| Chain sequence(s) |
A: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK
C: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK B: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK input PDB |
| Selected Chain(s) | A,B,C |
| 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 all 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 (00:05:18)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/a0e20bd23166c5f/tmp/folded.pdb (00:05:18)
[INFO] Main: Simulation completed successfully. (00:08:18)
|
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 | -0.3795 | |
| 2 | K | A | -2.6091 | |
| 3 | K | A | -3.4621 | |
| 4 | N | A | -3.4027 | |
| 5 | N | A | -3.4544 | |
| 6 | N | A | -2.7194 | |
| 7 | A | A | -1.8131 | |
| 8 | V | A | 0.0000 | |
| 9 | A | A | 0.0000 | |
| 10 | F | A | 0.0000 | |
| 11 | Y | A | 0.0000 | |
| 12 | A | A | 0.0000 | |
| 13 | Y | A | -0.6608 | |
| 14 | L | A | 0.0000 | |
| 15 | S | A | -1.2092 | |
| 16 | K | A | -2.1612 | |
| 17 | S | A | -1.2981 | |
| 18 | L | A | -0.8910 | |
| 19 | P | A | -1.2693 | |
| 20 | L | A | 0.0000 | |
| 21 | N | A | -1.7939 | |
| 22 | S | A | -0.8791 | |
| 23 | V | A | -0.8043 | |
| 24 | S | A | -1.5590 | |
| 25 | K | A | -2.6146 | |
| 26 | H | A | -1.9742 | |
| 27 | T | A | -1.1038 | |
| 28 | T | A | -0.7505 | |
| 29 | L | A | 0.0000 | |
| 30 | K | A | -2.1551 | |
| 31 | Y | A | 0.0000 | |
| 32 | D | A | -1.8220 | |
| 33 | L | A | -0.4280 | |
| 34 | V | A | -0.5889 | |
| 35 | D | A | -1.5262 | |
| 36 | L | A | 0.0000 | |
| 37 | N | A | -1.1467 | |
| 38 | L | A | -1.0807 | |
| 39 | G | A | -1.7138 | |
| 40 | N | A | -1.7278 | |
| 41 | G | A | 0.0000 | |
| 42 | Y | A | 0.0000 | |
| 43 | D | A | -2.5317 | |
| 44 | K | A | -2.9182 | |
| 45 | Q | A | -2.6553 | |
| 46 | T | A | -1.7000 | |
| 47 | G | A | 0.0000 | |
| 48 | L | A | -1.0559 | |
| 49 | F | A | 0.0000 | |
| 50 | T | A | -1.8288 | |
| 51 | A | A | 0.0000 | |
| 52 | P | A | -2.1491 | |
| 53 | S | A | -2.5452 | |
| 54 | N | A | -2.9840 | |
| 55 | G | A | -1.5803 | |
| 56 | L | A | -0.7663 | |
| 57 | Y | A | 0.0000 | |
| 58 | V | A | 0.0000 | |
| 59 | F | A | 0.0000 | |
| 60 | N | A | 0.0000 | |
| 61 | V | A | 0.0000 | |
| 62 | A | A | 0.0000 | |
| 63 | T | A | 0.0000 | |
| 64 | G | A | 0.0000 | |
| 65 | A | A | 0.0000 | |
| 66 | Q | A | -0.7311 | |
| 67 | D | A | -0.5378 | |
| 68 | S | A | -0.6973 | |
| 69 | S | A | 0.0000 | |
| 70 | H | A | -0.7694 | |
| 71 | S | A | 0.0000 | |
| 72 | C | A | 0.0000 | |
