| Chain sequence(s) |
A: GYCFTEVLQNMCQIGSSNRNPVTKSECCCDGGRGWGPHCEICPFQGTVAFKKLCPHGRGFMTNGADIDECKVIHDVCRNGECVNDRGSYHCICKTGYTPDITGTSCVDLNECNQAPKPCNFICKNTEGSYQCSCPKGYILQEDGRSCKDLDECATKQHNCQFLCVNTIGGFTCKCPPGFTQHHTSCIDNNECTSDINLCGSKGICQNTPGSFTCECQRGFSLDQTGSSCEDVDECEGNHRCQHGCQNIIGGYRCSCPQGYLQHYQWNQCVDENECLSAHICGGASCHNTLGSYKCMCPAGFQYEQFSGGCQDINECGSAQAPCSYGCSNTEGGYLCGCPPGYFRIGQGHCVSGMGMGRGNPEPPVSGEMDDNSLSPEACYECKINGYPKRGRKRR
input PDB |
| Selected Chain(s) | A |
| 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 A 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 (00:03:29)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8f8e9fb59503894/tmp/folded.pdb (00:03:29)
[INFO] Main: Simulation completed successfully. (00:05:08)
|
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 |
|---|---|---|---|---|
| 2337 | G | A | -0.9039 | |
| 2338 | Y | A | -0.3192 | |
| 2339 | C | A | 0.0000 | |
| 2340 | F | A | 0.0000 | |
| 2341 | T | A | -1.4329 | |
| 2342 | E | A | -1.2727 | |
| 2343 | V | A | -0.4451 | |
| 2344 | L | A | -0.2028 | |
| 2345 | Q | A | -1.0383 | |
| 2346 | N | A | -1.4081 | |
| 2347 | M | A | 0.3330 | |
| 2348 | C | A | 0.0193 | |
| 2349 | Q | A | 0.2471 | |
| 2350 | I | A | 1.3920 | |
| 2351 | G | A | -0.0811 | |
| 2352 | S | A | 0.0000 | |
| 2353 | S | A | 0.0000 | |
| 2354 | N | A | -1.5413 | |
| 2355 | R | A | -1.8158 | |
| 2356 | N | A | -1.6977 | |
| 2357 | P | A | -1.0964 | |
| 2358 | V | A | 0.0000 | |
| 2359 | T | A | -0.5087 | |
| 2360 | K | A | -0.8162 | |
| 2361 | S | A | -0.6454 | |
| 2362 | E | A | 0.0000 | |
| 2363 | C | A | 0.0000 | |
| 2364 | C | A | 0.0000 | |
| 2365 | C | A | 0.0000 | |
| 2366 | D | A | -1.4338 | |
| 2367 | G | A | -1.2266 | |
| 2368 | G | A | -1.0775 | |
| 2369 | R | A | -1.9152 | |
| 2370 | G | A | 0.0000 | |
| 2371 | W | A | -0.7563 | |
| 2372 | G | A | 0.0000 | |
| 2373 | P | A | -0.8484 | |
| 2374 | H | A | -1.2882 | |
| 2375 | C | A | -0.9021 | |
| 2376 | E | A | -1.4097 | |
| 2377 | I | A | -0.0686 | |
| 2378 | C | A | 0.0000 | |
| 2379 | P | A | 0.1615 | |
| 2380 | F | A | 1.0423 | |
| 2381 | Q | A | -0.9141 | |
| 2382 | G | A | -0.5462 | |
| 2383 | T | A | 0.1610 | |
| 2384 | V | A | 0.7342 | |
| 2385 | A | A | -0.1071 | |
| 2386 | F | A | 0.0000 | |
| 2387 | K | A | -2.3565 | |
| 2388 | K | A | -2.1217 | |
| 2389 | L | A | -1.3336 | |
| 2390 | C | A | 0.0000 | |
| 2391 | P | A | -2.0759 | |
| 2392 | H | A | -2.1619 | |
| 2393 | G | A | -2.2230 | |
| 2394 | R | A | -2.6435 | |
| 2395 | G | A | 0.0000 | |
| 2396 | F | A | -1.4381 | |
| 2397 | M | A | -1.0259 | |
