| Chain sequence(s) |
A: QIVLTQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKSGTSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQRRSFPPTFGGGTKLEIKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: EVQLQQSGPELVKPGASVKISCKASGYTFTDFYMNWVKQSHGKSLEWIGDINPNNGDTSYNQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARIYYYGSSDYWGQGTTLTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:09:15)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/9039c3c4ec9c63a/tmp/folded.pdb (00:09:15)
[INFO] Main: Simulation completed successfully. (00:16:29)
|
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 | Q | A | -0.3962 | |
| 2 | I | A | 0.5530 | |
| 3 | V | A | 1.3641 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | 0.1559 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.2541 | |
| 8 | P | A | -0.1318 | |
| 9 | A | A | -0.0467 | |
| 10 | I | A | 0.1565 | |
| 11 | M | A | 0.0739 | |
| 12 | S | A | -0.2502 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.3179 | |
| 15 | P | A | -1.9651 | |
| 16 | G | A | -2.4853 | |
| 17 | E | A | -3.1023 | |
| 18 | K | A | -3.2875 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6243 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.2535 | |
| 23 | C | A | 0.0000 | |
| 24 | S | A | -0.1249 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | 0.0574 | |
| 27 | S | A | -0.2749 | |
| 28 | S | A | -0.7328 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.8467 | |
| 31 | Y | A | -0.6132 | |
| 32 | M | A | 0.0000 | |
| 33 | H | A | 0.0000 | |
| 34 | W | A | 0.0000 | |
| 35 | F | A | 0.0000 | |
| 36 | Q | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -1.5567 | |
| 39 | S | A | -0.9709 | |
| 40 | G | A | -1.0140 | |
| 41 | T | A | -1.1095 | |
| 42 | S | A | -0.9974 | |
| 43 | P | A | 0.0000 | |
| 44 | K | A | -1.6950 | |
| 45 | L | A | -0.6200 | |
| 46 | W | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | 0.1179 | |
| 49 | S | A | -0.1159 | |
| 50 | T | A | -0.3210 | |
| 51 | S | A | -0.4723 | |
| 52 | N | A | -0.4874 | |
| 53 | L | A | 0.1248 | |
| 54 | A | A | -0.2696 | |
| 55 | S | A | -0.3558 | |
| 56 | G | A | -0.3921 | |
| 57 | V | A | -0.1156 | |
| 58 | P | A | -0.1663 | |
| 59 | A | A | -0.1347 | |
| 60 | R | A | -1.2115 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.3723 | |
| 63 | G | A | -0.3893 | |
| 64 | S | A | -0.5997 | |
| 65 | G | A | -0.6243 | |
| 66 | S | A | -0.5980 | |
| 67 | G | A | -0.6181 | |
| 68 | T | A | -0.5733 | |
| 69 | S | A | -0.5890 | |
| 70 | Y | A | 0.0000 | |
| 71 | S | A | -0.3538 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8049 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.2628 | |
| 76 | R | A | -3.4744 | |
| 77 | V | A | 0.0000 | |
| 78 | E | A | -2.6134 | |
| 79 | A | A | -1.4243 | |
| 80 | E | A | -2.1957 | |
| 81 | D | A | 0.0000 | |
| 82 | A | A | -1.0008 | |
| 83 | A | A | 0.0000 | |
| 84 | T | A | 0.0000 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | R | A | -1.0136 | |
| 91 | R | A | -1.7150 | |
| 92 | S | A | -0.4409 | |
| 93 | F | A | 1.1280 | |
| 94 | P | A | 0.0000 | |
| 95 | P | A | 0.0000 | |
| 96 | T | A | 0.0392 | |
| 97 | F | A | 0.0000 | |
| 98 | G | A | 0.0000 | |
