| Chain sequence(s) |
A: DIQMTQTPSSLSASLGDRVTINCRASQDIENHLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISNLEQEDIATYFCQQGNTLPATFGGGTKLEIKRTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: DVQLQESGPGLVKSSQSLSLTCSVTGYSITSGYFWNWIRQFPGNKLEWMGEMTYDGSNNYNPSLKNRISITRDTSKNQFFLKLNSVTAEDTATYYCARDGHLPFDYWGQGTTLTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC input PDB |
| Selected Chain(s) | A,B |
| 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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:09:48)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/73a95023fffd789/tmp/folded.pdb (00:09:48)
[INFO] Main: Simulation completed successfully. (00:15:19)
|
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 | D | A | -2.0726 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.1803 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.4238 | |
| 6 | Q | A | -1.1545 | |
| 7 | T | A | -0.7667 | |
| 8 | P | A | -0.5631 | |
| 9 | S | A | -0.7259 | |
| 10 | S | A | -0.7348 | |
| 11 | L | A | -0.4656 | |
| 12 | S | A | -0.8470 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.3877 | |
| 15 | L | A | -1.0824 | |
| 16 | G | A | -1.8244 | |
| 17 | D | A | -2.3604 | |
| 18 | R | A | -2.8183 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.7062 | |
| 21 | I | A | 0.0000 | |
| 22 | N | A | -1.3338 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -3.0116 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.2575 | |
| 27 | Q | A | -2.9881 | |
| 28 | D | A | -3.4660 | |
| 29 | I | A | 0.0000 | |
| 30 | E | A | -2.9245 | |
| 31 | N | A | -1.7962 | |
| 32 | H | A | -1.2495 | |
| 33 | L | A | 0.0000 | |
| 34 | N | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -1.4923 | |
| 40 | P | A | -1.3559 | |
| 41 | D | A | -2.2464 | |
| 42 | G | A | -1.4134 | |
| 43 | T | A | -1.2607 | |
| 44 | V | A | -0.8061 | |
| 45 | K | A | -0.8259 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.1323 | |
| 50 | Y | A | -0.0363 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -0.9069 | |
| 53 | R | A | -1.3553 | |
| 54 | L | A | -0.3891 | |
| 55 | H | A | -0.5628 | |
| 56 | S | A | -0.5823 | |
| 57 | G | A | -0.5509 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.4050 | |
| 60 | S | A | -0.6000 | |
| 61 | R | A | -1.1789 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6345 | |
| 64 | G | A | -0.5461 | |
| 65 | S | A | -0.8531 | |
| 66 | G | A | -1.3158 | |
| 67 | S | A | -1.7511 | |
| 68 | G | A | -2.4035 | |
| 69 | T | A | -2.5431 | |
| 70 | D | A | -2.3185 | |
| 71 | F | A | 0.0000 | |
| 72 | S | A | -0.9601 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.8514 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -2.0168 | |
| 77 | N | A | -2.5698 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.1460 | |
| 80 | Q | A | -2.1887 | |
| 81 | E | A | -2.4374 | |
| 82 | D | A | 0.0000 | |
| 83 | I | A | -0.7815 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | F | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | G | A | -0.6600 | |
| 92 | N | A | -1.1309 | |
| 93 | T | A | -0.1764 | |
| 94 | L | A | 0.5400 | |
| 95 | P | A | 0.0000 | |
| 96 | A | A | 0.0000 | |
