| Chain sequence(s) |
A: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK
C: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK B: MKKNNNAVAFYAYLSKSLPLNSVSKHTTLKYDLVDLNLGNGYDKQTGLFTAPSNGLYVFNVATGAQDSSHSCLELAVNGVVKDLTWADSMDHVDRAFATTATPMSLNENDKVLARLGEAHGGNELESNKYLRTSFSGFK input PDB |
| Selected Chain(s) | A,B,C |
| Distance of aggregation | 10 Å |
| FoldX usage | No |
| 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] runJob: FoldX not utilized. Treating input pdb file as it was already optimized. (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:03)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/c0dbf708b566f4e/tmp/folded.pdb (00:00:03)
[INFO] Main: Simulation completed successfully. (00:03:39)
|
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 | -3.4059 | |
| 6 | N | A | -2.6483 | |
| 7 | A | A | -1.6976 | |
| 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 | -0.6314 | |
| 14 | L | A | 0.0000 | |
| 15 | S | A | -1.3092 | |
| 16 | K | A | -2.1851 | |
| 17 | S | A | -1.2629 | |
| 18 | L | A | -0.8317 | |
| 19 | P | A | -1.1350 | |
| 20 | L | A | 0.0000 | |
| 21 | N | A | -1.7770 | |
| 22 | S | A | -0.8653 | |
| 23 | V | A | -0.7711 | |
| 24 | S | A | -1.4341 | |
| 25 | K | A | -2.3228 | |
| 26 | H | A | -1.6011 | |
| 27 | T | A | -1.0533 | |
| 28 | T | A | -0.7929 | |
| 29 | L | A | 0.0000 | |
| 30 | K | A | -2.3954 | |
| 31 | Y | A | 0.0000 | |
| 32 | D | A | -1.8211 | |
| 33 | L | A | -0.2378 | |
| 34 | V | A | -0.3197 | |
| 35 | D | A | -1.2827 | |
| 36 | L | A | -0.6161 | |
| 37 | N | A | -0.9285 | |
| 38 | L | A | -0.7603 | |
| 39 | G | A | -1.5149 | |
| 40 | N | A | -1.5944 | |
| 41 | G | A | 0.0000 | |
| 42 | Y | A | 0.0000 | |
| 43 | D | A | -2.2493 | |
| 44 | K | A | -2.5199 | |
| 45 | Q | A | -2.5106 | |
| 46 | T | A | -1.6197 | |
| 47 | G | A | 0.0000 | |
| 48 | L | A | -0.9918 | |
| 49 | F | A | 0.0000 | |
| 50 | T | A | -1.9201 | |
| 51 | A | A | 0.0000 | |
| 52 | P | A | -2.1811 | |
| 53 | S | A | -2.5303 | |
| 54 | N | A | -2.9772 | |
| 55 | G | A | -1.5516 | |
| 56 | L | A | -0.6936 | |
| 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 | -0.6916 | |
| 67 | D | A | -0.4360 | |
| 68 | S | A | -0.6379 | |
| 69 | S | A | 0.0000 | |
| 70 | H | A | -0.7500 | |
| 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 | -1.5355 | |
| 79 | G | A | -0.3881 | |
| 80 | V | A | 1.2822 | |
| 81 | V | A | 0.6298 | |
| 82 | K | A | -0.1356 | |
| 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 | -0.2359 | |
| 91 | D | A | -0.9192 | |
| 92 | H | A | -0.2100 | |
| 93 | V | A | 0.8028 | |
| 94 | D | A | 0.0000 | |
| 95 | R | A | -0.2386 | |
| 96 | A | A | -0.0760 | |
| 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 | -0.9029 | |
| 106 | L | A | 0.0000 | |
| 107 | N | A | -3.3681 | |
| 108 | E | A | -3.8621 | |
| 109 | N | A | -3.3043 | |
| 110 | D | A | -2.9215 | |
| 111 | K | A | -2.5226 | |
| 112 | V | A | 0.0000 | |
| 113 | L | A | -0.4922 | |
| 114 | A | A | 0.0000 | |
| 115 | R | A | -0.9570 | |
| 116 | L | A | 0.0000 | |
| 117 | G | A | 0.0000 | |
| 118 | E | A | -1.9191 | |
| 119 | A | A | -1.1554 | |
| 120 | H | A | -1.1080 | |
| 121 | G | A | -0.8918 | |
| 122 | G | A | -1.4693 | |
| 123 | N | A | -1.9171 | |
| 124 | E | A | -1.6596 | |
| 125 | L | A | 0.0000 | |