| 2398 | T | A | -1.3733 | |
| 2399 | N | A | -1.4625 | |
| 2400 | G | A | -1.0464 | |
| 2401 | A | A | -1.0474 | |
| 2402 | D | A | -1.9388 | |
| 2403 | I | A | 0.0000 | |
| 2404 | D | A | -1.4279 | |
| 2405 | E | A | 0.0000 | |
| 2406 | C | A | -0.9540 | |
| 2407 | K | A | -1.5056 | |
| 2408 | V | A | 0.0000 | |
| 2409 | I | A | -0.9879 | |
| 2410 | H | A | -1.9823 | |
| 2411 | D | A | -2.8337 | |
| 2412 | V | A | -1.6175 | |
| 2413 | C | A | 0.0000 | |
| 2414 | R | A | -2.8750 | |
| 2415 | N | A | -2.1556 | |
| 2416 | G | A | -1.8168 | |
| 2417 | E | A | -1.8914 | |
| 2418 | C | A | -0.8687 | |
| 2419 | V | A | 0.0281 | |
| 2420 | N | A | -1.3605 | |
| 2421 | D | A | -2.1205 | |
| 2422 | R | A | -2.6681 | |
| 2423 | G | A | -2.0509 | |
| 2424 | S | A | -1.6040 | |
| 2425 | Y | A | -0.8917 | |
| 2426 | H | A | -0.3178 | |
| 2427 | C | A | 0.0000 | |
| 2428 | I | A | 0.7060 | |
| 2429 | C | A | -0.7157 | |
| 2430 | K | A | -1.9190 | |
| 2431 | T | A | -0.7601 | |
| 2432 | G | A | 0.0000 | |
| 2433 | Y | A | -0.7607 | |
| 2434 | T | A | 0.1888 | |
| 2435 | P | A | 0.4056 | |
| 2436 | D | A | 0.5831 | |
| 2437 | I | A | 1.7782 | |
| 2438 | T | A | 0.6019 | |
| 2439 | G | A | 0.5306 | |
| 2440 | T | A | 0.2106 | |
| 2441 | S | A | -0.3575 | |
| 2442 | C | A | -0.2902 | |
| 2443 | V | A | 0.0683 | |
| 2444 | D | A | -1.0731 | |
| 2445 | L | A | -0.8160 | |
| 2446 | N | A | -1.9308 | |
| 2447 | E | A | 0.0000 | |
| 2448 | C | A | -1.7160 | |
| 2449 | N | A | -2.1278 | |
| 2450 | Q | A | -1.7754 | |
| 2451 | A | A | -1.0710 | |
| 2452 | P | A | -1.2249 | |
| 2453 | K | A | -1.7984 | |
| 2454 | P | A | 0.0000 | |
| 2455 | C | A | 0.0000 | |
| 2456 | N | A | -1.0844 | |
| 2457 | F | A | 0.6644 | |
| 2458 | I | A | 0.3608 | |
| 2459 | C | A | -1.0398 | |
| 2460 | K | A | -1.8768 | |
| 2461 | N | A | -2.3276 | |
| 2462 | T | A | -1.9031 | |
| 2463 | E | A | -2.0519 | |
| 2464 | G | A | -1.4175 | |
| 2465 | S | A | -1.2485 | |
| 2466 | Y | A | -1.2030 | |
| 2467 | Q | A | -1.5782 | |
| 2468 | C | A | 0.0000 | |
| 2469 | S | A | -0.2711 | |
| 2470 | C | A | 0.1206 | |
| 2471 | P | A | -0.2422 | |
| 2472 | K | A | -1.5198 | |
| 2473 | G | A | 0.0000 | |
| 2474 | Y | A | 0.0899 | |
| 2475 | I | A | 0.2951 | |
| 2476 | L | A | -0.5285 | |
| 2477 | Q | A | -2.1707 | |
| 2478 | E | A | -3.0135 | |
| 2479 | D | A | -3.2469 | |
| 2480 | G | A | -2.4798 | |
| 2481 | R | A | -2.5266 | |
| 2482 | S | A | -1.5658 | |
| 2483 | C | A | -0.7785 | |
| 2484 | K | A | -0.6589 | |
| 2485 | D | A | -0.2267 | |