| 97 | T | A | -0.6405 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.4774 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.3306 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.1254 | |
| 106 | I | A | -1.0855 | |
| 107 | K | A | -1.4976 | |
| 108 | R | A | -2.0809 | |
| 109 | T | A | -1.1179 | |
| 110 | A | A | -1.0306 | |
| 111 | S | A | -0.9763 | |
| 112 | T | A | -1.0991 | |
| 113 | K | A | -1.8049 | |
| 114 | G | A | -1.7532 | |
| 115 | P | A | 0.0000 | |
| 116 | S | A | -0.6111 | |
| 117 | V | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -1.1483 | |
| 120 | L | A | 0.0000 | |
| 121 | A | A | -1.3486 | |
| 122 | P | A | 0.0000 | |
| 123 | S | A | -1.1665 | |
| 124 | S | A | -0.9079 | |
| 125 | K | A | -1.0873 | |
| 126 | S | A | 0.0000 | |
| 127 | T | A | -0.7078 | |
| 128 | S | A | -0.7589 | |
| 129 | G | A | -0.8297 | |
| 130 | G | A | -0.8906 | |
| 131 | T | A | -0.6253 | |
| 132 | A | A | 0.0000 | |
| 133 | A | A | 0.0000 | |
| 134 | L | A | 0.0000 | |
| 135 | G | A | 0.0000 | |
| 136 | C | A | 0.0000 | |
| 137 | L | A | 0.0000 | |
| 138 | V | A | 0.0000 | |
| 139 | K | A | -0.4518 | |
| 140 | D | A | -0.8575 | |
| 141 | Y | A | 0.0000 | |
| 142 | F | A | 0.0000 | |
| 143 | P | A | 0.0000 | |
| 144 | E | A | -0.6474 | |
| 145 | P | A | -0.6706 | |
| 146 | V | A | -0.5626 | |
| 147 | T | A | -0.4781 | |
| 148 | V | A | -0.1489 | |
| 149 | S | A | -0.3589 | |
| 150 | W | A | 0.0000 | |
| 151 | N | A | -0.7327 | |
| 152 | S | A | -0.6582 | |
| 153 | G | A | -0.5729 | |
| 154 | A | A | -0.2454 | |
| 155 | L | A | 0.0103 | |
| 156 | T | A | -0.1834 | |
| 157 | S | A | -0.1922 | |
| 158 | G | A | -0.2326 | |
| 159 | V | A | 0.1368 | |
| 160 | H | A | -0.1277 | |
| 161 | T | A | 0.0439 | |
| 162 | F | A | 0.0000 | |
| 163 | P | A | -0.3524 | |
| 164 | A | A | 0.0364 | |
| 165 | V | A | 0.0904 | |
| 166 | L | A | 0.2796 | |
| 167 | Q | A | -0.1754 | |
| 168 | S | A | -0.2432 | |
| 169 | S | A | -0.3450 | |
| 170 | G | A | -0.5165 | |
| 171 | L | A | -0.5786 | |
| 172 | Y | A | 0.0000 | |
| 173 | S | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | S | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | V | A | 0.0000 | |
| 178 | V | A | 0.0000 | |
| 179 | T | A | -0.1493 | |
| 180 | V | A | 0.0000 | |
| 181 | P | A | -0.5343 | |
| 182 | S | A | -0.5720 | |
| 183 | S | A | -0.5838 | |
| 184 | S | A | -0.5709 | |
| 185 | L | A | -0.7653 | |
| 186 | G | A | -0.9445 | |
| 187 | T | A | -0.7130 | |
| 188 | Q | A | -1.1747 | |
| 189 | T | A | -1.0625 | |
| 190 | Y | A | 0.0000 | |
| 191 | I | A | -1.1566 | |
| 192 | C | A | 0.0000 | |
| 193 | N | A | -1.4381 | |
| 194 | V | A | 0.0000 | |
| 195 | N | A | -1.7821 | |
| 196 | H | A | 0.0000 | |
| 197 | K | A | -2.6883 | |
| 198 | P | A | -1.7136 | |
| 199 | S | A | -2.0166 | |
| 200 | N | A | -2.6417 | |
| 201 | T | A | -2.1353 | |
| 202 | K | A | -2.6808 | |
| 203 | V | A | -1.6421 | |
| 204 | D | A | -2.5507 | |
| 205 | K | A | -2.2510 | |
| 206 | K | A | -2.4350 | |
| 207 | V | A | 0.0000 | |
| 208 | E | A | -2.8055 | |
| 209 | P | A | -1.9541 | |
| 210 | K | A | -2.2340 | |
| 211 | S | A | -1.5861 | |
| 1 | D | B | -2.1221 | |
| 2 | V | B | 0.0000 | |
