| Chain sequence(s) |
A: EVQLVESGGGLVQPGGSLRLSCAASGFNISYYYIHWVRQAPGKGLEWVASISSSYGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREVMWRFSHIGLRYESSMDITYVMDYWGQGTLVTVSSASASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV
B: DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSAHYHHAPITFGQGTKVEIKRGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 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] (00:00:12)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:12)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:12)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:12)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:13)
[INFO] FoldX: Starting FoldX energy minimization (00:00:13)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:43)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/bcbfc8bdd3aae3e/tmp/folded.pdb (00:03:43)
[INFO] Main: Simulation completed successfully. (00:06:49)
|
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 | E | A | -2.1151 | |
| 2 | V | A | -1.2843 | |
| 3 | Q | A | -1.0601 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 1.1130 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.3065 | |
| 8 | G | A | -0.9033 | |
| 9 | G | A | -0.4616 | |
| 10 | G | A | 0.0000 | |
| 11 | L | A | -0.0630 | |
| 12 | V | A | 0.0000 | |
| 13 | Q | A | -1.7989 | |
| 14 | P | A | -1.9558 | |
| 15 | G | A | -1.5867 | |
| 16 | G | A | -1.2198 | |
| 17 | S | A | -1.4313 | |
| 18 | L | A | -1.0934 | |
| 19 | R | A | -2.1661 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.2889 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | 0.0095 | |
| 24 | A | A | -0.4108 | |
| 25 | S | A | -1.0730 | |
| 26 | G | A | -1.4025 | |
| 27 | F | A | -0.5644 | |
| 28 | N | A | -0.5428 | |
| 29 | I | A | 0.0000 | |
| 30 | S | A | 0.4515 | |
| 31 | Y | A | 1.4255 | |
| 32 | Y | A | 0.9657 | |
| 33 | Y | A | 0.7072 | |
| 34 | I | A | 0.0000 | |
| 35 | H | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.7894 | |
| 40 | A | A | -1.1965 | |
| 41 | P | A | -0.9654 | |
| 42 | G | A | -1.4755 | |
| 43 | K | A | -2.3882 | |
| 44 | G | A | -1.6422 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -1.0710 | |
| 47 | W | A | 0.0000 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | S | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | S | A | 0.0000 | |
| 53 | S | A | 0.2358 | |
| 54 | S | A | 0.5882 | |
| 55 | Y | A | 1.0940 | |
| 56 | G | A | 0.0159 | |
| 57 | S | A | 0.0325 | |
| 58 | T | A | -0.0422 | |
| 59 | S | A | -0.5111 | |
| 60 | Y | A | -0.9722 | |
| 61 | A | A | -1.4555 | |
| 62 | D | A | -2.5278 | |
| 63 | S | A | -1.7948 | |
| 64 | V | A | 0.0000 | |
| 65 | K | A | -2.6519 | |
| 66 | G | A | -1.7813 | |