| 2486 | L | A | -0.1199 | |
| 2487 | D | A | -0.7880 | |
| 2488 | E | A | 0.0000 | |
| 2489 | C | A | -0.8162 | |
| 2490 | A | A | -0.8698 | |
| 2491 | T | A | -1.3941 | |
| 2492 | K | A | -2.6021 | |
| 2493 | Q | A | -2.3551 | |
| 2494 | H | A | -1.9540 | |
| 2495 | N | A | -1.8822 | |
| 2496 | C | A | -0.9861 | |
| 2497 | Q | A | -0.8785 | |
| 2498 | F | A | 0.8691 | |
| 2499 | L | A | 1.1973 | |
| 2500 | C | A | 0.3694 | |
| 2501 | V | A | 0.6120 | |
| 2502 | N | A | 0.4010 | |
| 2503 | T | A | 0.9134 | |
| 2504 | I | A | 1.6398 | |
| 2505 | G | A | 0.3179 | |
| 2506 | G | A | 0.3762 | |
| 2507 | F | A | 0.6609 | |
| 2508 | T | A | 0.1883 | |
| 2509 | C | A | -0.4403 | |
| 2510 | K | A | -0.9214 | |
| 2511 | C | A | -0.2865 | |
| 2512 | P | A | -0.0462 | |
| 2513 | P | A | -0.5154 | |
| 2514 | G | A | -0.3917 | |
| 2515 | F | A | -0.3920 | |
| 2516 | T | A | -0.6595 | |
| 2517 | Q | A | -1.6156 | |
| 2518 | H | A | -1.6201 | |
| 2519 | H | A | -1.8097 | |
| 2520 | T | A | -1.4194 | |
| 2521 | S | A | -1.0790 | |
| 2522 | C | A | -0.3245 | |
| 2523 | I | A | 0.4558 | |
| 2524 | D | A | -0.5433 | |
| 2525 | N | A | -0.9340 | |
| 2526 | N | A | -1.4454 | |
| 2527 | E | A | -0.9839 | |
| 2528 | C | A | -0.3054 | |
| 2529 | T | A | -0.5472 | |
| 2530 | S | A | -0.7329 | |
| 2531 | D | A | -0.7252 | |
| 2532 | I | A | 1.0555 | |
| 2533 | N | A | -0.4864 | |
| 2534 | L | A | 0.1011 | |
| 2535 | C | A | 0.0000 | |
| 2536 | G | A | -0.5451 | |
| 2537 | S | A | -0.6458 | |
| 2538 | K | A | -1.4826 | |
| 2539 | G | A | -0.8922 | |
| 2540 | I | A | 0.8605 | |
| 2541 | C | A | 0.0320 | |
| 2542 | Q | A | -1.1396 | |
| 2543 | N | A | -1.0202 | |
| 2544 | T | A | -0.8056 | |
| 2545 | P | A | -0.4761 | |
| 2546 | G | A | -0.4678 | |
| 2547 | S | A | -0.6314 | |
| 2548 | F | A | -0.3921 | |
| 2549 | T | A | -0.3463 | |
| 2550 | C | A | 0.0000 | |
| 2551 | E | A | -1.6875 | |
| 2552 | C | A | -1.5778 | |
| 2553 | Q | A | -2.4339 | |
| 2554 | R | A | -2.6682 | |
| 2555 | G | A | -1.3613 | |
| 2556 | F | A | -1.5942 | |
| 2557 | S | A | -1.4470 | |
| 2558 | L | A | -0.7260 | |
| 2559 | D | A | -1.2954 | |
| 2560 | Q | A | -1.5756 | |
| 2561 | T | A | -0.7938 | |
| 2562 | G | A | -0.7439 | |
| 2563 | S | A | -0.7430 | |
| 2564 | S | A | -0.9381 | |
| 2565 | C | A | 0.0000 | |
| 2566 | E | A | -2.0992 | |
| 2567 | D | A | -1.2289 | |
| 2568 | V | A | -1.1752 | |
| 2569 | D | A | -2.4418 | |
| 2570 | E | A | -3.0265 | |
| 2571 | C | A | -2.8319 | |
| 2572 | E | A | -3.0810 | |
| 2573 | G | A | -2.7037 | |
| 2574 | N | A | -2.5470 | |
