 | |
305 | K | A | -1.8830 | |
306 | G | A | -1.4231 | |
307 | P | A | -0.8740 | |
308 | F | A | -0.3576 | |
309 | Q | A | -1.0462 | |
310 | V | A | -0.2114 | |
311 | V | A | -0.5769 | |
312 | R | A | -0.8152 | |
313 | P | A | -0.5190 | |
314 | P | A | -0.4265 | |
315 | L | A | 0.0051 | |
316 | R | A | -2.0255 | |
317 | Q | A | -1.9092 | |
318 | P | A | -0.9756 | |
319 | Y | A | -0.6511 | |
320 | E | A | -2.6365 | |
321 | S | A | -2.4620 | |
322 | E | A | -3.0122 | |
323 | E | A | -3.1205 | |
324 | W | A | -1.6055 | |
325 | R | A | -2.8352 | |
326 | H | A | -2.4047 | |
327 | P | A | -2.0231 | |
328 | R | A | -2.9364 | |
329 | S | A | -1.9724 | |
330 | P | A | -1.7248 | |
331 | Q | A | -2.1674 | |
332 | G | A | -1.9313 | |
333 | N | A | -2.2506 | |
334 | G | A | -1.2860 | |
335 | L | A | -0.0425 | |
336 | E | A | -2.0778 | |
337 | E | A | -2.2720 | |
338 | T | A | -0.4921 | |
339 | I | A | 1.4327 | |
340 | C | A | 0.0427 | |
341 | S | A | -0.9012 | |
342 | M | A | -0.4574 | |
343 | R | A | -1.5366 | |
344 | S | A | 0.0000 | |
345 | H | A | -0.7247 | |
346 | E | A | 0.0000 | |
347 | N | A | -1.0424 | |
348 | I | A | 0.0000 | |
349 | D | A | 0.0000 | |
350 | D | A | -1.3181 | |
351 | P | A | -0.7849 | |
352 | A | A | -0.7136 | |
353 | R | A | -1.3147 | |
354 | A | A | -0.9493 | |
355 | D | A | -1.4680 | |
356 | V | A | -0.0412 | |
357 | Y | A | 0.6874 | |
358 | K | A | 0.0599 | |
359 | P | A | -0.3319 | |
360 | S | A | -0.8412 | |
361 | L | A | 0.0000 | |
362 | G | A | 0.0000 | |
363 | R | A | 0.0000 | |
364 | V | A | -0.0649 | |
365 | T | A | 0.0000 | |
366 | S | A | -0.5851 | |
367 | V | A | 0.0000 | |
368 | N | A | -0.5023 | |
369 | S | A | -0.4051 | |
370 | Y | A | 0.8298 | |
371 | T | A | 0.2610 | |
372 | L | A | 0.0000 | |
373 | P | A | -0.6090 | |
374 | I | A | 0.0000 | |
375 | L | A | 0.0000 | |
376 | E | A | -1.7654 | |
377 | Y | A | -0.4094 | |
378 | V | A | 0.0000 | |
379 | R | A | -1.4044 | |
380 | L | A | 0.0000 | |
381 | S | A | 0.0000 | |
382 | A | A | 0.0000 | |
383 | T | A | 0.0000 | |
384 | R | A | 0.0000 | |
385 | G | A | 0.0000 | |
386 | V | A | 0.0000 | |
387 | L | A | 0.0000 | |
388 | Q | A | -2.2118 | |
389 | G | A | -2.3935 | |
390 | N | A | -2.7111 | |
391 | A | A | 0.0000 | |
392 | M | A | -1.0821 | |
393 | V | A | 0.0000 | |
394 | L | A | 0.0000 | |
395 | P | A | 0.1678 | |
396 | K | A | 0.0000 | |
397 | Y | A | 0.4954 | |
398 | N | A | 0.0000 | |
399 | M | A | 0.5110 | |
400 | N | A | -0.1738 | |
401 | A | A | 0.0000 | |
402 | N | A | -0.7125 | |
403 | E | A | 0.0000 | |
404 | I | A | 0.0000 | |
405 | L | A | 0.0000 | |
406 | Y | A | 0.0000 | |
407 | C | A | 0.0000 | |
408 | T | A | 0.0000 | |
409 | G | A | -1.3365 | |
410 | G | A | -1.9876 | |
411 | Q | A | -2.4503 | |
412 | G | A | 0.0000 | |
413 | R | A | -2.4665 | |
414 | I | A | 0.0000 | |
415 | Q | A | -1.3058 | |
416 | V | A | 0.0000 | |
417 | V | A | -1.4454 | |
418 | N | A | 0.0000 | |
419 | D | A | -3.1808 | |
420 | N | A | -3.1133 | |
421 | G | A | -2.2288 | |
422 | Q | A | -2.8115 | |
423 | N | A | -2.5012 | |
424 | V | A | 0.0000 | |
