| Chain sequence(s) |
A: EVQLLESGGGLVQPGGSLRLSCAASGFTFSIYSMNWVRQAPGKGLEWVSSIGSSGGTTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAGSQWLYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH
B: DIQMTQSPSSLSASVGDRVTITCRSSQRIMTYLNWYQQKPGKAPKLLIFVASHSQSGVPSRFRGSGSETDFTLTISGLQPEDSATYYCQQSFWTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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] (00:00:00)
[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 (00:05:22)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/e3191f3ae7c5594/tmp/folded.pdb (00:05:22)
[INFO] Main: Simulation completed successfully. (00:07:27)
|
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 |
|---|---|---|---|---|
| 4 | E | A | -1.3947 | |
| 5 | V | A | 0.1500 | |
| 6 | Q | A | -0.5215 | |
| 7 | L | A | 0.0000 | |
| 8 | L | A | 0.3071 | |
| 9 | E | A | 0.0000 | |
| 10 | S | A | -0.4785 | |
| 11 | G | A | -0.7662 | |
| 12 | G | A | -0.7211 | |
| 13 | G | A | -0.5688 | |
| 14 | L | A | -0.3446 | |
| 15 | V | A | 0.0000 | |
| 16 | Q | A | -1.7413 | |
| 17 | P | A | -1.9201 | |
| 18 | G | A | -1.6117 | |
| 19 | G | A | -1.1346 | |
| 20 | S | A | -0.9070 | |
| 21 | L | A | -0.7262 | |
| 22 | R | A | -1.3473 | |
| 23 | L | A | 0.0000 | |
| 24 | S | A | -0.3465 | |
| 25 | C | A | 0.0000 | |
| 26 | A | A | -0.3936 | |
| 27 | A | A | -0.3080 | |
| 28 | S | A | -0.3998 | |
| 29 | G | A | -0.5158 | |
| 30 | F | A | 0.2129 | |
| 31 | T | A | 0.4261 | |
| 32 | F | A | 0.0000 | |
| 33 | S | A | 0.1217 | |
| 34 | I | A | 1.3007 | |
| 35 | Y | A | 0.7507 | |
| 36 | S | A | 0.3514 | |
| 37 | M | A | 0.0000 | |
| 38 | N | A | 0.0000 | |
| 39 | W | A | 0.0000 | |
| 40 | V | A | 0.0000 | |
| 41 | R | A | 0.0000 | |
| 42 | Q | A | -0.9274 | |
| 43 | A | A | -1.3468 | |
| 44 | P | A | -1.2843 | |
| 45 | G | A | -1.4730 | |
| 46 | K | A | -2.3042 | |
| 47 | G | A | -1.5166 | |
| 48 | L | A | 0.0000 | |
| 49 | E | A | -1.1823 | |
| 50 | W | A | 0.0000 | |
| 51 | V | A | 0.0000 | |
| 52 | S | A | 0.0000 | |
| 53 | S | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | G | A | 0.0211 | |
| 56 | S | A | 0.1106 | |
| 57 | S | A | -0.2917 | |
| 58 | G | A | -0.7522 | |
| 59 | G | A | -0.5854 | |
| 60 | T | A | -0.2606 | |
| 61 | T | A | 0.1337 | |
| 62 | Y | A | 0.2567 | |
| 63 | Y | A | -0.5693 | |
| 64 | A | A | -1.4892 | |
| 65 | D | A | -2.6247 | |
| 66 | S | A | -1.8941 | |
| 67 | V | A | 0.0000 | |
| 68 | K | A | -2.5627 | |
| 69 | G | A | -1.7861 | |
| 70 | R | A | -1.3349 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.6579 | |
| 73 | I | A | 0.0000 | |
| 74 | S | A | -0.5026 | |
| 75 | R | A | -1.1652 | |
| 76 | D | A | -1.7716 | |
| 77 | N | A | -1.8004 | |
| 78 | S | A | -1.7394 | |
| 79 | K | A | -2.4896 | |
| 80 | N | A | -1.9639 | |
| 81 | T | A | -1.1819 | |
| 82 | L | A | 0.0000 | |
| 83 | Y | A | -0.4278 | |
| 84 | L | A | 0.0000 | |
| 85 | Q | A | -0.8407 | |
| 86 | M | A | 0.0000 | |
| 87 | N | A | -1.3343 | |
| 88 | S | A | -1.3961 | |
| 89 | L | A | 0.0000 | |
| 90 | R | A | -2.8687 | |
| 91 | A | A | -2.0409 | |
| 92 | E | A | -2.4435 | |
| 93 | D | A | 0.0000 | |