| 2575 | H | A | -2.8322 | |
| 2576 | R | A | -2.8571 | |
| 2577 | C | A | -2.6372 | |
| 2578 | Q | A | -2.3577 | |
| 2579 | H | A | -1.9322 | |
| 2580 | G | A | -1.7325 | |
| 2581 | C | A | -2.2859 | |
| 2582 | Q | A | -2.4096 | |
| 2583 | N | A | -1.6810 | |
| 2584 | I | A | 0.2931 | |
| 2585 | I | A | 1.6347 | |
| 2586 | G | A | -0.2045 | |
| 2587 | G | A | -0.5167 | |
| 2588 | Y | A | -1.0141 | |
| 2589 | R | A | -2.3212 | |
| 2590 | C | A | 0.0000 | |
| 2591 | S | A | -1.3937 | |
| 2592 | C | A | -0.7573 | |
| 2593 | P | A | -0.7331 | |
| 2594 | Q | A | -1.0983 | |
| 2595 | G | A | 0.0000 | |
| 2596 | Y | A | 0.1645 | |
| 2597 | L | A | 0.6285 | |
| 2598 | Q | A | -0.1344 | |
| 2599 | H | A | 0.0228 | |
| 2600 | Y | A | 0.5529 | |
| 2601 | Q | A | -0.3371 | |
| 2602 | W | A | 0.2279 | |
| 2603 | N | A | -0.9698 | |
| 2604 | Q | A | -1.4644 | |
| 2605 | C | A | -0.1801 | |
| 2606 | V | A | 0.5293 | |
| 2607 | D | A | -0.0484 | |
| 2608 | E | A | -0.2330 | |
| 2609 | N | A | -0.1460 | |
| 2610 | E | A | -0.2392 | |
| 2611 | C | A | 0.3020 | |
| 2612 | L | A | 1.2103 | |
| 2613 | S | A | 0.4559 | |
| 2614 | A | A | 0.0697 | |
| 2615 | H | A | -0.7598 | |
| 2616 | I | A | 0.0624 | |
| 2617 | C | A | 0.0000 | |
| 2618 | G | A | -0.9582 | |
| 2619 | G | A | -0.7254 | |
| 2620 | A | A | -0.5650 | |
| 2621 | S | A | -0.3420 | |
| 2622 | C | A | -0.1809 | |
| 2623 | H | A | -0.8783 | |
| 2624 | N | A | -0.5170 | |
| 2625 | T | A | -0.0508 | |
| 2626 | L | A | 1.3116 | |
| 2627 | G | A | 0.3250 | |
| 2628 | S | A | -0.2815 | |
| 2629 | Y | A | -0.2015 | |
| 2630 | K | A | -1.0966 | |
| 2631 | C | A | -0.4977 | |
| 2632 | M | A | 0.1486 | |
| 2633 | C | A | -0.1967 | |
| 2634 | P | A | -0.2390 | |
| 2635 | A | A | -0.0746 | |
| 2636 | G | A | -0.7703 | |
| 2637 | F | A | -0.8143 | |
| 2638 | Q | A | -0.9763 | |
| 2639 | Y | A | -0.5543 | |
| 2640 | E | A | -0.7561 | |
| 2641 | Q | A | -0.5969 | |
| 2642 | F | A | 1.1116 | |
| 2643 | S | A | 0.0418 | |
| 2644 | G | A | -0.4535 | |
| 2645 | G | A | -0.7144 | |
| 2646 | C | A | -0.8202 | |
| 2647 | Q | A | -1.6207 | |
| 2648 | D | A | -1.6198 | |
| 2649 | I | A | -0.9750 | |
| 2650 | N | A | -1.7514 | |
| 2651 | E | A | -0.8578 | |
| 2652 | C | A | -0.6399 | |
| 2653 | G | A | -1.0531 | |
| 2654 | S | A | -0.9372 | |
| 2655 | A | A | -0.7044 | |
| 2656 | Q | A | -1.3009 | |
| 2657 | A | A | -0.6173 | |
| 2658 | P | A | -0.2214 | |
| 2659 | C | A | 0.0000 | |
| 2660 | S | A | 0.3280 | |
| 2661 | Y | A | 0.9911 | |
| 2662 | G | A | 0.2855 | |
| 2663 | C | A | 0.2080 | |