| 99 | G | A | -0.4361 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -0.6932 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | 0.0000 | |
| 105 | I | A | -0.4405 | |
| 106 | K | A | -0.3936 | |
| 107 | A | A | -0.4170 | |
| 108 | S | A | -0.6351 | |
| 109 | T | A | -0.9327 | |
| 110 | K | A | -1.7002 | |
| 111 | G | A | -1.8226 | |
| 112 | P | A | 0.0000 | |
| 113 | S | A | -0.6943 | |
| 114 | V | A | 0.0000 | |
| 115 | F | A | 0.0000 | |
| 116 | P | A | -1.2048 | |
| 117 | L | A | 0.0000 | |
| 118 | A | A | -1.3224 | |
| 119 | P | A | 0.0000 | |
| 120 | S | A | -0.9465 | |
| 121 | S | A | -0.7256 | |
| 122 | K | A | -1.0071 | |
| 123 | S | A | 0.0000 | |
| 124 | T | A | -0.6904 | |
| 125 | S | A | -0.7520 | |
| 126 | G | A | -0.8336 | |
| 127 | G | A | -0.8981 | |
| 128 | T | A | -0.6221 | |
| 129 | A | A | 0.0000 | |
| 130 | A | A | 0.0000 | |
| 131 | L | A | 0.0000 | |
| 132 | G | A | 0.0000 | |
| 133 | C | A | 0.0000 | |
| 134 | L | A | 0.0000 | |
| 135 | V | A | 0.0000 | |
| 136 | K | A | 0.0000 | |
| 137 | D | A | -0.7579 | |
| 138 | Y | A | 0.0000 | |
| 139 | F | A | 0.0000 | |
| 140 | P | A | 0.0000 | |
| 141 | E | A | -0.5571 | |
| 142 | P | A | -0.6230 | |
| 143 | V | A | 0.0000 | |
| 144 | T | A | -0.7773 | |
| 145 | V | A | -0.4949 | |
| 146 | S | A | -0.4370 | |
| 147 | W | A | 0.0000 | |
| 148 | N | A | -0.6898 | |
| 149 | S | A | -0.6437 | |
| 150 | G | A | -0.5149 | |
| 151 | A | A | -0.2491 | |
| 152 | L | A | -0.0019 | |
| 153 | T | A | -0.1809 | |
| 154 | S | A | -0.1900 | |
| 155 | G | A | -0.3825 | |
| 156 | V | A | 0.1607 | |
| 157 | H | A | -0.2720 | |
| 158 | T | A | 0.0181 | |
| 159 | F | A | 0.0000 | |
| 160 | P | A | -0.3334 | |
| 161 | A | A | 0.1781 | |
| 162 | V | A | 0.3992 | |
| 163 | L | A | 1.1216 | |
| 164 | Q | A | 0.1941 | |
| 165 | S | A | -0.2004 | |
| 166 | S | A | -0.2894 | |
| 167 | G | A | -0.1285 | |
| 168 | L | A | -0.1677 | |
| 169 | Y | A | 0.2457 | |
| 170 | S | A | 0.0000 | |
| 171 | L | A | 0.0000 | |
| 172 | S | A | 0.0000 | |
| 173 | S | A | 0.0000 | |
| 174 | V | A | 0.0000 | |
| 175 | V | A | 0.0000 | |
| 176 | T | A | -0.1259 | |
| 177 | V | A | 0.0000 | |
| 178 | P | A | -0.6200 | |
| 179 | S | A | -0.5828 | |
| 180 | S | A | -0.5817 | |
| 181 | S | A | -0.6062 | |
| 182 | L | A | -0.7484 | |
| 183 | G | A | -0.9270 | |
| 184 | T | A | -0.6858 | |
| 185 | Q | A | -1.1441 | |
| 186 | T | A | -1.0237 | |
| 187 | Y | A | 0.0000 | |
| 188 | I | A | -1.1130 | |
| 189 | C | A | 0.0000 | |
| 190 | N | A | -1.4835 | |
| 191 | V | A | 0.0000 | |
| 192 | N | A | -2.3995 | |
| 193 | H | A | 0.0000 | |
| 194 | K | A | -2.8818 | |
| 195 | P | A | -1.7443 | |
| 196 | S | A | -2.0250 | |
| 197 | N | A | -2.7424 | |
| 198 | T | A | -2.2973 | |
| 199 | K | A | -2.8649 | |
| 200 | V | A | -1.6246 | |
| 201 | D | A | -2.4272 | |
| 202 | K | A | -2.0044 | |
| 203 | K | A | -2.3147 | |
| 204 | V | A | 0.0000 | |
| 205 | E | A | -2.8114 | |
| 206 | P | A | -1.9298 | |
| 207 | K | A | -2.4695 | |
| 208 | S | A | -1.1575 | |
| 1 | E | B | -2.0830 | |
| 2 | V | B | -1.1959 | |
| 3 | Q | B | -1.7861 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.0784 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.1795 | |