| 126 | E | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | N | A | -1.9748 | |
| 129 | K | A | -2.2668 | |
| 130 | Y | A | -1.0070 | |
| 131 | L | A | 0.0000 | |
| 132 | R | A | -0.8529 | |
| 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 | -1.4215 | |
| 1 | M | B | -0.4126 | |
| 2 | K | B | -2.5842 | |
| 3 | K | B | -3.4455 | |
| 4 | N | B | -3.3991 | |
| 5 | N | B | -3.3531 | |
| 6 | N | B | -2.6505 | |
| 7 | A | B | -1.4665 | |
| 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 | -0.6297 | |
| 14 | L | B | 0.0000 | |
| 15 | S | B | -1.3066 | |
| 16 | K | B | -2.1761 | |
| 17 | S | B | -1.2507 | |
| 18 | L | B | -0.8216 | |
| 19 | P | B | -1.1207 | |
| 20 | L | B | 0.0000 | |
| 21 | N | B | -1.7721 | |
| 22 | S | B | -0.8654 | |
| 23 | V | B | -0.7588 | |
| 24 | S | B | -1.4075 | |
| 25 | K | B | -2.2504 | |
| 26 | H | B | -1.5648 | |
| 27 | T | B | -1.0366 | |
| 28 | T | B | -0.7917 | |
| 29 | L | B | 0.0000 | |
| 30 | K | B | -2.4502 | |
| 31 | Y | B | 0.0000 | |
| 32 | D | B | -1.8278 | |
| 33 | L | B | -0.2216 | |
| 34 | V | B | -0.3188 | |
| 35 | D | B | -1.2553 | |
| 36 | L | B | -0.6110 | |
| 37 | N | B | -0.9488 | |
| 38 | L | B | -0.8092 | |
| 39 | G | B | -1.5021 | |
| 40 | N | B | -1.6149 | |
| 41 | G | B | 0.0000 | |
| 42 | Y | B | 0.0000 | |
| 43 | D | B | -2.3843 | |
| 44 | K | B | -2.5734 | |
| 45 | Q | B | -2.5590 | |
| 46 | T | B | -1.6749 | |
| 47 | G | B | 0.0000 | |
| 48 | L | B | -1.0580 | |
| 49 | F | B | 0.0000 | |
| 50 | T | B | -1.9647 | |
| 51 | A | B | 0.0000 | |
| 52 | P | B | -2.1688 | |
| 53 | S | B | -2.5237 | |
| 54 | N | B | -2.9908 | |
| 55 | G | B | -1.9252 | |
| 56 | L | B | -0.7040 | |
| 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 | -0.6891 | |
| 67 | D | B | -0.4379 | |
| 68 | S | B | -0.6292 | |
| 69 | S | B | 0.0000 | |
| 70 | H | B | -0.7550 | |
| 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 | -1.5460 | |
| 79 | G | B | -0.3922 | |
| 80 | V | B | 1.2823 | |
| 81 | V | B | 0.6331 | |
| 82 | K | B | -0.1428 | |
| 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 | -0.2542 | |
| 91 | D | B | -0.9273 | |
| 92 | H | B | -0.2078 | |
| 93 | V | B | 0.8048 | |
| 94 | D | B | 0.0000 | |
| 95 | R | B | -0.2374 | |
| 96 | A | B | -0.0754 | |
| 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 | -0.9075 | |
| 106 | L | B | 0.0000 | |
| 107 | N | B | -3.3709 | |
| 108 | E | B | -3.8672 | |
| 109 | N | B | -3.3145 | |
| 110 | D | B | -2.9422 | |
| 111 | K | B | -2.5723 | |
| 112 | V | B | 0.0000 | |
| 113 | L | B | -0.5036 | |
| 114 | A | B | 0.0000 | |
| 115 | R | B | -0.9427 | |
| 116 | L | B | 0.0000 | |
| 117 | G | B | 0.0000 | |
| 118 | E | B | -1.8574 | |
| 119 | A | B | -1.1235 | |
| 120 | H | B | -1.0916 | |
| 121 | G | B | -0.9154 | |
| 122 | G | B | -1.4701 | |
| 123 | N | B | -1.9031 | |
| 124 | E | B | -1.6391 | |
| 125 | L | B | 0.0000 | |
| 126 | E | B | 0.0000 | |
| 127 | S | B | 0.0000 | |
| 128 | N | B | -1.9633 | |
| 129 | K | B | -2.2609 | |
| 130 | Y | B | -1.0077 | |
| 131 | L | B | 0.0000 | |
| 132 | R | B | -0.8501 | |
| 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 | -1.4554 | |
| 1 | M | C | -0.4069 | |
| 2 | K | C | -2.6037 | |
| 3 | K | C | -3.4336 | |
| 4 | N | C | -3.3914 | |
| 5 | N | C | -3.3697 | |
| 6 | N | C | -2.6287 | |