| 94 | T | A | -0.9545 | |
| 95 | A | A | 0.0000 | |
| 96 | V | A | -0.0078 | |
| 97 | Y | A | 0.0000 | |
| 98 | Y | A | 0.0000 | |
| 99 | C | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | G | A | 0.0000 | |
| 102 | S | A | 0.0000 | |
| 103 | Q | A | 0.6215 | |
| 104 | W | A | 1.5761 | |
| 105 | L | A | 1.6985 | |
| 106 | Y | A | 1.3353 | |
| 107 | G | A | 0.0000 | |
| 108 | M | A | 0.0000 | |
| 109 | D | A | -0.7829 | |
| 110 | V | A | 0.0000 | |
| 111 | W | A | -0.3088 | |
| 112 | G | A | 0.0000 | |
| 113 | Q | A | -1.4548 | |
| 114 | G | A | -0.7536 | |
| 115 | T | A | -0.2507 | |
| 116 | T | A | -0.1267 | |
| 117 | V | A | 0.0000 | |
| 118 | T | A | 0.0000 | |
| 119 | V | A | 0.0000 | |
| 120 | S | A | -0.8825 | |
| 121 | S | A | -0.7719 | |
| 122 | A | A | -0.5414 | |
| 123 | S | A | -0.6671 | |
| 124 | T | A | -0.9393 | |
| 125 | K | A | -1.5813 | |
| 126 | G | A | -1.6246 | |
| 127 | P | A | 0.0000 | |
| 128 | S | A | -0.4648 | |
| 129 | V | A | 0.0000 | |
| 130 | F | A | 0.0000 | |
| 131 | P | A | -1.1810 | |
| 132 | L | A | 0.0000 | |
| 133 | A | A | -1.0985 | |
| 134 | P | A | 0.0000 | |
| 135 | S | A | -1.1271 | |
| 136 | S | A | -1.5924 | |
| 137 | K | A | -1.9508 | |
| 138 | S | A | -1.1448 | |
| 139 | T | A | -1.0759 | |
| 140 | S | A | -0.7997 | |
| 141 | G | A | -0.9706 | |
| 142 | G | A | -0.8973 | |
| 143 | T | A | -0.6159 | |
| 144 | A | A | 0.0000 | |
| 145 | A | A | 0.0000 | |
| 146 | L | A | 0.0000 | |
| 147 | G | A | 0.0000 | |
| 148 | C | A | 0.0000 | |
| 149 | L | A | 0.0000 | |
| 150 | V | A | 0.0000 | |
| 151 | K | A | 0.0000 | |
| 152 | D | A | -0.6501 | |
| 153 | Y | A | 0.0000 | |
| 154 | F | A | 0.0000 | |
| 155 | P | A | 0.0000 | |
| 156 | E | A | -0.5306 | |
| 157 | P | A | -0.6608 | |
| 158 | V | A | -0.6594 | |
| 159 | T | A | -0.6243 | |
| 160 | V | A | -0.3893 | |
| 161 | S | A | -0.4723 | |
| 162 | W | A | 0.0000 | |
| 163 | N | A | -0.9421 | |
| 164 | S | A | -0.7533 | |
| 165 | G | A | -0.6283 | |
| 166 | A | A | -0.2777 | |
| 167 | L | A | -0.0259 | |
| 168 | T | A | -0.1949 | |
| 169 | S | A | -0.2198 | |
| 170 | G | A | -0.2260 | |
| 171 | V | A | 0.1371 | |
| 172 | H | A | -0.3628 | |
| 173 | T | A | -0.1931 | |
| 174 | F | A | 0.0000 | |
| 175 | P | A | -0.3647 | |
| 176 | A | A | 0.2816 | |
| 177 | V | A | 0.6966 | |
| 178 | L | A | 1.4516 | |
| 179 | Q | A | 0.4293 | |
| 180 | S | A | -0.0415 | |
| 181 | S | A | -0.2566 | |
| 182 | G | A | -0.0719 | |
| 183 | L | A | 0.0229 | |
| 184 | Y | A | 0.6062 | |
| 185 | S | A | 0.0000 | |
| 186 | L | A | 0.0000 | |
| 187 | S | A | 0.0000 | |
| 188 | S | A | 0.0000 | |
| 189 | V | A | 0.0000 | |
| 190 | V | A | 0.0000 | |
| 191 | T | A | -0.1807 | |
| 192 | V | A | 0.0000 | |
| 193 | P | A | -0.6299 | |
| 194 | S | A | -0.8565 | |
| 195 | S | A | -0.5839 | |
| 196 | S | A | -0.6332 | |
| 197 | L | A | -0.8150 | |
| 198 | G | A | -1.0357 | |
| 199 | T | A | -0.7312 | |
| 200 | Q | A | -1.2488 | |
| 201 | T | A | -1.2199 | |
| 202 | Y | A | 0.0000 | |
| 203 | I | A | -1.5048 | |
| 204 | C | A | 0.0000 | |
| 205 | N | A | -1.6269 | |
| 206 | V | A | 0.0000 | |
