| Chain sequence(s) |
A: PEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF
C: PEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF B: PEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF D: PEVQVLHSSVCSTLGDDSVELLCVITGFSPPPVEVEWLVDGAPAHLVATMTRPQREAGSKTYMATSQTNVSREDWKAGKAFTCRVKHPATGGTAQGHARFCPEF input PDB |
| Selected Chain(s) | A,C,B,D |
| 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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[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 (00:05:14)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/a36188f53252671/tmp/folded.pdb (00:05:14)
[INFO] Main: Simulation completed successfully. (00:07:11)
|
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 | P | A | -0.5705 | |
| 2 | E | A | -0.8239 | |
| 3 | V | A | -0.8388 | |
| 4 | Q | A | -0.8535 | |
| 5 | V | A | 0.0000 | |
| 6 | L | A | 0.0000 | |
| 7 | H | A | 0.0000 | |
| 8 | S | A | -0.4832 | |
| 9 | S | A | -0.2712 | |
| 10 | V | A | -0.5900 | |
| 11 | C | A | -0.0304 | |
| 12 | S | A | -0.0016 | |
| 13 | T | A | -0.1064 | |
| 14 | L | A | 0.7288 | |
| 15 | G | A | -0.9214 | |
| 16 | D | A | -2.5632 | |
| 17 | D | A | -3.0467 | |
| 18 | S | A | -2.3022 | |
| 19 | V | A | 0.0000 | |
| 20 | E | A | -0.9502 | |
| 21 | L | A | 0.0000 | |
| 22 | L | A | 0.0000 | |
| 23 | C | A | 0.0000 | |
| 24 | V | A | 0.1028 | |
| 25 | I | A | 0.0000 | |
| 26 | T | A | -0.5009 | |
| 27 | G | A | -1.0069 | |
| 28 | F | A | 0.0000 | |
| 29 | S | A | -0.8953 | |
| 30 | P | A | -0.8338 | |
| 31 | P | A | -0.9904 | |
| 32 | P | A | -1.0730 | |
| 33 | V | A | 0.0000 | |
| 34 | E | A | -2.2214 | |
| 35 | V | A | -1.5510 | |
| 36 | E | A | -2.0084 | |
| 37 | W | A | 0.0000 | |
| 38 | L | A | 0.0000 | |
| 39 | V | A | -1.1842 | |
| 40 | D | A | -2.0884 | |
| 41 | G | A | -1.4687 | |
| 42 | A | A | -0.8682 | |
| 43 | P | A | -1.0738 | |
| 44 | A | A | -0.5960 | |
| 45 | H | A | -0.5658 | |
| 46 | L | A | 0.4009 | |
| 47 | V | A | 1.4851 | |
| 48 | A | A | 0.5547 | |
| 49 | T | A | 0.1731 | |
| 50 | M | A | -0.2082 | |
| 51 | T | A | -1.1139 | |
| 52 | R | A | -2.3695 | |
| 53 | P | A | -1.6048 | |
| 54 | Q | A | -2.0305 | |
| 55 | R | A | -2.7735 | |
| 56 | E | A | -1.8513 | |
| 57 | A | A | -1.1889 | |
| 58 | G | A | -0.9259 | |
| 59 | S | A | -1.5479 | |
| 60 | K | A | -2.3477 | |
| 61 | T | A | -1.7182 | |
| 62 | Y | A | -1.6137 | |
| 63 | M | A | -0.8908 | |
| 64 | A | A | 0.0000 | |
| 65 | T | A | 0.0000 | |
| 66 | S | A | 0.0000 | |