| 73 | L | A | 0.0000 | |
| 74 | E | A | 0.0000 | |
| 75 | L | A | 0.0000 | |
| 76 | A | A | 0.0000 | |
| 77 | V | A | 0.0000 | |
| 78 | N | A | -1.4311 | |
| 79 | G | A | -0.3637 | |
| 80 | V | A | 1.2764 | |
| 81 | V | A | 0.6243 | |
| 82 | K | A | -0.1565 | |
| 83 | D | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | T | A | 0.0000 | |
| 86 | W | A | 0.0000 | |
| 87 | A | A | 0.0000 | |
| 88 | D | A | 0.0000 | |
| 89 | S | A | 0.0000 | |
| 90 | M | A | -0.3351 | |
| 91 | D | A | -0.9938 | |
| 92 | H | A | -0.2740 | |
| 93 | V | A | 0.7467 | |
| 94 | D | A | 0.0000 | |
| 95 | R | A | -0.2524 | |
| 96 | A | A | -0.0850 | |
| 97 | F | A | 0.0000 | |
| 98 | A | A | 0.0000 | |
| 99 | T | A | 0.0000 | |
| 100 | T | A | 0.0000 | |
| 101 | A | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | P | A | 0.0000 | |
| 104 | M | A | 0.0000 | |
| 105 | S | A | -0.9923 | |
| 106 | L | A | 0.0000 | |
| 107 | N | A | -3.2938 | |
| 108 | E | A | -3.8019 | |
| 109 | N | A | -3.2163 | |
| 110 | D | A | -2.7886 | |
| 111 | K | A | -2.1939 | |
| 112 | V | A | 0.0000 | |
| 113 | L | A | -0.3854 | |
| 114 | A | A | 0.0000 | |
| 115 | R | A | -1.0071 | |
| 116 | L | A | 0.0000 | |
| 117 | G | A | 0.0000 | |
| 118 | E | A | -2.7110 | |
| 119 | A | A | -1.5315 | |
| 120 | H | A | -1.2605 | |
| 121 | G | A | -0.8755 | |
| 122 | G | A | -1.4276 | |
| 123 | N | A | -1.9738 | |
| 124 | E | A | -1.8315 | |
| 125 | L | A | 0.0000 | |
| 126 | E | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | N | A | -1.8835 | |
| 129 | K | A | -2.2708 | |
| 130 | Y | A | -1.0828 | |
| 131 | L | A | 0.0000 | |
| 132 | R | A | -0.8425 | |
| 133 | T | A | 0.0000 | |
| 134 | S | A | 0.0000 | |
| 135 | F | A | 0.0000 | |
| 136 | S | A | 0.0000 | |
| 137 | G | A | 0.0000 | |
| 138 | F | A | 0.0000 | |
| 139 | K | A | -1.6165 | |
| 1 | M | B | -0.4126 | |
| 2 | K | B | -2.5842 | |
| 3 | K | B | -3.4455 | |
| 4 | N | B | -3.3991 | |
| 5 | N | B | -3.3777 | |
| 6 | N | B | -2.7044 | |
| 7 | A | B | -1.5532 | |
| 8 | V | B | 0.0000 | |
| 9 | A | B | 0.0000 | |
| 10 | F | B | 0.0000 | |
| 11 | Y | B | 0.0000 | |
| 12 | A | B | 0.0000 | |
| 13 | Y | B | 0.0000 | |
| 14 | L | B | 0.0000 | |
| 15 | S | B | -1.2383 | |
| 16 | K | B | -2.1216 | |
| 17 | S | B | -1.2314 | |
| 18 | L | B | -0.8767 | |
| 19 | P | B | -1.1931 | |
| 20 | L | B | 0.0000 | |
| 21 | N | B | -1.7642 | |
| 22 | S | B | -0.8802 | |
| 23 | V | B | -0.7721 | |
| 24 | S | B | -1.4085 | |