| 67 | R | A | -1.6096 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.9693 | |
| 70 | I | A | 0.0000 | |
| 71 | S | A | -0.3558 | |
| 72 | A | A | -0.6399 | |
| 73 | D | A | -1.1438 | |
| 74 | T | A | -1.1850 | |
| 75 | S | A | -1.3430 | |
| 76 | K | A | -2.1545 | |
| 77 | N | A | -1.4791 | |
| 78 | T | A | 0.0000 | |
| 79 | A | A | 0.0000 | |
| 80 | Y | A | -0.6017 | |
| 81 | L | A | 0.0000 | |
| 82 | Q | A | -1.5769 | |
| 83 | M | A | 0.0000 | |
| 84 | N | A | -1.5879 | |
| 85 | S | A | -1.4296 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -2.9500 | |
| 88 | A | A | -2.0277 | |
| 89 | E | A | -2.4403 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | -0.8481 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.2083 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | 0.0000 | |
| 99 | E | A | 0.0000 | |
| 100 | V | A | 0.0000 | |
| 101 | M | A | 0.5386 | |
| 102 | W | A | 0.1848 | |
| 103 | R | A | -1.0932 | |
| 104 | F | A | 0.0848 | |
| 105 | S | A | -0.3009 | |
| 106 | H | A | -0.5348 | |
| 107 | I | A | 1.3273 | |
| 108 | G | A | 0.1827 | |
| 109 | L | A | 0.7972 | |
| 110 | R | A | -0.9767 | |
| 111 | Y | A | 0.0364 | |
| 112 | E | A | -1.5555 | |
| 113 | S | A | -0.6485 | |
| 114 | S | A | -0.6528 | |
| 115 | M | A | -0.2347 | |
| 116 | D | A | -0.2905 | |
| 117 | I | A | 0.1049 | |
| 118 | T | A | 0.0000 | |
| 119 | Y | A | 0.0000 | |
| 120 | V | A | 0.0000 | |
| 121 | M | A | 0.0000 | |
| 122 | D | A | -0.1704 | |
| 123 | Y | A | -0.1797 | |
| 124 | W | A | 0.0000 | |
| 125 | G | A | 0.0000 | |
| 126 | Q | A | -1.2664 | |
| 127 | G | A | 0.0000 | |
| 128 | T | A | 0.0023 | |
| 129 | L | A | 0.1395 | |
| 130 | V | A | 0.0000 | |
| 131 | T | A | -0.4994 | |
| 132 | V | A | 0.0000 | |
| 133 | S | A | -1.0921 | |
| 134 | S | A | -0.9281 | |
| 135 | A | A | -0.4108 | |
| 136 | S | A | -0.4713 | |
| 137 | A | A | -0.3789 | |
| 138 | S | A | -0.3963 | |
| 139 | T | A | -0.6337 | |
| 140 | K | A | -1.0332 | |
| 141 | G | A | -1.2198 | |
| 142 | P | A | 0.0000 | |
| 143 | S | A | -0.2196 | |
| 144 | V | A | 0.0000 | |
| 145 | F | A | 0.0000 | |
| 146 | P | A | -0.5248 | |
| 147 | L | A | 0.0000 | |
| 148 | A | A | -0.0388 | |
| 149 | P | A | -0.1545 | |
| 150 | S | A | -0.7922 | |
| 151 | S | A | -1.0280 | |
| 152 | K | A | -1.4775 | |
| 153 | S | A | -0.7534 | |
| 154 | T | A | -0.8546 | |
| 155 | S | A | -0.8640 | |
| 156 | G | A | -0.8492 | |
| 157 | G | A | -0.9078 | |
| 158 | T | A | -0.6053 | |
| 159 | A | A | 0.0000 | |
| 160 | A | A | -0.2501 | |
| 161 | L | A | 0.0000 | |
| 162 | G | A | 0.0000 | |
| 163 | C | A | 0.0000 | |
| 164 | L | A | 0.0000 | |
| 165 | V | A | 0.0000 | |
| 166 | K | A | 0.0000 | |
| 167 | D | A | -0.1935 | |
| 168 | Y | A | 0.0000 | |
| 169 | F | A | -0.0589 | |