| 207 | N | A | -2.0105 | |
| 208 | H | A | 0.0000 | |
| 209 | K | A | -2.5543 | |
| 210 | P | A | -1.5711 | |
| 211 | S | A | -1.9164 | |
| 212 | N | A | -2.3970 | |
| 213 | T | A | -2.0745 | |
| 214 | K | A | -2.7121 | |
| 215 | V | A | -1.7726 | |
| 216 | D | A | -2.4843 | |
| 217 | K | A | -2.3163 | |
| 218 | R | A | -2.7894 | |
| 219 | V | A | 0.0000 | |
| 220 | E | A | -2.9098 | |
| 221 | P | A | -1.9613 | |
| 222 | K | A | -2.8758 | |
| 223 | S | A | -2.1666 | |
| 224 | C | A | -2.5151 | |
| 225 | D | A | -3.3477 | |
| 226 | K | A | -3.3904 | |
| 227 | T | A | -2.7565 | |
| 228 | H | A | -2.4408 | |
| 1 | D | B | -2.3537 | |
| 2 | I | B | 0.0000 | |
| 3 | Q | B | -2.1904 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -0.9429 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.5904 | |
| 8 | P | B | -0.6241 | |
| 9 | S | B | -0.8668 | |
| 10 | S | B | -0.9219 | |
| 11 | L | B | -0.5381 | |
| 12 | S | B | -0.7233 | |
| 13 | A | B | -0.9442 | |
| 14 | S | B | -0.8958 | |
| 15 | V | B | -0.2634 | |
| 16 | G | B | -1.0165 | |
| 17 | D | B | -2.0449 | |
| 18 | R | B | -2.4213 | |
| 19 | V | B | 0.0000 | |
| 20 | T | B | -0.7516 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.6734 | |
| 23 | C | B | 0.0000 | |
| 24 | R | B | -2.2016 | |
| 25 | S | B | 0.0000 | |
| 26 | S | B | -2.2802 | |
| 27 | Q | B | -2.7954 | |
| 28 | R | B | -2.6282 | |
| 29 | I | B | 0.0000 | |
| 30 | M | B | -0.4972 | |
| 31 | T | B | -0.1161 | |
| 32 | Y | B | 0.8673 | |
| 33 | L | B | 0.0000 | |
| 34 | N | 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 | -1.5680 | |
| 40 | P | B | -1.5186 | |
| 41 | G | B | -1.7610 | |
| 42 | K | B | -2.3774 | |
| 43 | A | B | -1.5079 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.2790 | |
| 46 | L | B | 0.0000 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | F | B | 0.2900 | |
| 50 | V | B | 0.5652 | |
| 51 | A | B | 0.0000 | |
| 52 | S | B | -0.7830 | |
| 53 | H | B | -1.0457 | |
| 54 | S | B | -0.9464 | |
| 55 | Q | B | -0.8688 | |
| 56 | S | B | -0.7228 | |
| 57 | G | B | -0.5825 | |
| 58 | V | B | -0.3951 | |
| 59 | P | B | -0.5312 | |
| 60 | S | B | -0.7508 | |
| 61 | R | B | -1.0646 | |
| 62 | F | B | 0.0000 | |
| 63 | R | B | -1.5189 | |
| 64 | G | B | 0.0000 | |
| 65 | S | B | -0.9133 | |
| 66 | G | B | -0.9683 | |
| 67 | S | B | -1.1269 | |
| 68 | E | B | -1.8535 | |
| 69 | T | B | -2.1845 | |
| 70 | D | B | -2.2057 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.7965 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -0.9449 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.4831 | |
| 77 | G | B | -1.2448 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -0.9497 | |
| 80 | P | B | -1.5921 | |
| 81 | E | B | -1.9133 | |
| 82 | D | B | 0.0000 | |
| 83 | S | B | 0.0000 | |
| 84 | A | B | 0.0000 | |
| 85 | T | B | -0.8493 | |
| 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 | F | B | 1.2160 | |
| 93 | W | B | 0.8403 | |
| 94 | T | B | 0.4323 | |
| 95 | P | B | -0.1764 | |
| 96 | L | B | 0.0866 | |
| 97 | T | B | -0.5442 | |
| 98 | F | B | 0.0000 | |
| 99 | G | B | 0.0000 | |