| 25 | K | B | -2.2548 | |
| 26 | H | B | -1.9986 | |
| 27 | T | B | -1.1979 | |
| 28 | T | B | -0.8889 | |
| 29 | L | B | 0.0000 | |
| 30 | K | B | -2.5052 | |
| 31 | Y | B | 0.0000 | |
| 32 | D | B | -1.8670 | |
| 33 | L | B | -0.3824 | |
| 34 | V | B | -0.4763 | |
| 35 | D | B | -1.5227 | |
| 36 | L | B | 0.0000 | |
| 37 | N | B | -1.0196 | |
| 38 | L | B | -0.9575 | |
| 39 | G | B | -1.6367 | |
| 40 | N | B | -1.6085 | |
| 41 | G | B | 0.0000 | |
| 42 | Y | B | 0.0000 | |
| 43 | D | B | -2.1701 | |
| 44 | K | B | -2.7347 | |
| 45 | Q | B | -2.5942 | |
| 46 | T | B | -1.6793 | |
| 47 | G | B | 0.0000 | |
| 48 | L | B | -1.0017 | |
| 49 | F | B | 0.0000 | |
| 50 | T | B | -1.8017 | |
| 51 | A | B | 0.0000 | |
| 52 | P | B | -2.1432 | |
| 53 | S | B | -2.5511 | |
| 54 | N | B | -3.0172 | |
| 55 | G | B | -1.9774 | |
| 56 | L | B | -0.8368 | |
| 57 | Y | B | 0.0000 | |
| 58 | V | B | 0.0000 | |
| 59 | F | B | 0.0000 | |
| 60 | N | B | 0.0000 | |
| 61 | V | B | 0.0000 | |
| 62 | A | B | 0.0000 | |
| 63 | T | B | 0.0000 | |
| 64 | G | B | 0.0000 | |
| 65 | A | B | 0.0000 | |
| 66 | Q | B | -0.7559 | |
| 67 | D | B | -0.5767 | |
| 68 | S | B | -0.6933 | |
| 69 | S | B | 0.0000 | |
| 70 | H | B | -0.7480 | |
| 71 | S | B | 0.0000 | |
| 72 | C | B | 0.0000 | |
| 73 | L | B | 0.0000 | |
| 74 | E | B | 0.0000 | |
| 75 | L | B | 0.0000 | |
| 76 | A | B | 0.0000 | |
| 77 | V | B | 0.0000 | |
| 78 | N | B | -1.4413 | |
| 79 | G | B | -0.4000 | |
| 80 | V | B | 1.2924 | |
| 81 | V | B | 0.6601 | |
| 82 | K | B | -0.1632 | |
| 83 | D | B | 0.0000 | |
| 84 | L | B | 0.0000 | |
| 85 | T | B | 0.0000 | |
| 86 | W | B | 0.0000 | |
| 87 | A | B | 0.0000 | |
| 88 | D | B | 0.0000 | |
| 89 | S | B | 0.0000 | |
| 90 | M | B | -0.3247 | |
| 91 | D | B | -0.9768 | |
| 92 | H | B | -0.2955 | |
| 93 | V | B | 0.6586 | |
| 94 | D | B | 0.0000 | |
| 95 | R | B | -0.3071 | |
| 96 | A | B | -0.1113 | |
| 97 | F | B | 0.0000 | |
| 98 | A | B | 0.0000 | |
| 99 | T | B | 0.0000 | |
| 100 | T | B | 0.0000 | |
| 101 | A | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | P | B | 0.0000 | |
| 104 | M | B | 0.0000 | |
| 105 | S | B | -1.0329 | |
| 106 | L | B | 0.0000 | |
| 107 | N | B | -3.3341 | |
| 108 | E | B | -3.8196 | |
| 109 | N | B | -3.2248 | |
| 110 | D | B | -2.7894 | |
| 111 | K | B | -2.2799 | |
| 112 | V | B | 0.0000 | |
| 113 | L | B | -0.4527 | |
| 114 | A | B | 0.0000 | |
| 115 | R | B | -1.0324 | |
| 116 | L | B | 0.0000 | |