425 | L | A | 0.0000 | |
426 | D | A | -2.1630 | |
427 | Q | A | -2.5031 | |
428 | Q | A | -2.4341 | |
429 | V | A | 0.0000 | |
430 | Q | A | -2.6822 | |
431 | K | A | -2.4994 | |
432 | G | A | -1.5497 | |
433 | Q | A | -1.5457 | |
434 | L | A | 0.0000 | |
435 | V | A | 0.0000 | |
436 | V | A | 0.0000 | |
437 | I | A | 0.0000 | |
438 | P | A | 0.0000 | |
439 | Q | A | -1.1789 | |
440 | G | A | -1.0248 | |
441 | F | A | 0.0000 | |
442 | A | A | -0.2348 | |
443 | Y | A | 0.0000 | |
444 | V | A | -0.0547 | |
445 | V | A | 0.0000 | |
446 | Q | A | -1.6988 | |
447 | S | A | 0.0000 | |
448 | H | A | -2.6768 | |
449 | G | A | -2.2644 | |
450 | N | A | -2.5711 | |
451 | K | A | -2.2726 | |
452 | F | A | 0.0000 | |
453 | E | A | -1.0291 | |
454 | W | A | 0.0000 | |
455 | I | A | 0.0000 | |
456 | S | A | 0.0000 | |
457 | F | A | 0.0000 | |
458 | K | A | 0.0000 | |
459 | T | A | -0.6472 | |
460 | N | A | -1.0125 | |
461 | E | A | -1.1873 | |
462 | N | A | -0.5390 | |
463 | A | A | 0.1245 | |
464 | M | A | 1.1499 | |
465 | I | A | 1.2432 | |
466 | S | A | 1.0085 | |
467 | T | A | 0.0000 | |
468 | L | A | 0.6417 | |
469 | A | A | 0.2880 | |
470 | G | A | 0.0000 | |
471 | R | A | -1.1518 | |
472 | T | A | -0.5486 | |
473 | S | A | 0.0000 | |
474 | L | A | 0.8855 | |
475 | L | A | 0.9179 | |
476 | R | A | -0.3232 | |
477 | A | A | 0.0713 | |
478 | L | A | 0.5500 | |
479 | P | A | -0.1337 | |
480 | L | A | -1.1129 | |
481 | E | A | -1.6097 | |
482 | V | A | 0.2002 | |
483 | I | A | 0.0000 | |
484 | S | A | -1.3255 | |
485 | N | A | -1.4634 | |
486 | G | A | -0.5045 | |
487 | F | A | 0.3270 | |
488 | Q | A | -1.0662 | |
489 | I | A | -1.0423 | |
490 | S | A | -1.7219 | |
491 | P | A | -2.2718 | |
492 | E | A | -3.1639 | |
493 | E | A | -2.5063 | |
494 | A | A | 0.0000 | |
495 | R | A | -3.2709 | |
496 | K | A | -2.8316 | |
497 | I | A | -0.6787 | |
498 | K | A | -0.7520 | |
499 | F | A | -0.3008 | |
500 | N | A | -1.0730 | |
501 | T | A | -0.0609 | |
502 | L | A | 0.7294 | |
503 | E | A | -0.4454 | |
504 | T | A | -0.4379 | |
505 | T | A | 0.0303 | |
506 | L | A | 0.0000 | |
507 | T | A | -1.0463 | |
508 | R | A | -2.3686 | |
509 | A | A | -1.7992 | |
510 | A | A | -1.5690 | |
511 | G | A | -2.2484 | |
512 | R | A | -2.8945 | |
513 | Q | A | -2.7321 | |
514 | Q | A | -2.1103 | |
515 | Q | A | -2.3151 | |
516 | Q | A | -2.3312 | |
517 | L | A | -0.4972 | |
518 | I | A | 0.1503 | |
519 | E | A | -1.7915 | |
520 | E | A | -1.4775 | |
521 | I | A | 1.3738 | |
522 | V | A | 1.0571 | |
523 | E | A | -1.1407 | |
524 | A | A | -0.1877 |
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 | -0.2692 | 7.0174 | View | CSV | PDB |
4.5 | -0.3223 | 7.0174 | View | CSV | PDB |
5.0 | -0.3901 | 7.0174 | View | CSV | PDB |
5.5 | -0.4619 | 7.0174 | View | CSV | PDB |
6.0 | -0.5258 | 7.0174 | View | CSV | PDB |
6.5 | -0.5721 | 7.0174 | View | CSV | PDB |
7.0 | -0.597 | 7.0174 | View | CSV | PDB |
7.5 | -0.6052 | 7.0174 | View | CSV | PDB |
8.0 | -0.6028 | 7.0174 | View | CSV | PDB |
8.5 | -0.593 | 7.0174 | View | CSV | PDB |
9.0 | -0.5771 | 7.0174 | View | CSV | PDB |