| 3 | Q | B | -2.0091 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -1.6535 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.8243 | |
| 8 | G | B | -0.5851 | |
| 9 | P | B | -0.2710 | |
| 10 | G | B | -0.0630 | |
| 11 | L | B | 0.4640 | |
| 12 | V | B | 0.0000 | |
| 13 | K | B | -1.9779 | |
| 14 | S | B | -1.6659 | |
| 15 | S | B | -1.5560 | |
| 16 | Q | B | -2.1303 | |
| 17 | S | B | -1.7248 | |
| 18 | L | B | 0.0000 | |
| 19 | S | B | -0.9916 | |
| 20 | L | B | 0.0000 | |
| 21 | T | B | -0.5161 | |
| 22 | C | B | 0.0000 | |
| 23 | S | B | -1.0853 | |
| 24 | V | B | 0.0000 | |
| 25 | T | B | -1.2595 | |
| 26 | G | B | -1.1260 | |
| 27 | Y | B | -0.3219 | |
| 28 | S | B | -0.2001 | |
| 29 | I | B | 0.0000 | |
| 30 | T | B | -0.2517 | |
| 31 | S | B | -0.0856 | |
| 32 | G | B | -0.1923 | |
| 33 | Y | B | 0.1539 | |
| 34 | F | B | 0.2820 | |
| 35 | W | B | 0.0000 | |
| 36 | N | B | 0.0000 | |
| 37 | W | B | 0.0000 | |
| 38 | I | B | 0.0000 | |
| 39 | R | B | 0.0000 | |
| 40 | Q | B | 0.0000 | |
| 41 | F | B | -1.4426 | |
| 42 | P | B | -1.7948 | |
| 43 | G | B | -1.8719 | |
| 44 | N | B | -1.9460 | |
| 45 | K | B | -2.2585 | |
| 46 | L | B | 0.0000 | |
| 47 | E | B | -0.6639 | |
| 48 | W | B | 0.0000 | |
| 49 | M | B | 0.0000 | |
| 50 | G | B | 0.0000 | |
| 51 | E | B | 0.0000 | |
| 52 | M | B | 0.0000 | |
| 53 | T | B | 0.0000 | |
| 54 | Y | B | -0.0714 | |
| 55 | D | B | -1.5110 | |
| 56 | G | B | -1.0564 | |
| 57 | S | B | -0.8598 | |
| 58 | N | B | -0.7974 | |
| 59 | N | B | -0.5978 | |
| 60 | Y | B | -0.6314 | |
| 61 | N | B | 0.0000 | |
| 62 | P | B | -1.1679 | |
| 63 | S | B | -1.1752 | |
| 64 | L | B | 0.0000 | |
| 65 | K | B | -2.5569 | |
| 66 | N | B | -2.4687 | |
| 67 | R | B | -2.1501 | |
| 68 | I | B | 0.0000 | |
| 69 | S | B | -1.2250 | |
| 70 | I | B | 0.0000 | |
| 71 | T | B | -0.6323 | |
| 72 | R | B | -0.9623 | |
| 73 | D | B | -1.3552 | |
| 74 | T | B | -1.2337 | |
| 75 | S | B | -1.3635 | |
| 76 | K | B | -2.2210 | |
| 77 | N | B | -1.4851 | |
| 78 | Q | B | -1.2954 | |
| 79 | F | B | 0.0000 | |
| 80 | F | B | -0.2539 | |
| 81 | L | B | 0.0000 | |
| 82 | K | B | -1.4403 | |
| 83 | L | B | 0.0000 | |
| 84 | N | B | -1.9644 | |
| 85 | S | B | -1.4423 | |
| 86 | V | B | 0.0000 | |
| 87 | T | B | -1.6673 | |
| 88 | A | B | -1.9674 | |
| 89 | E | B | -2.3204 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | T | B | -0.2647 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | D | B | -0.1829 | |
| 100 | G | B | -0.5352 | |
| 101 | H | B | -0.9451 | |
| 102 | L | B | -0.3626 | |
| 103 | P | B | -0.1575 | |
| 104 | F | B | 0.0000 | |
| 105 | D | B | 0.0000 | |
| 106 | Y | B | -0.4284 | |
| 107 | W | B | -0.5759 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.7607 | |
| 110 | G | B | 0.0000 | |
| 111 | T | B | -0.6749 | |
| 112 | T | B | -0.1057 | |
| 113 | L | B | 0.0000 | |
| 114 | T | B | 0.0000 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.5359 | |
| 117 | S | B | 0.1644 | |
| 118 | V | B | 0.8262 | |
| 119 | A | B | 0.0685 | |
| 120 | A | B | -0.0375 | |
| 121 | P | B | 0.0000 | |
| 122 | S | B | -0.2479 | |
| 123 | V | B | 0.0000 | |
| 124 | F | B | 0.0000 | |
| 125 | I | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -0.5182 | |