| 7 | A | C | -1.4414 | |
| 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 | -0.6042 | |
| 14 | L | C | 0.0000 | |
| 15 | S | C | -1.2828 | |
| 16 | K | C | -2.1642 | |
| 17 | S | C | -1.2413 | |
| 18 | L | C | -0.8065 | |
| 19 | P | C | -1.0997 | |
| 20 | L | C | 0.0000 | |
| 21 | N | C | -1.7545 | |
| 22 | S | C | -0.8557 | |
| 23 | V | C | -0.7664 | |
| 24 | S | C | -1.4332 | |
| 25 | K | C | -2.3049 | |
| 26 | H | C | -1.5905 | |
| 27 | T | C | -1.0496 | |
| 28 | T | C | -0.7935 | |
| 29 | L | C | 0.0000 | |
| 30 | K | C | -2.3641 | |
| 31 | Y | C | 0.0000 | |
| 32 | D | C | -1.7166 | |
| 33 | L | C | -0.1740 | |
| 34 | V | C | -0.2748 | |
| 35 | D | C | -1.2165 | |
| 36 | L | C | -0.5875 | |
| 37 | N | C | -0.9115 | |
| 38 | L | C | -0.7624 | |
| 39 | G | C | -1.3762 | |
| 40 | N | C | -1.5814 | |
| 41 | G | C | 0.0000 | |
| 42 | Y | C | 0.0000 | |
| 43 | D | C | -2.2290 | |
| 44 | K | C | -2.4636 | |
| 45 | Q | C | -2.4851 | |
| 46 | T | C | -1.6133 | |
| 47 | G | C | 0.0000 | |
| 48 | L | C | -0.9907 | |
| 49 | F | C | 0.0000 | |
| 50 | T | C | -1.9174 | |
| 51 | A | C | 0.0000 | |
| 52 | P | C | -2.1696 | |
| 53 | S | C | -2.5305 | |
| 54 | N | C | -2.9806 | |
| 55 | G | C | -1.6773 | |
| 56 | L | C | -0.6931 | |
| 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 | -0.6793 | |
| 67 | D | C | -0.4299 | |
| 68 | S | C | -0.6233 | |
| 69 | S | C | 0.0000 | |
| 70 | H | C | -0.7394 | |
| 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 | -1.5282 | |
| 79 | G | C | -0.3819 | |
| 80 | V | C | 1.2843 | |
| 81 | V | C | 0.6383 | |
| 82 | K | C | -0.1350 | |
| 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 | -0.2399 | |
| 91 | D | C | -0.9271 | |
| 92 | H | C | -0.2139 | |
| 93 | V | C | 0.8027 | |
| 94 | D | C | 0.0000 | |
| 95 | R | C | -0.2420 | |
| 96 | A | C | -0.0784 | |
| 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 | -0.9060 | |
| 106 | L | C | 0.0000 | |
| 107 | N | C | -3.3704 | |
| 108 | E | C | -3.8684 | |
| 109 | N | C | -3.3047 | |
| 110 | D | C | -2.9167 | |
| 111 | K | C | -2.5238 | |
| 112 | V | C | 0.0000 | |
| 113 | L | C | -0.4874 | |
| 114 | A | C | 0.0000 | |
| 115 | R | C | -0.9487 | |
| 116 | L | C | 0.0000 | |
| 117 | G | C | 0.0000 | |
| 118 | E | C | -1.8583 | |
| 119 | A | C | -1.1270 | |
| 120 | H | C | -1.0886 | |
| 121 | G | C | -0.8974 | |
| 122 | G | C | -1.4389 | |
| 123 | N | C | -1.8364 | |
| 124 | E | C | -1.6079 | |
| 125 | L | C | 0.0000 | |
| 126 | E | C | 0.0000 | |
| 127 | S | C | 0.0000 | |
| 128 | N | C | -1.9635 | |
| 129 | K | C | -2.2700 | |
| 130 | Y | C | -1.0217 | |
| 131 | L | C | 0.0000 | |
| 132 | R | C | -0.8617 | |
| 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 | -1.3302 |
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 | -0.848 | 1.4229 | View | CSV | PDB |
| 4.5 | -0.8846 | 1.2998 | View | CSV | PDB |
| 5.0 | -0.9258 | 1.2636 | View | CSV | PDB |
| 5.5 | -0.9609 | 1.2658 | View | CSV | PDB |
| 6.0 | -0.9767 | 1.274 | View | CSV | PDB |
| 6.5 | -0.9641 | 1.2886 | View | CSV | PDB |
| 7.0 | -0.9266 | 1.3081 | View | CSV | PDB |
| 7.5 | -0.8752 | 1.33 | View | CSV | PDB |
| 8.0 | -0.8169 | 1.3528 | View | CSV | PDB |
| 8.5 | -0.7531 | 1.3758 | View | CSV | PDB |
| 9.0 | -0.6834 | 1.3987 | 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