| 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. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:43)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d3330a5a0aff874/tmp/folded.pdb (00:03:43)
[INFO] Main: Simulation completed successfully. (00:08:17)
|
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 | -0.4538 | |
| 2 | K | A | -2.5987 | |
| 3 | K | A | -3.4122 | |
| 4 | N | A | -3.5023 | |
| 5 | N | A | -3.3840 | |
| 6 | N | A | -2.6755 | |
| 7 | A | A | -1.3130 | |
| 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 | -0.6636 | |
| 14 | L | A | 0.0000 | |
| 15 | S | A | -1.3203 | |
| 16 | K | A | -2.1764 | |
| 17 | S | A | -1.2213 | |
| 18 | L | A | -0.7232 | |
| 19 | P | A | -1.1552 | |
| 20 | L | A | 0.0000 | |
| 21 | N | A | -1.7183 | |
| 22 | S | A | -0.8631 | |
| 23 | V | A | -0.7827 | |
| 24 | S | A | -1.4998 | |
| 25 | K | A | -2.3908 | |
| 26 | H | A | -1.8658 | |
| 27 | T | A | -1.1698 | |
| 28 | T | A | -0.8012 | |
| 29 | L | A | 0.0000 | |
| 30 | K | A | -2.2656 | |
| 31 | Y | A | 0.0000 | |
| 32 | D | A | -1.9264 | |
| 33 | L | A | -0.4075 | |
| 34 | V | A | -0.2946 | |
| 35 | D | A | -0.7392 | |
| 36 | L | A | -0.4075 | |
| 37 | N | A | -0.7793 | |
| 38 | L | A | -0.5262 | |
| 39 | G | A | -0.9588 | |
| 40 | N | A | -1.5170 | |
| 41 | G | A | 0.0000 | |
| 42 | Y | A | 0.0000 | |
| 43 | D | A | -2.5078 | |
| 44 | K | A | -2.9858 | |
| 45 | Q | A | -2.6837 | |
| 46 | T | A | -1.6982 | |
| 47 | G | A | 0.0000 | |
| 48 | L | A | -0.9455 | |
| 49 | F | A | 0.0000 | |
| 50 | T | A | -1.5583 | |
| 51 | A | A | 0.0000 | |
| 52 | P | A | -1.8039 | |
| 53 | S | A | -2.7671 | |
| 54 | N | A | -2.8404 | |
| 55 | G | A | -1.4964 | |
| 56 | L | A | -0.7346 | |
| 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 | -0.8040 | |
| 67 | D | A | -0.8126 | |
| 68 | S | A | -1.1724 | |
| 69 | S | A | 0.0000 | |
| 70 | H | A | -0.9175 | |
| 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 | -1.4129 | |
| 79 | G | A | -0.2860 | |
| 80 | V | A | 1.2670 | |
| 81 | V | A | 0.6297 | |
| 82 | K | A | -0.1410 | |
| 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 | -0.4963 | |
| 91 | D | A | -1.3529 | |
| 92 | H | A | -0.3914 | |
| 93 | V | A | 0.7251 | |
| 94 | D | A | -0.1770 | |
| 95 | R | A | -0.2330 | |
| 96 | A | A | -0.1829 | |
| 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 | -0.7812 | |
| 106 | L | A | 0.0000 | |
| 107 | N | A | -3.1273 | |
| 108 | E | A | -3.4408 | |
| 109 | N | A | -3.0242 | |
| 110 | D | A | -2.6324 | |
| 111 | K | A | -2.0626 | |
| 112 | V | A | 0.0000 | |
| 113 | L | A | -0.3299 | |
| 114 | A | A | 0.0000 | |
| 115 | R | A | -0.9751 | |
| 116 | L | A | 0.0000 | |
| 117 | G | A | 0.0000 | |
| 118 | E | A | -1.6249 | |
| 119 | A | A | -1.0926 | |
| 120 | H | A | -1.1379 | |
| 121 | G | A | -0.9574 | |
| 122 | G | A | -1.7438 | |
| 123 | N | A | -1.8666 | |
| 124 | E | A | -1.6644 | |
| 125 | L | A | 0.0000 | |
| 126 | E | A | 0.0000 | |
| 127 | S | A | 0.0000 | |
| 128 | N | A | -1.8305 | |
| 129 | K | A | -2.0749 | |
| 130 | Y | A | -0.9057 | |
| 131 | L | A | 0.0000 | |
| 132 | R | A | -0.8135 | |
| 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 | -1.5018 | |