| 8 | G | B | -1.0131 | |
| 9 | P | B | -0.4067 | |
| 10 | E | B | -0.3066 | |
| 11 | L | B | 0.8401 | |
| 12 | V | B | -0.2469 | |
| 13 | K | B | -1.3590 | |
| 14 | P | B | -1.4807 | |
| 15 | G | B | -1.4113 | |
| 16 | A | B | -1.2842 | |
| 17 | S | B | -1.7895 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.1437 | |
| 20 | I | B | 0.0000 | |
| 21 | S | B | -0.9260 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.8097 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.2648 | |
| 26 | G | B | -1.2158 | |
| 27 | Y | B | -0.7269 | |
| 28 | T | B | -0.5673 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.7415 | |
| 31 | D | B | -1.6179 | |
| 32 | F | B | -0.1795 | |
| 33 | Y | B | 0.1102 | |
| 34 | M | B | 0.0000 | |
| 35 | N | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | -0.2153 | |
| 39 | Q | B | 0.0000 | |
| 40 | S | B | -1.3117 | |
| 41 | H | B | -1.8121 | |
| 42 | G | B | -1.4846 | |
| 43 | K | B | -1.2674 | |
| 44 | S | B | -0.9373 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.6353 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | D | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | N | B | -1.5970 | |
| 53 | P | B | 0.0000 | |
| 54 | N | B | -2.8964 | |
| 55 | N | B | -2.7632 | |
| 56 | G | B | -2.2922 | |
| 57 | D | B | -2.4849 | |
| 58 | T | B | -1.0956 | |
| 59 | S | B | -0.5847 | |
| 60 | Y | B | -0.8833 | |
| 61 | N | B | 0.0000 | |
| 62 | Q | B | -2.8419 | |
| 63 | K | B | -2.9070 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9389 | |
| 66 | G | B | -2.1413 | |
| 67 | K | B | -2.2105 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.1998 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.7551 | |
| 72 | V | B | -1.2942 | |
| 73 | D | B | -1.8417 | |
| 74 | K | B | -2.5538 | |
| 75 | S | B | -1.3108 | |
| 76 | S | B | -1.2046 | |
| 77 | S | B | -1.3152 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5844 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.9225 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.6604 | |
| 85 | S | B | -1.6098 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.3972 | |
| 88 | S | B | -1.8798 | |
| 89 | E | B | -2.2097 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.8578 | |
| 92 | A | B | -0.6840 | |
| 93 | V | B | -0.0579 | |
| 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 | I | B | 0.0000 | |
| 100 | Y | B | 1.1824 | |
| 101 | Y | B | 1.6259 | |
| 102 | Y | B | 0.8968 | |
| 103 | G | B | 0.0000 | |
| 104 | S | B | 0.0000 | |
| 105 | S | B | 0.0000 | |
| 106 | D | B | -0.0154 | |
| 107 | Y | B | -0.0873 | |
| 108 | W | B | -0.6044 | |
| 109 | G | B | 0.0000 | |
| 110 | Q | B | -1.5764 | |
| 111 | G | B | -0.8729 | |
| 112 | T | B | 0.0000 | |
| 113 | T | B | -0.1631 | |
| 114 | L | B | 0.0000 | |
| 115 | T | B | 0.0000 | |
| 116 | V | B | 0.0000 | |
| 117 | S | B | 0.0000 | |
| 118 | S | B | 0.2167 | |
| 119 | V | B | 0.9739 | |
| 120 | A | B | 0.2443 | |
| 121 | A | B | 0.0578 | |
| 122 | P | B | 0.0000 | |
| 123 | S | B | -0.2249 | |
| 124 | V | B | 0.0000 | |
| 125 | F | B | 0.0000 | |
| 126 | I | B | 0.0000 | |
| 127 | F | B | 0.0000 | |
| 128 | P | B | -0.7752 | |