| 170 | P | A | 0.0000 | |
| 171 | E | A | -0.2342 | |
| 172 | P | A | -0.5051 | |
| 173 | V | A | -0.5774 | |
| 174 | T | A | -0.5864 | |
| 175 | V | A | -0.2110 | |
| 176 | S | A | -0.3587 | |
| 177 | W | A | 0.0000 | |
| 178 | N | A | -0.6949 | |
| 179 | S | A | -0.6053 | |
| 180 | G | A | -0.4649 | |
| 181 | A | A | -0.2023 | |
| 182 | L | A | 0.0284 | |
| 183 | T | A | -0.1904 | |
| 184 | S | A | -0.2767 | |
| 185 | G | A | -0.3546 | |
| 186 | V | A | 0.1580 | |
| 187 | H | A | -0.1330 | |
| 188 | T | A | 0.0057 | |
| 189 | F | A | 0.0000 | |
| 190 | P | A | -0.2309 | |
| 191 | A | A | 0.1112 | |
| 192 | V | A | 0.0000 | |
| 193 | L | A | 1.1714 | |
| 194 | Q | A | 0.2547 | |
| 195 | S | A | -0.1500 | |
| 196 | S | A | -0.1789 | |
| 197 | G | A | 0.0882 | |
| 198 | L | A | 0.2354 | |
| 199 | Y | A | 0.5047 | |
| 200 | S | A | 0.0000 | |
| 201 | L | A | 0.0000 | |
| 202 | S | A | 0.0000 | |
| 203 | S | A | 0.0000 | |
| 204 | V | A | 0.1608 | |
| 205 | V | A | 0.0000 | |
| 206 | T | A | -0.2302 | |
| 207 | V | A | 0.0000 | |
| 208 | P | A | -0.5610 | |
| 209 | S | A | -0.4947 | |
| 210 | S | A | -0.4679 | |
| 211 | S | A | -0.3757 | |
| 212 | L | A | 0.0039 | |
| 213 | G | A | -0.4889 | |
| 214 | T | A | -0.5483 | |
| 215 | Q | A | -0.7905 | |
| 216 | T | A | -0.5694 | |
| 217 | Y | A | 0.0000 | |
| 218 | I | A | -0.8527 | |
| 219 | C | A | 0.0000 | |
| 220 | N | A | -1.4817 | |
| 221 | V | A | 0.0000 | |
| 222 | N | A | -2.0309 | |
| 223 | H | A | 0.0000 | |
| 224 | K | A | -2.3006 | |
| 225 | P | A | -1.2571 | |
| 226 | S | A | -1.6455 | |
| 227 | N | A | -2.4179 | |
| 228 | T | A | -2.0125 | |
| 229 | K | A | -2.7252 | |
| 230 | V | A | -1.6552 | |
| 231 | D | A | -2.3077 | |
| 232 | K | A | -1.8187 | |
| 233 | K | A | -1.8018 | |
| 234 | V | A | -0.3631 | |
| 1 | D | B | -2.1283 | |
| 2 | I | B | -1.5078 | |
| 3 | Q | B | -2.1549 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -1.3949 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9042 | |
| 8 | P | B | -0.6110 | |
| 9 | S | B | -0.8701 | |
| 10 | S | B | -0.8272 | |
| 11 | L | B | -0.5228 | |
| 12 | S | B | -1.2544 | |
| 13 | A | B | 0.0000 | |
| 14 | S | B | -0.9147 | |
| 15 | V | B | 0.1048 | |
| 16 | G | B | -0.8370 | |
| 17 | D | B | -1.5940 | |
| 18 | R | B | -2.2334 | |
| 19 | V | B | 0.0000 | |
| 20 | T | B | -0.5975 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8183 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -2.6372 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -1.8057 | |
| 27 | Q | B | -1.8384 | |
| 28 | S | B | -1.0187 | |
| 29 | V | B | 0.0000 | |
| 30 | S | B | -0.1183 | |
| 31 | S | B | -0.3995 | |
| 32 | A | B | 0.0000 | |
| 33 | V | B | 0.0000 | |
| 34 | A | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | 0.0000 | |