| 117 | G | B | 0.0000 | |
| 118 | E | B | -2.0413 | |
| 119 | A | B | -1.2015 | |
| 120 | H | B | -1.0362 | |
| 121 | G | B | -0.8648 | |
| 122 | G | B | -1.3924 | |
| 123 | N | B | -1.9065 | |
| 124 | E | B | -1.6887 | |
| 125 | L | B | 0.0000 | |
| 126 | E | B | 0.0000 | |
| 127 | S | B | 0.0000 | |
| 128 | N | B | -1.7671 | |
| 129 | K | B | -2.2915 | |
| 130 | Y | B | -1.1291 | |
| 131 | L | B | 0.0000 | |
| 132 | R | B | -0.8532 | |
| 133 | T | B | 0.0000 | |
| 134 | S | B | 0.0000 | |
| 135 | F | B | 0.0000 | |
| 136 | S | B | 0.0000 | |
| 137 | G | B | 0.0000 | |
| 138 | F | B | 0.0000 | |
| 139 | K | B | -1.7036 | |
| 1 | M | C | -0.4069 | |
| 2 | K | C | -2.6037 | |
| 3 | K | C | -3.4336 | |
| 4 | N | C | -3.3914 | |
| 5 | N | C | -3.4064 | |
| 6 | N | C | -2.6581 | |
| 7 | A | C | -1.4802 | |
| 8 | V | C | 0.0000 | |
| 9 | A | C | 0.0000 | |
| 10 | F | C | 0.0000 | |
| 11 | Y | C | 0.0000 | |
| 12 | A | C | 0.0000 | |
| 13 | Y | C | 0.0000 | |
| 14 | L | C | 0.0000 | |
| 15 | S | C | -1.2092 | |
| 16 | K | C | -2.1760 | |
| 17 | S | C | -1.3355 | |
| 18 | L | C | -0.9254 | |
| 19 | P | C | -1.3139 | |
| 20 | L | C | 0.0000 | |
| 21 | N | C | -1.8303 | |
| 22 | S | C | -0.8881 | |
| 23 | V | C | -0.7640 | |
| 24 | S | C | -1.5005 | |
| 25 | K | C | -2.4841 | |
| 26 | H | C | -1.6905 | |
| 27 | T | C | -0.9845 | |
| 28 | T | C | -0.6694 | |
| 29 | L | C | 0.0000 | |
| 30 | K | C | -2.1777 | |
| 31 | Y | C | 0.0000 | |
| 32 | D | C | -1.8069 | |
| 33 | L | C | -0.3178 | |
| 34 | V | C | -0.4442 | |
| 35 | D | C | -1.3083 | |
| 36 | L | C | 0.0000 | |
| 37 | N | C | -1.0198 | |
| 38 | L | C | -0.9515 | |
| 39 | G | C | -1.5140 | |
| 40 | N | C | -1.6750 | |
| 41 | G | C | 0.0000 | |
| 42 | Y | C | 0.0000 | |
| 43 | D | C | -2.4949 | |
| 44 | K | C | -2.9613 | |
| 45 | Q | C | -2.6749 | |
| 46 | T | C | -1.6809 | |
| 47 | G | C | 0.0000 | |
| 48 | L | C | -0.8145 | |
| 49 | F | C | 0.0000 | |
| 50 | T | C | -1.6391 | |
| 51 | A | C | 0.0000 | |
| 52 | P | C | -2.0965 | |
| 53 | S | C | -2.5099 | |
| 54 | N | C | -2.9682 | |
| 55 | G | C | -1.6693 | |
| 56 | L | C | -0.7282 | |
| 57 | Y | C | 0.0000 | |
| 58 | V | C | 0.0000 | |
| 59 | F | C | 0.0000 | |
| 60 | N | C | 0.0000 | |
| 61 | V | C | 0.0000 | |
| 62 | A | C | 0.0000 | |
| 63 | T | C | 0.0000 | |
| 64 | G | C | 0.0000 | |
| 65 | A | C | 0.0000 | |
| 66 | Q | C | -0.7907 | |
| 67 | D | C | -0.5613 | |
| 68 | S | C | -0.7253 | |
| 69 | S | C | 0.0000 | |