| 1 | M | B | -0.4463 | |
| 2 | K | B | -2.5911 | |
| 3 | K | B | -3.4094 | |
| 4 | N | B | -3.4971 | |
| 5 | N | B | -3.3789 | |
| 6 | N | B | -2.7235 | |
| 7 | A | B | -1.3699 | |
| 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 | -0.6442 | |
| 14 | L | B | 0.0000 | |
| 15 | S | B | -1.2789 | |
| 16 | K | B | -2.1499 | |
| 17 | S | B | -1.1735 | |
| 18 | L | B | -0.6585 | |
| 19 | P | B | -1.0577 | |
| 20 | L | B | 0.0000 | |
| 21 | N | B | -1.6731 | |
| 22 | S | B | -0.8335 | |
| 23 | V | B | -0.7913 | |
| 24 | S | B | -1.5174 | |
| 25 | K | B | -2.4199 | |
| 26 | H | B | -1.9248 | |
| 27 | T | B | -1.2018 | |
| 28 | T | B | -0.8200 | |
| 29 | L | B | 0.0000 | |
| 30 | K | B | -2.1954 | |
| 31 | Y | B | 0.0000 | |
| 32 | D | B | -1.7732 | |
| 33 | L | B | -0.3698 | |
| 34 | V | B | -0.3733 | |
| 35 | D | B | -1.0765 | |
| 36 | L | B | 0.0000 | |
| 37 | N | B | -0.9730 | |
| 38 | L | B | -0.7061 | |
| 39 | G | B | -1.2143 | |
| 40 | N | B | -1.6564 | |
| 41 | G | B | 0.0000 | |
| 42 | Y | B | 0.0000 | |
| 43 | D | B | -2.4224 | |
| 44 | K | B | -2.7806 | |
| 45 | Q | B | -2.5876 | |
| 46 | T | B | -1.6394 | |
| 47 | G | B | 0.0000 | |
| 48 | L | B | -0.9181 | |
| 49 | F | B | 0.0000 | |
| 50 | T | B | -1.5949 | |
| 51 | A | B | 0.0000 | |
| 52 | P | B | -1.8728 | |
| 53 | S | B | -2.8264 | |
| 54 | N | B | -2.8528 | |
| 55 | G | B | -1.5051 | |
| 56 | L | B | -0.7467 | |
| 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 | -0.7242 | |
| 67 | D | B | -0.8678 | |
| 68 | S | B | -1.1856 | |
| 69 | S | B | 0.0000 | |
| 70 | H | B | -0.9230 | |
| 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 | -1.4169 | |
| 79 | G | B | -0.2862 | |
| 80 | V | B | 1.2689 | |
| 81 | V | B | 0.6305 | |
| 82 | K | B | -0.1518 | |
| 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 | -0.6306 | |
| 91 | D | B | -1.3973 | |
| 92 | H | B | -0.4158 | |
| 93 | V | B | 0.7311 | |
| 94 | D | B | 0.0000 | |
| 95 | R | B | -0.2229 | |
| 96 | A | B | -0.1898 | |
| 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 | -0.7606 | |
| 106 | L | B | 0.0000 | |
| 107 | N | B | -3.1395 | |
| 108 | E | B | -3.4711 | |
| 109 | N | B | -3.0445 | |
| 110 | D | B | -2.6475 | |
| 111 | K | B | -2.0753 | |
| 112 | V | B | 0.0000 | |
| 113 | L | B | -0.3338 | |
| 114 | A | B | 0.0000 | |
| 115 | R | B | -0.9948 | |
| 116 | L | B | 0.0000 | |
| 117 | G | B | 0.0000 | |
| 118 | E | B | -1.6418 | |
| 119 | A | B | -1.1059 | |
| 120 | H | B | -1.1201 | |
| 121 | G | B | -0.9202 | |
| 122 | G | B | -1.6807 | |
| 123 | N | B | -1.6889 | |
| 124 | E | B | -1.5088 | |
| 125 | L | B | 0.0000 | |
| 126 | E | B | 0.0000 | |
| 127 | S | B | 0.0000 | |
| 128 | N | B | -1.8319 | |
| 129 | K | B | -2.0422 | |
| 130 | Y | B | -0.8731 | |
| 131 | L | B | 0.0000 | |
| 132 | R | B | -0.8210 | |
| 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 | -1.5693 | |
| 1 | M | C | -0.4451 | |
| 2 | K | C | -2.5942 | |
| 3 | K | C | -3.4103 | |
| 4 | N | C | -3.5043 | |
| 5 | N | C | -3.3748 | |
| 6 | N | C | -2.6745 | |
| 7 | A | C | -1.3118 | |
| 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 | -0.6645 | |
| 14 | L | C | 0.0000 | |
| 15 | S | C | -1.2989 | |