| 67 | Q | A | -0.1746 | |
| 68 | T | A | 0.0000 | |
| 69 | N | A | -1.0348 | |
| 70 | V | A | 0.0000 | |
| 71 | S | A | -2.0879 | |
| 72 | R | A | -2.6639 | |
| 73 | E | A | -2.9451 | |
| 74 | D | A | -2.0276 | |
| 75 | W | A | 0.0000 | |
| 76 | K | A | -2.4211 | |
| 77 | A | A | -1.5215 | |
| 78 | G | A | -1.4679 | |
| 79 | K | A | -1.8814 | |
| 80 | A | A | -1.5220 | |
| 81 | F | A | 0.0000 | |
| 82 | T | A | 0.0000 | |
| 83 | C | A | 0.0000 | |
| 84 | R | A | -2.4505 | |
| 85 | V | A | 0.0000 | |
| 86 | K | A | -2.4023 | |
| 87 | H | A | 0.0000 | |
| 88 | P | A | -1.0395 | |
| 89 | A | A | -0.4801 | |
| 90 | T | A | -0.5799 | |
| 91 | G | A | -0.8856 | |
| 92 | G | A | -0.7949 | |
| 93 | T | A | -1.3126 | |
| 94 | A | A | -1.0082 | |
| 95 | Q | A | -1.6799 | |
| 96 | G | A | 0.0000 | |
| 97 | H | A | -1.5292 | |
| 98 | A | A | 0.0000 | |
| 99 | R | A | -1.3140 | |
| 100 | F | A | -0.8043 | |
| 101 | C | A | -0.5791 | |
| 102 | P | A | -1.4273 | |
| 103 | E | A | -1.7632 | |
| 104 | F | A | -0.5631 | |
| 1 | P | B | -1.3126 | |
| 2 | E | B | -2.1502 | |
| 3 | V | B | 0.0000 | |
| 4 | Q | B | -1.3317 | |
| 5 | V | B | 0.0000 | |
| 6 | L | B | 0.0000 | |
| 7 | H | B | 0.0000 | |
| 8 | S | B | -0.3978 | |
| 9 | S | B | -0.2479 | |
| 10 | V | B | -0.4963 | |
| 11 | C | B | 0.0442 | |
| 12 | S | B | 0.0502 | |
| 13 | T | B | -0.0452 | |
| 14 | L | B | 0.7638 | |
| 15 | G | B | -0.8561 | |
| 16 | D | B | -2.4902 | |
| 17 | D | B | -2.9151 | |
| 18 | S | B | -2.0897 | |
| 19 | V | B | 0.0000 | |
| 20 | E | B | -0.5307 | |
| 21 | L | B | 0.0000 | |
| 22 | L | B | 0.0000 | |
| 23 | C | B | 0.0000 | |
| 24 | V | B | -0.3382 | |
| 25 | I | B | 0.0000 | |
| 26 | T | B | -1.0748 | |
| 27 | G | B | -1.4008 | |
| 28 | F | B | 0.0000 | |
| 29 | S | B | -0.8748 | |
| 30 | P | B | -0.7874 | |
| 31 | P | B | -0.6258 | |
| 32 | P | B | -0.5568 | |
| 33 | V | B | 0.0000 | |
| 34 | E | B | -1.4346 | |
| 35 | V | B | -1.0102 | |
| 36 | E | B | -1.4352 | |
| 37 | W | B | 0.0000 | |
| 38 | L | B | 0.0000 | |
| 39 | V | B | -1.1323 | |
| 40 | D | B | -2.0957 | |
| 41 | G | B | -1.4514 | |
| 42 | A | B | -0.7958 | |
| 43 | P | B | -0.8383 | |
| 44 | A | B | -0.4640 | |
| 45 | H | B | -0.4150 | |
| 46 | L | B | -0.0281 | |
| 47 | V | B | -0.0819 | |
| 48 | A | B | -0.1041 | |
| 49 | T | B | -0.1952 | |
| 50 | M | B | 0.0000 | |
| 51 | T | B | -0.5947 | |
| 52 | R | B | -1.1364 | |
| 53 | P | B | -0.9200 | |
| 54 | Q | B | -1.5917 | |
| 55 | R | B | -2.7898 | |