| 70 | H | C | -0.7899 | |
| 71 | S | C | 0.0000 | |
| 72 | C | C | 0.0000 | |
| 73 | L | C | 0.0000 | |
| 74 | E | C | 0.0000 | |
| 75 | L | C | 0.0000 | |
| 76 | A | C | 0.0000 | |
| 77 | V | C | 0.0000 | |
| 78 | N | C | -1.3052 | |
| 79 | G | C | -0.2775 | |
| 80 | V | C | 1.2804 | |
| 81 | V | C | 0.6380 | |
| 82 | K | C | -0.2346 | |
| 83 | D | C | 0.0000 | |
| 84 | L | C | 0.0000 | |
| 85 | T | C | 0.0000 | |
| 86 | W | C | 0.0000 | |
| 87 | A | C | 0.0000 | |
| 88 | D | C | 0.0000 | |
| 89 | S | C | 0.0000 | |
| 90 | M | C | -0.3047 | |
| 91 | D | C | -0.9757 | |
| 92 | H | C | -0.2940 | |
| 93 | V | C | 0.6793 | |
| 94 | D | C | 0.0000 | |
| 95 | R | C | -0.2856 | |
| 96 | A | C | -0.0962 | |
| 97 | F | C | 0.0000 | |
| 98 | A | C | 0.0000 | |
| 99 | T | C | 0.0000 | |
| 100 | T | C | 0.0000 | |
| 101 | A | C | 0.0000 | |
| 102 | T | C | 0.0000 | |
| 103 | P | C | 0.0000 | |
| 104 | M | C | 0.0000 | |
| 105 | S | C | -0.9747 | |
| 106 | L | C | 0.0000 | |
| 107 | N | C | -3.2827 | |
| 108 | E | C | -3.7635 | |
| 109 | N | C | -3.1117 | |
| 110 | D | C | -2.5583 | |
| 111 | K | C | -1.8136 | |
| 112 | V | C | 0.0000 | |
| 113 | L | C | -0.2434 | |
| 114 | A | C | 0.0000 | |
| 115 | R | C | -0.9361 | |
| 116 | L | C | 0.0000 | |
| 117 | G | C | 0.0000 | |
| 118 | E | C | -2.5896 | |
| 119 | A | C | -1.4783 | |
| 120 | H | C | -1.2731 | |
| 121 | G | C | -0.9356 | |
| 122 | G | C | -1.4962 | |
| 123 | N | C | -2.1364 | |
| 124 | E | C | -1.9568 | |
| 125 | L | C | 0.0000 | |
| 126 | E | C | 0.0000 | |
| 127 | S | C | 0.0000 | |
| 128 | N | C | -1.8772 | |
| 129 | K | C | -2.3384 | |
| 130 | Y | C | -1.1179 | |
| 131 | L | C | 0.0000 | |
| 132 | R | C | -0.8651 | |
| 133 | T | C | 0.0000 | |
| 134 | S | C | 0.0000 | |
| 135 | F | C | 0.0000 | |
| 136 | S | C | 0.0000 | |
| 137 | G | C | 0.0000 | |
| 138 | F | C | 0.0000 | |
| 139 | K | C | -1.2818 |
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 | -0.8583 | 1.4103 | View | CSV | PDB |
| 4.5 | -0.8976 | 1.2666 | View | CSV | PDB |
| 5.0 | -0.9409 | 1.2678 | View | CSV | PDB |
| 5.5 | -0.9766 | 1.2713 | View | CSV | PDB |
| 6.0 | -0.9915 | 1.2795 | View | CSV | PDB |
| 6.5 | -0.9775 | 1.2943 | View | CSV | PDB |
| 7.0 | -0.9389 | 1.3143 | View | CSV | PDB |
| 7.5 | -0.8866 | 1.3368 | View | CSV | PDB |
| 8.0 | -0.8282 | 1.3603 | View | CSV | PDB |
| 8.5 | -0.7648 | 1.3841 | View | CSV | PDB |
| 9.0 | -0.696 | 1.4077 | 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