| 16 | K | C | -2.1680 | |
| 17 | S | C | -1.1872 | |
| 18 | L | C | -0.6712 | |
| 19 | P | C | -1.0790 | |
| 20 | L | C | 0.0000 | |
| 21 | N | C | -1.6834 | |
| 22 | S | C | -0.8470 | |
| 23 | V | C | -0.8003 | |
| 24 | S | C | -1.5158 | |
| 25 | K | C | -2.4094 | |
| 26 | H | C | -1.8821 | |
| 27 | T | C | -1.1748 | |
| 28 | T | C | -0.8008 | |
| 29 | L | C | 0.0000 | |
| 30 | K | C | -2.1815 | |
| 31 | Y | C | 0.0000 | |
| 32 | D | C | -1.7961 | |
| 33 | L | C | -0.3767 | |
| 34 | V | C | -0.3795 | |
| 35 | D | C | -1.1099 | |
| 36 | L | C | -0.5787 | |
| 37 | N | C | -0.8538 | |
| 38 | L | C | -0.5590 | |
| 39 | G | C | -0.9524 | |
| 40 | N | C | -1.5154 | |
| 41 | G | C | 0.0000 | |
| 42 | Y | C | 0.0000 | |
| 43 | D | C | -2.4266 | |
| 44 | K | C | -2.7975 | |
| 45 | Q | C | -2.5970 | |
| 46 | T | C | -1.6426 | |
| 47 | G | C | 0.0000 | |
| 48 | L | C | -0.8935 | |
| 49 | F | C | 0.0000 | |
| 50 | T | C | -1.6639 | |
| 51 | A | C | 0.0000 | |
| 52 | P | C | -1.8092 | |
| 53 | S | C | -2.7821 | |
| 54 | N | C | -2.8482 | |
| 55 | G | C | -1.4966 | |
| 56 | L | C | -0.7333 | |
| 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 | -0.7894 | |
| 67 | D | C | -0.9203 | |
| 68 | S | C | -1.2033 | |
| 69 | S | C | 0.0000 | |
| 70 | H | C | -0.9219 | |
| 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 | -0.1929 | |
| 78 | N | C | -1.3056 | |
| 79 | G | C | -0.2029 | |
| 80 | V | C | 1.3738 | |
| 81 | V | C | 0.7530 | |
| 82 | K | C | 0.0869 | |
| 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 | -0.5341 | |
| 91 | D | C | -1.4006 | |
| 92 | H | C | -0.4542 | |
| 93 | V | C | 0.6587 | |
| 94 | D | C | -0.2358 | |
| 95 | R | C | -0.2824 | |
| 96 | A | C | -0.2163 | |
| 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 | -0.7576 | |
| 106 | L | C | 0.0000 | |
| 107 | N | C | -3.1379 | |
| 108 | E | C | -3.4683 | |
| 109 | N | C | -3.0372 | |
| 110 | D | C | -2.5957 | |
| 111 | K | C | -1.9976 | |
| 112 | V | C | 0.0000 | |
| 113 | L | C | -0.2796 | |
| 114 | A | C | 0.0000 | |
| 115 | R | C | -0.9784 | |
| 116 | L | C | 0.0000 | |
| 117 | G | C | 0.0000 | |
| 118 | E | C | -1.6881 | |
| 119 | A | C | -1.1248 | |
| 120 | H | C | -1.1294 | |
| 121 | G | C | -0.9136 | |
| 122 | G | C | -1.6878 | |
| 123 | N | C | -1.7467 | |
| 124 | E | C | -1.5193 | |
| 125 | L | C | 0.0000 | |
| 126 | E | C | 0.0000 | |
| 127 | S | C | 0.0000 | |
| 128 | N | C | -1.8822 | |
| 129 | K | C | -2.0884 | |
| 130 | Y | C | -0.9060 | |
| 131 | L | C | 0.0000 | |
| 132 | R | C | -0.8368 | |
| 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 | -1.5189 |
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 | -0.868 | 1.3646 | View | CSV | PDB |
| 4.5 | -0.9028 | 1.3648 | View | CSV | PDB |
| 5.0 | -0.9407 | 1.3653 | View | CSV | PDB |
| 5.5 | -0.9702 | 1.367 | View | CSV | PDB |
| 6.0 | -0.9793 | 1.3712 | View | CSV | PDB |
| 6.5 | -0.9629 | 1.3798 | View | CSV | PDB |
| 7.0 | -0.9266 | 1.3928 | View | CSV | PDB |
| 7.5 | -0.8793 | 1.4084 | View | CSV | PDB |
| 8.0 | -0.8263 | 1.425 | View | CSV | PDB |
| 8.5 | -0.7681 | 1.442 | View | CSV | PDB |
| 9.0 | -0.7032 | 1.4591 | 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