| 56 | E | B | -2.0998 | |
| 57 | A | B | -1.4195 | |
| 58 | G | B | -1.2076 | |
| 59 | S | B | -1.6844 | |
| 60 | K | B | -2.4265 | |
| 61 | T | B | -1.7027 | |
| 62 | Y | B | -1.4148 | |
| 63 | M | B | -0.8438 | |
| 64 | A | B | 0.0000 | |
| 65 | T | B | -0.1438 | |
| 66 | S | B | 0.0000 | |
| 67 | Q | B | -0.3692 | |
| 68 | T | B | 0.0000 | |
| 69 | N | B | -0.7180 | |
| 70 | V | B | 0.0000 | |
| 71 | S | B | -1.9166 | |
| 72 | R | B | 0.0000 | |
| 73 | E | B | -2.9293 | |
| 74 | D | B | -2.1534 | |
| 75 | W | B | 0.0000 | |
| 76 | K | B | -2.3321 | |
| 77 | A | B | -1.5274 | |
| 78 | G | B | -1.5115 | |
| 79 | K | B | -1.9578 | |
| 80 | A | B | -1.5709 | |
| 81 | F | B | 0.0000 | |
| 82 | T | B | 0.0000 | |
| 83 | C | B | 0.0000 | |
| 84 | R | B | -2.0510 | |
| 85 | V | B | 0.0000 | |
| 86 | K | B | -1.7836 | |
| 87 | H | B | 0.0000 | |
| 88 | P | B | -0.8135 | |
| 89 | A | B | -0.3824 | |
| 90 | T | B | -0.5217 | |
| 91 | G | B | -0.8055 | |
| 92 | G | B | -0.7056 | |
| 93 | T | B | -1.2952 | |
| 94 | A | B | -1.3124 | |
| 95 | Q | B | -1.8768 | |
| 96 | G | B | 0.0000 | |
| 97 | H | B | -1.5686 | |
| 98 | A | B | 0.0000 | |
| 99 | R | B | -1.3578 | |
| 100 | F | B | -0.8280 | |
| 101 | C | B | -0.6109 | |
| 102 | P | B | -1.4616 | |
| 103 | E | B | -1.8046 | |
| 104 | F | B | -0.6457 | |
| 1 | P | C | -0.5417 | |
| 2 | E | C | -0.8753 | |
| 3 | V | C | 0.0000 | |
| 4 | Q | C | -0.9386 | |
| 5 | V | C | 0.0000 | |
| 6 | L | C | 0.0000 | |
| 7 | H | C | 0.0000 | |
| 8 | S | C | -0.6226 | |
| 9 | S | C | -0.3003 | |
| 10 | V | C | -0.6256 | |
| 11 | C | C | -0.0771 | |
| 12 | S | C | -0.0394 | |
| 13 | T | C | -0.0976 | |
| 14 | L | C | 0.7282 | |
| 15 | G | C | -0.9047 | |
| 16 | D | C | -2.5130 | |
| 17 | D | C | -3.0147 | |
| 18 | S | C | -2.4008 | |
| 19 | V | C | 0.0000 | |
| 20 | E | C | -1.3389 | |
| 21 | L | C | 0.0000 | |
| 22 | L | C | 0.0000 | |
| 23 | C | C | 0.0000 | |
| 24 | V | C | -0.0002 | |
| 25 | I | C | 0.0000 | |
| 26 | T | C | -0.5403 | |
| 27 | G | C | -1.0304 | |
| 28 | F | C | 0.0000 | |
| 29 | S | C | -0.9074 | |
| 30 | P | C | -0.8477 | |
| 31 | P | C | -1.0406 | |
| 32 | P | C | -1.0810 | |
| 33 | V | C | 0.0000 | |
| 34 | E | C | -2.5678 | |
| 35 | V | C | -1.9193 | |
| 36 | E | C | -2.6846 | |
| 37 | W | C | 0.0000 | |
| 38 | L | C | 0.0000 | |
| 39 | V | C | -1.1878 | |
| 40 | D | C | -2.0934 | |
| 41 | G | C | -1.5107 | |
| 42 | A | C | -0.8666 | |
| 43 | P | C | -1.2291 | |
| 44 | A | C | -0.6780 | |