| 129 | P | B | 0.0000 | |
| 130 | S | B | 0.0000 | |
| 131 | D | B | -2.9067 | |
| 132 | E | B | -2.6027 | |
| 133 | Q | B | 0.0000 | |
| 134 | L | B | -2.1485 | |
| 135 | K | B | -2.7171 | |
| 136 | S | B | -1.7018 | |
| 137 | G | B | -1.3438 | |
| 138 | T | B | -1.0189 | |
| 139 | A | B | 0.0000 | |
| 140 | S | B | 0.0000 | |
| 141 | V | B | 0.0000 | |
| 142 | V | B | 0.0000 | |
| 143 | C | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | N | B | 0.0000 | |
| 147 | N | B | -0.8861 | |
| 148 | F | B | 0.0000 | |
| 149 | Y | B | 0.0000 | |
| 150 | P | B | 0.0000 | |
| 151 | R | B | -3.0174 | |
| 152 | E | B | -3.2409 | |
| 153 | A | B | -2.3534 | |
| 154 | K | B | -2.4302 | |
| 155 | V | B | -1.1467 | |
| 156 | Q | B | -0.5900 | |
| 157 | W | B | 0.0000 | |
| 158 | K | B | -0.3942 | |
| 159 | V | B | 0.0000 | |
| 160 | D | B | -1.5251 | |
| 161 | N | B | -1.1515 | |
| 162 | A | B | -0.1507 | |
| 163 | L | B | 0.7159 | |
| 164 | Q | B | -0.2996 | |
| 165 | S | B | -0.6382 | |
| 166 | G | B | -1.2309 | |
| 167 | N | B | -1.5059 | |
| 168 | S | B | -1.4774 | |
| 169 | Q | B | -1.5341 | |
| 170 | E | B | -1.9640 | |
| 171 | S | B | -1.0318 | |
| 172 | V | B | -1.0178 | |
| 173 | T | B | -1.2159 | |
| 174 | E | B | -2.3547 | |
| 175 | Q | B | -2.2573 | |
| 176 | D | B | -2.1851 | |
| 177 | S | B | -2.2420 | |
| 178 | K | B | -2.7075 | |
| 179 | D | B | -2.1480 | |
| 180 | S | B | -1.6874 | |
| 181 | T | B | 0.0000 | |
| 182 | Y | B | -1.3929 | |
| 183 | S | B | 0.0000 | |
| 184 | L | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | T | B | -0.8243 | |
| 188 | L | B | 0.0000 | |
| 189 | T | B | -0.6262 | |
| 190 | L | B | -0.8146 | |
| 191 | S | B | -1.0745 | |
| 192 | K | B | -2.0829 | |
| 193 | A | B | -1.8799 | |
| 194 | D | B | -2.5826 | |
| 195 | Y | B | 0.0000 | |
| 196 | E | B | -3.4799 | |
| 197 | K | B | -3.5763 | |
| 198 | H | B | -2.9087 | |
| 199 | K | B | -3.0553 | |
| 200 | V | B | -1.3157 | |
| 201 | Y | B | 0.0000 | |
| 202 | A | B | 0.0000 | |
| 203 | C | B | 0.0000 | |
| 204 | E | B | -0.7564 | |
| 205 | V | B | 0.0000 | |
| 206 | T | B | -1.2140 | |
| 207 | H | B | 0.0000 | |
| 208 | Q | B | -1.6641 | |
| 209 | G | B | -0.2672 | |
| 210 | L | B | -0.3347 | |
| 211 | S | B | -0.4485 | |
| 212 | S | B | -0.4491 | |
| 213 | P | B | -0.5764 | |
| 214 | V | B | -0.0247 | |
| 215 | T | B | -0.3903 | |
| 216 | K | B | -0.7130 | |
| 217 | S | B | -0.6340 | |
| 218 | F | B | 0.0000 | |
| 219 | N | B | -1.9455 | |
| 220 | R | B | -2.4795 | |
| 221 | G | B | -1.8816 | |
| 222 | E | B | -2.1235 | |
| 223 | C | B | -0.6785 |
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 | -0.7799 | 2.5906 | View | CSV | PDB |
| 4.5 | -0.8185 | 2.5906 | View | CSV | PDB |
| 5.0 | -0.8648 | 2.5906 | View | CSV | PDB |
| 5.5 | -0.9084 | 2.5906 | View | CSV | PDB |
| 6.0 | -0.9371 | 2.5906 | View | CSV | PDB |
| 6.5 | -0.9402 | 2.5906 | View | CSV | PDB |
| 7.0 | -0.9169 | 2.5906 | View | CSV | PDB |
| 7.5 | -0.8757 | 2.5906 | View | CSV | PDB |
| 8.0 | -0.8249 | 2.5906 | View | CSV | PDB |
| 8.5 | -0.7685 | 2.5906 | View | CSV | PDB |
| 9.0 | -0.7077 | 2.5905 | 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