| 128 | P | B | -0.7756 | |
| 129 | S | B | -1.8143 | |
| 130 | D | B | -2.9491 | |
| 131 | E | B | -3.0239 | |
| 132 | Q | B | 0.0000 | |
| 133 | L | B | -2.2013 | |
| 134 | K | B | -2.8165 | |
| 135 | S | B | -1.7490 | |
| 136 | G | B | -1.3671 | |
| 137 | T | B | -1.0488 | |
| 138 | A | B | 0.0000 | |
| 139 | S | B | 0.0000 | |
| 140 | V | B | 0.0000 | |
| 141 | V | B | 0.0000 | |
| 142 | C | B | 0.0000 | |
| 143 | L | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | N | B | -0.3246 | |
| 146 | N | B | -0.9444 | |
| 147 | F | B | 0.0000 | |
| 148 | Y | B | -0.7986 | |
| 149 | P | B | -1.3580 | |
| 150 | R | B | -2.9836 | |
| 151 | E | B | -3.2515 | |
| 152 | A | B | -2.3471 | |
| 153 | K | B | -2.5082 | |
| 154 | V | B | -1.1963 | |
| 155 | Q | B | -0.7383 | |
| 156 | W | B | 0.0000 | |
| 157 | K | B | -0.5118 | |
| 158 | V | B | 0.0000 | |
| 159 | D | B | -1.9486 | |
| 160 | N | B | -1.5124 | |
| 161 | A | B | -0.2332 | |
| 162 | L | B | 0.7431 | |
| 163 | Q | B | -0.0986 | |
| 164 | S | B | -0.4609 | |
| 165 | G | B | -0.8600 | |
| 166 | N | B | -0.7251 | |
| 167 | S | B | -0.9994 | |
| 168 | Q | B | -1.3215 | |
| 169 | E | B | -1.4742 | |
| 170 | S | B | -0.6416 | |
| 171 | V | B | -0.3305 | |
| 172 | T | B | -1.0493 | |
| 173 | E | B | -2.2291 | |
| 174 | Q | B | 0.0000 | |
| 175 | D | B | -2.2477 | |
| 176 | S | B | -2.3487 | |
| 177 | K | B | -2.8842 | |
| 178 | D | B | -2.2976 | |
| 179 | S | B | 0.0000 | |
| 180 | T | B | 0.0000 | |
| 181 | Y | B | 0.0000 | |
| 182 | S | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | T | B | -0.5795 | |
| 187 | L | B | 0.0000 | |
| 188 | T | B | -0.4234 | |
| 189 | L | B | -0.6651 | |
| 190 | S | B | -1.0690 | |
| 191 | K | B | -1.9915 | |
| 192 | A | B | -1.8853 | |
| 193 | D | B | -2.7799 | |
| 194 | Y | B | 0.0000 | |
| 195 | E | B | -3.2816 | |
| 196 | K | B | -3.5908 | |
| 197 | H | B | -3.0205 | |
| 198 | K | B | -3.3055 | |
| 199 | V | B | -1.5338 | |
| 200 | Y | B | 0.0000 | |
| 201 | A | B | 0.0000 | |
| 202 | C | B | 0.0000 | |
| 203 | E | B | -0.9614 | |
| 204 | V | B | 0.0000 | |
| 205 | T | B | -1.2733 | |
| 206 | H | B | 0.0000 | |
| 207 | Q | B | -1.6903 | |
| 208 | G | B | -0.3459 | |
| 209 | L | B | -0.2043 | |
| 210 | S | B | -0.4432 | |
| 211 | S | B | -0.4521 | |
| 212 | P | B | -0.6269 | |
| 213 | V | B | -0.1070 | |
| 214 | T | B | -0.4923 | |
| 215 | K | B | -0.8204 | |
| 216 | S | B | -0.6516 | |
| 217 | F | B | 0.0000 | |
| 218 | N | B | -1.9889 | |
| 219 | R | B | -2.5304 | |
| 220 | G | B | -2.0358 | |
| 221 | E | B | -2.3958 | |
| 222 | C | B | -1.4036 |
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 | -0.8645 | 1.4297 | View | CSV | PDB |
| 4.5 | -0.914 | 1.3644 | View | CSV | PDB |
| 5.0 | -0.9696 | 1.2916 | View | CSV | PDB |
| 5.5 | -1.0214 | 1.2589 | View | CSV | PDB |
| 6.0 | -1.058 | 1.2589 | View | CSV | PDB |
| 6.5 | -1.0706 | 1.2589 | View | CSV | PDB |
| 7.0 | -1.059 | 1.2589 | View | CSV | PDB |
| 7.5 | -1.0309 | 1.2589 | View | CSV | PDB |
| 8.0 | -0.9925 | 1.2589 | View | CSV | PDB |
| 8.5 | -0.9456 | 1.2763 | View | CSV | PDB |
| 9.0 | -0.891 | 1.3865 | 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