| 45 | H | C | -0.6632 | |
| 46 | L | C | 0.2380 | |
| 47 | V | C | 1.3930 | |
| 48 | A | C | 0.3336 | |
| 49 | T | C | 0.0181 | |
| 50 | M | C | -0.3401 | |
| 51 | T | C | -0.9700 | |
| 52 | R | C | -2.4099 | |
| 53 | P | C | -1.6640 | |
| 54 | Q | C | -2.1444 | |
| 55 | R | C | -2.9475 | |
| 56 | E | C | -1.8516 | |
| 57 | A | C | -1.2223 | |
| 58 | G | C | -1.0200 | |
| 59 | S | C | -1.5484 | |
| 60 | K | C | -2.3728 | |
| 61 | T | C | -1.7712 | |
| 62 | Y | C | -1.7005 | |
| 63 | M | C | -0.9035 | |
| 64 | A | C | 0.0000 | |
| 65 | T | C | -0.2857 | |
| 66 | S | C | 0.0000 | |
| 67 | Q | C | -0.6583 | |
| 68 | T | C | 0.0000 | |
| 69 | N | C | -1.5071 | |
| 70 | V | C | 0.0000 | |
| 71 | S | C | -2.1217 | |
| 72 | R | C | 0.0000 | |
| 73 | E | C | -2.8994 | |
| 74 | D | C | -2.0375 | |
| 75 | W | C | 0.0000 | |
| 76 | K | C | -2.4513 | |
| 77 | A | C | -1.5577 | |
| 78 | G | C | -1.5514 | |
| 79 | K | C | -1.9238 | |
| 80 | A | C | -1.5238 | |
| 81 | F | C | 0.0000 | |
| 82 | T | C | 0.0000 | |
| 83 | C | C | 0.0000 | |
| 84 | R | C | -2.9729 | |
| 85 | V | C | 0.0000 | |
| 86 | K | C | -2.3226 | |
| 87 | H | C | 0.0000 | |
| 88 | P | C | -1.0205 | |
| 89 | A | C | -0.4408 | |
| 90 | T | C | -0.5387 | |
| 91 | G | C | -0.8188 | |
| 92 | G | C | -0.7077 | |
| 93 | T | C | -1.2874 | |
| 94 | A | C | -1.0063 | |
| 95 | Q | C | -1.7658 | |
| 96 | G | C | 0.0000 | |
| 97 | H | C | -1.5452 | |
| 98 | A | C | 0.0000 | |
| 99 | R | C | -1.3538 | |
| 100 | F | C | -0.8601 | |
| 101 | C | C | -0.6239 | |
| 102 | P | C | -1.3526 | |
| 103 | E | C | -1.7551 | |
| 104 | F | C | -0.5237 | |
| 1 | P | D | -1.3475 | |
| 2 | E | D | -2.1605 | |
| 3 | V | D | 0.0000 | |
| 4 | Q | D | -1.3935 | |
| 5 | V | D | 0.0000 | |
| 6 | L | D | 0.0000 | |
| 7 | H | D | 0.0000 | |
| 8 | S | D | -0.3445 | |
| 9 | S | D | -0.2388 | |
| 10 | V | D | -0.5041 | |
| 11 | C | D | -0.0349 | |
| 12 | S | D | 0.0282 | |
| 13 | T | D | -0.0410 | |
| 14 | L | D | 0.7652 | |
| 15 | G | D | -0.8613 | |
| 16 | D | D | -2.5020 | |
| 17 | D | D | -2.9052 | |
| 18 | S | D | -2.0121 | |
| 19 | V | D | 0.0000 | |
| 20 | E | D | -0.3131 | |
| 21 | L | D | 0.0000 | |
| 22 | L | D | 0.0000 | |
| 23 | C | D | 0.0000 | |
| 24 | V | D | -0.2791 | |
| 25 | I | D | 0.0000 | |
| 26 | T | D | -1.0777 | |
| 27 | G | D | -1.3941 | |
| 28 | F | D | 0.0000 | |
| 29 | S | D | -0.8719 | |
| 30 | P | D | -0.7878 | |
| 31 | P | D | -0.5058 | |
| 32 | P | D | -0.3742 | |
| 33 | V | D | 0.0000 | |