| 39 | K | B | -1.6928 | |
| 40 | P | B | -1.4171 | |
| 41 | G | B | -1.6411 | |
| 42 | K | B | -2.5971 | |
| 43 | A | B | -1.6202 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.4836 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | Y | B | 0.4179 | |
| 50 | S | B | -0.0844 | |
| 51 | A | B | 0.0000 | |
| 52 | S | B | -0.3251 | |
| 53 | S | B | 0.2737 | |
| 54 | L | B | 0.4724 | |
| 55 | Y | B | 0.1464 | |
| 56 | S | B | -0.1757 | |
| 57 | G | B | -0.4023 | |
| 58 | V | B | -0.2172 | |
| 59 | P | B | -0.2673 | |
| 60 | S | B | -0.3241 | |
| 61 | R | B | -0.7084 | |
| 62 | F | B | 0.0000 | |
| 63 | S | B | -0.2823 | |
| 64 | G | B | -0.4005 | |
| 65 | S | B | -0.8839 | |
| 66 | R | B | -1.5554 | |
| 67 | S | B | -1.2389 | |
| 68 | G | B | -1.3015 | |
| 69 | T | B | -1.5357 | |
| 70 | D | B | -1.6968 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.8093 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -0.6057 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.2958 | |
| 77 | S | B | -1.1895 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -0.9365 | |
| 80 | P | B | -0.9101 | |
| 81 | E | B | -1.5565 | |
| 82 | D | B | 0.0000 | |
| 83 | F | B | -0.7742 | |
| 84 | A | B | 0.0000 | |
| 85 | T | B | -0.8950 | |
| 86 | Y | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | C | B | 0.0000 | |
| 89 | Q | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | A | B | -0.3512 | |
| 93 | H | B | -0.0379 | |
| 94 | Y | B | 0.6540 | |
| 95 | H | B | -0.5419 | |
| 96 | H | B | -0.3714 | |
| 97 | A | B | -0.3452 | |
| 98 | P | B | -0.7939 | |
| 99 | I | B | 0.0000 | |
| 100 | T | B | -0.6785 | |
| 101 | F | B | -0.4700 | |
| 102 | G | B | 0.0000 | |
| 103 | Q | B | -1.9071 | |
| 104 | G | B | 0.0000 | |
| 105 | T | B | 0.0000 | |
| 106 | K | B | -1.5903 | |
| 107 | V | B | 0.0000 | |
| 108 | E | B | -1.3458 | |
| 109 | I | B | -1.0901 | |
| 110 | K | B | -2.1398 | |
| 111 | R | B | -2.7809 | |
| 112 | G | B | -2.0566 | |
| 113 | Q | B | -1.5374 | |
| 114 | P | B | -1.6822 | |
| 115 | K | B | -2.5493 | |
| 116 | A | B | -1.9770 | |
| 117 | N | B | -2.1918 | |
| 118 | P | B | 0.0000 | |
| 119 | T | B | -0.5445 | |
| 120 | V | B | 0.0000 | |
| 121 | T | B | -0.4167 | |
| 122 | L | B | 0.0000 | |
| 123 | F | B | 0.0000 | |
| 124 | P | B | -0.2669 | |
| 125 | P | B | 0.0000 | |
| 126 | S | B | -0.7790 | |
| 127 | S | B | -1.3593 | |
| 128 | E | B | -2.1982 | |
| 129 | E | B | 0.0000 | |
| 130 | L | B | -1.9069 | |
| 131 | Q | B | -2.2731 | |
| 132 | A | B | -1.8137 | |
| 133 | N | B | -2.5058 | |
| 134 | K | B | -2.2252 | |
| 135 | A | B | 0.0000 | |
| 136 | T | B | 0.0000 | |
| 137 | L | B | 0.0000 | |
| 138 | V | B | 0.0000 | |
| 139 | C | B | 0.0000 | |