| 2664 | S | A | -0.2228 | |
| 2665 | N | A | -0.8857 | |
| 2666 | T | A | -1.0618 | |
| 2667 | E | A | -2.2145 | |
| 2668 | G | A | -1.4137 | |
| 2669 | G | A | -0.7118 | |
| 2670 | Y | A | -0.0527 | |
| 2671 | L | A | 0.0599 | |
| 2672 | C | A | 0.0462 | |
| 2673 | G | A | 0.3169 | |
| 2674 | C | A | 0.6033 | |
| 2675 | P | A | 0.4580 | |
| 2676 | P | A | 0.2813 | |
| 2677 | G | A | 0.3057 | |
| 2678 | Y | A | 1.2817 | |
| 2679 | F | A | 1.5362 | |
| 2680 | R | A | -0.4135 | |
| 2681 | I | A | 0.4418 | |
| 2682 | G | A | -0.8269 | |
| 2683 | Q | A | -1.5927 | |
| 2684 | G | A | -1.1444 | |
| 2685 | H | A | -1.0333 | |
| 2686 | C | A | -0.0182 | |
| 2687 | V | A | 0.8630 | |
| 2688 | S | A | 0.6177 | |
| 2689 | G | A | 0.6662 | |
| 2690 | M | A | 0.8289 | |
| 2691 | G | A | 0.0728 | |
| 2692 | M | A | 0.3178 | |
| 2693 | G | A | -1.1332 | |
| 2694 | R | A | -2.4512 | |
| 2695 | G | A | -2.2485 | |
| 2696 | N | A | -2.6242 | |
| 2697 | P | A | -2.1652 | |
| 2698 | E | A | -2.2872 | |
| 2699 | P | A | -1.0441 | |
| 2700 | P | A | -0.1066 | |
| 2701 | V | A | 0.9440 | |
| 2702 | S | A | -0.0443 | |
| 2703 | G | A | -0.9493 | |
| 2704 | E | A | -2.1038 | |
| 2705 | M | A | -1.5468 | |
| 2706 | D | A | -3.1217 | |
| 2707 | D | A | -3.0449 | |
| 2708 | N | A | -2.2447 | |
| 2709 | S | A | -1.0200 | |
| 2710 | L | A | 0.4293 | |
| 2711 | S | A | -0.3500 | |
| 2712 | P | A | -0.5677 | |
| 2713 | E | A | -1.2972 | |
| 2714 | A | A | -0.3844 | |
| 2715 | C | A | 0.5330 | |
| 2716 | Y | A | 0.3827 | |
| 2717 | E | A | -0.9420 | |
| 2718 | C | A | -0.1061 | |
| 2719 | K | A | -1.2384 | |
| 2720 | I | A | 0.5336 | |
| 2721 | N | A | -0.6091 | |
| 2722 | G | A | -0.4129 | |
| 2723 | Y | A | 0.1958 | |
| 2724 | P | A | -1.3147 | |
| 2725 | K | A | -2.8214 | |
| 2726 | R | A | -3.4818 | |
| 2727 | G | A | -3.4675 | |
| 2728 | R | A | -4.3343 | |
| 2729 | K | A | -4.3487 | |
| 2730 | R | A | -4.1627 | |
| 2731 | R | A | -3.4431 |
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 | -0.3605 | 3.3571 | View | CSV | PDB |
| 4.5 | -0.4209 | 3.3579 | View | CSV | PDB |
| 5.0 | -0.4923 | 3.3601 | View | CSV | PDB |
| 5.5 | -0.5606 | 3.3667 | View | CSV | PDB |
| 6.0 | -0.6102 | 3.3832 | View | CSV | PDB |
| 6.5 | -0.632 | 3.4152 | View | CSV | PDB |
| 7.0 | -0.6294 | 3.4615 | View | CSV | PDB |
| 7.5 | -0.6124 | 3.5155 | View | CSV | PDB |
| 8.0 | -0.5872 | 3.5727 | View | CSV | PDB |
| 8.5 | -0.5549 | 3.6308 | View | CSV | PDB |
| 9.0 | -0.5147 | 3.6889 | 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