| 34 | E | D | -1.1696 | |
| 35 | V | D | -1.0441 | |
| 36 | E | D | -1.8312 | |
| 37 | W | D | 0.0000 | |
| 38 | L | D | 0.0000 | |
| 39 | V | D | -1.1111 | |
| 40 | D | D | -2.0941 | |
| 41 | G | D | -1.4385 | |
| 42 | A | D | -0.7905 | |
| 43 | P | D | -0.9316 | |
| 44 | A | D | -0.5895 | |
| 45 | H | D | -0.6772 | |
| 46 | L | D | -0.3250 | |
| 47 | V | D | 0.0000 | |
| 48 | A | D | -0.2584 | |
| 49 | T | D | -0.1664 | |
| 50 | M | D | 0.0214 | |
| 51 | T | D | -0.2549 | |
| 52 | R | D | -0.6658 | |
| 53 | P | D | -0.7585 | |
| 54 | Q | D | -1.5421 | |
| 55 | R | D | -2.8121 | |
| 56 | E | D | -2.1127 | |
| 57 | A | D | -1.4289 | |
| 58 | G | D | -1.2094 | |
| 59 | S | D | -1.6862 | |
| 60 | K | D | -2.4260 | |
| 61 | T | D | -1.7110 | |
| 62 | Y | D | -1.3812 | |
| 63 | M | D | -0.7785 | |
| 64 | A | D | 0.0000 | |
| 65 | T | D | 0.0000 | |
| 66 | S | D | 0.0000 | |
| 67 | Q | D | -0.1134 | |
| 68 | T | D | 0.0000 | |
| 69 | N | D | -0.5704 | |
| 70 | V | D | 0.0000 | |
| 71 | S | D | -1.8089 | |
| 72 | R | D | 0.0000 | |
| 73 | E | D | -2.8367 | |
| 74 | D | D | -1.9770 | |
| 75 | W | D | 0.0000 | |
| 76 | K | D | -2.1938 | |
| 77 | A | D | -1.4482 | |
| 78 | G | D | -1.4760 | |
| 79 | K | D | -1.8942 | |
| 80 | A | D | -1.5080 | |
| 81 | F | D | 0.0000 | |
| 82 | T | D | 0.0000 | |
| 83 | C | D | 0.0000 | |
| 84 | R | D | -2.1236 | |
| 85 | V | D | 0.0000 | |
| 86 | K | D | -1.9500 | |
| 87 | H | D | 0.0000 | |
| 88 | P | D | -0.8068 | |
| 89 | A | D | -0.4134 | |
| 90 | T | D | -0.5545 | |
| 91 | G | D | -0.8624 | |
| 92 | G | D | -0.7795 | |
| 93 | T | D | -1.3477 | |
| 94 | A | D | -1.3689 | |
| 95 | Q | D | -1.9466 | |
| 96 | G | D | 0.0000 | |
| 97 | H | D | -1.4559 | |
| 98 | A | D | 0.0000 | |
| 99 | R | D | -1.2852 | |
| 100 | F | D | -0.7925 | |
| 101 | C | D | -0.6111 | |
| 102 | P | D | -1.4639 | |
| 103 | E | D | -1.8237 | |
| 104 | F | D | -0.6486 |
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 | -0.5277 | 2.0155 | View | CSV | PDB |
| 4.5 | -0.5935 | 1.8871 | View | CSV | PDB |
| 5.0 | -0.6753 | 1.7416 | View | CSV | PDB |
| 5.5 | -0.7603 | 1.7424 | View | CSV | PDB |
| 6.0 | -0.8355 | 1.7507 | View | CSV | PDB |
| 6.5 | -0.8884 | 1.7675 | View | CSV | PDB |
| 7.0 | -0.9144 | 1.7925 | View | CSV | PDB |
| 7.5 | -0.921 | 1.8308 | View | CSV | PDB |
| 8.0 | -0.9172 | 1.8977 | View | CSV | PDB |
| 8.5 | -0.9053 | 1.9657 | View | CSV | PDB |
| 9.0 | -0.8837 | 2.0335 | 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