| 140 | L | B | 0.0000 | |
| 141 | I | B | 0.0000 | |
| 142 | S | B | -0.7543 | |
| 143 | D | B | -1.4027 | |
| 144 | F | B | 0.0000 | |
| 145 | Y | B | 0.0000 | |
| 146 | P | B | -1.4219 | |
| 147 | G | B | -0.8695 | |
| 148 | A | B | -0.4165 | |
| 149 | V | B | -0.2862 | |
| 150 | T | B | -0.0865 | |
| 151 | V | B | 0.1188 | |
| 152 | A | B | -0.4043 | |
| 153 | W | B | 0.0000 | |
| 154 | K | B | -1.1274 | |
| 155 | A | B | 0.0000 | |
| 156 | D | B | -1.5637 | |
| 157 | G | B | -1.1940 | |
| 158 | S | B | -0.7808 | |
| 159 | P | B | -0.9186 | |
| 160 | V | B | -0.8788 | |
| 161 | K | B | -1.6530 | |
| 162 | A | B | -0.8172 | |
| 163 | G | B | -0.6665 | |
| 164 | V | B | -0.4856 | |
| 165 | E | B | -0.3320 | |
| 166 | T | B | -0.3239 | |
| 167 | T | B | -0.7526 | |
| 168 | K | B | -1.7775 | |
| 169 | P | B | -1.0330 | |
| 170 | S | B | -0.9672 | |
| 171 | K | B | -1.3023 | |
| 172 | Q | B | -1.1340 | |
| 173 | S | B | -1.2411 | |
| 174 | N | B | -1.6058 | |
| 175 | N | B | -1.2961 | |
| 176 | K | B | -1.5166 | |
| 177 | Y | B | -0.9457 | |
| 178 | A | B | 0.0000 | |
| 179 | A | B | 0.0000 | |
| 180 | S | B | 0.0000 | |
| 181 | S | B | 0.0000 | |
| 182 | Y | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | -0.4358 | |
| 185 | L | B | -1.0083 | |
| 186 | T | B | -1.6959 | |
| 187 | P | B | -2.3526 | |
| 188 | E | B | -3.1223 | |
| 189 | Q | B | -2.2691 | |
| 190 | W | B | 0.0000 | |
| 191 | K | B | -3.1124 | |
| 192 | S | B | -2.3810 | |
| 193 | H | B | -2.4294 | |
| 194 | R | B | -2.6073 | |
| 195 | S | B | -1.8252 | |
| 196 | Y | B | 0.0000 | |
| 197 | S | B | 0.0000 | |
| 198 | C | B | 0.0000 | |
| 199 | Q | B | -0.7466 | |
| 200 | V | B | 0.0000 | |
| 201 | T | B | -0.8004 | |
| 202 | H | B | 0.0000 | |
| 203 | E | B | -2.5154 | |
| 204 | G | B | -1.4063 | |
| 205 | S | B | -1.0753 | |
| 206 | T | B | -0.8619 | |
| 207 | V | B | -0.7344 | |
| 208 | E | B | -1.4841 | |
| 209 | K | B | -1.1905 | |
| 210 | T | B | -0.8661 | |
| 211 | V | B | 0.0000 | |
| 212 | A | B | -1.4538 | |
| 213 | P | B | -1.5744 | |
| 214 | T | B | -1.4652 | |
| 215 | E | B | -1.9101 | |
| 216 | C | B | -0.7104 | |
| 217 | S | B | -0.6534 |
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 | -0.7817 | 1.4851 | View | CSV | PDB |
| 4.5 | -0.8138 | 1.4652 | View | CSV | PDB |
| 5.0 | -0.8495 | 1.4377 | View | CSV | PDB |
| 5.5 | -0.8803 | 1.406 | View | CSV | PDB |
| 6.0 | -0.896 | 1.3741 | View | CSV | PDB |
| 6.5 | -0.8892 | 1.3459 | View | CSV | PDB |
| 7.0 | -0.8618 | 1.3319 | View | CSV | PDB |
| 7.5 | -0.823 | 1.3317 | View | CSV | PDB |
| 8.0 | -0.7791 | 1.3541 | View | CSV | PDB |
| 8.5 | -0.7319 | 1.5113 | View | CSV | PDB |
| 9.0 | -0.6815 | 1.6684 | 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