| 100 | G | B | -1.2407 | |
| 101 | G | B | -0.9990 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -1.6999 | |
| 104 | V | B | 0.0000 | |
| 105 | E | B | -1.1377 | |
| 106 | I | B | 0.0000 | |
| 107 | K | B | -1.0657 | |
| 108 | R | B | -0.7500 | |
| 109 | T | B | -0.0482 | |
| 110 | V | B | 0.3777 | |
| 111 | A | B | -0.0098 | |
| 112 | A | B | -0.0695 | |
| 113 | P | B | 0.0000 | |
| 114 | S | B | -0.2085 | |
| 115 | V | B | 0.0000 | |
| 116 | F | B | 0.0059 | |
| 117 | I | B | 0.0086 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | -0.5042 | |
| 120 | P | B | -0.7714 | |
| 121 | S | B | -1.3703 | |
| 122 | D | B | -2.6990 | |
| 123 | E | B | -2.3290 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -1.9619 | |
| 126 | K | B | -2.5221 | |
| 127 | S | B | -1.5990 | |
| 128 | G | B | -1.2350 | |
| 129 | T | B | -0.9254 | |
| 130 | A | B | 0.0000 | |
| 131 | S | B | 0.0000 | |
| 132 | V | B | 0.0000 | |
| 133 | V | B | 0.0000 | |
| 134 | C | B | 0.0000 | |
| 135 | L | B | 0.0000 | |
| 136 | L | B | 0.0000 | |
| 137 | N | B | 0.0000 | |
| 138 | N | B | -0.8625 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -1.4813 | |
| 142 | R | B | -2.6167 | |
| 143 | E | B | -2.9826 | |
| 144 | A | B | -2.2118 | |
| 145 | K | B | -2.5766 | |
| 146 | V | B | -1.1308 | |
| 147 | Q | B | -0.6067 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | 0.0000 | |
| 150 | V | B | 0.0000 | |
| 151 | D | B | -1.7528 | |
| 152 | N | B | -1.3733 | |
| 153 | A | B | -0.1207 | |
| 154 | L | B | 0.8988 | |
| 155 | Q | B | -0.0839 | |
| 156 | S | B | -0.5650 | |
| 157 | G | B | -1.0942 | |
| 158 | N | B | -1.2505 | |
| 159 | S | B | -1.2378 | |
| 160 | Q | B | -1.1941 | |
| 161 | E | B | -1.9929 | |
| 162 | S | B | -0.9475 | |
| 163 | V | B | -0.9447 | |
| 164 | T | B | -1.1058 | |
| 165 | E | B | -2.2078 | |
| 166 | Q | B | 0.0000 | |
| 167 | D | B | -2.0760 | |
| 168 | S | B | -2.2157 | |
| 169 | K | B | -2.6813 | |
| 170 | D | B | -2.1278 | |
| 171 | S | B | 0.0000 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | 0.0000 | |
| 174 | S | B | 0.0000 | |
| 175 | L | B | 0.0000 | |
| 176 | S | B | 0.0000 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | -0.6148 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | -0.4397 | |
| 181 | L | B | -0.8797 | |
| 182 | S | B | -1.2495 | |
| 183 | K | B | -2.3420 | |
| 184 | A | B | -2.1292 | |
| 185 | D | B | -2.8073 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.8495 | |
| 188 | K | B | -3.7834 | |
| 189 | H | B | -3.0467 | |
| 190 | K | B | -3.2847 | |
| 191 | V | B | -1.6652 | |
| 192 | Y | B | 0.0000 | |
| 193 | A | B | 0.0000 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -1.0598 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -1.1907 | |
| 198 | H | B | 0.0000 | |
| 199 | Q | B | -1.7048 | |
| 200 | G | B | -0.4571 | |
| 201 | L | B | -0.2575 | |
| 202 | S | B | -0.4755 | |
| 203 | S | B | -0.4986 | |
| 204 | P | B | -0.7338 | |
| 205 | V | B | -0.1385 | |
| 206 | T | B | -0.5753 | |
| 207 | K | B | -0.8642 | |
| 208 | S | B | -0.7122 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -1.9852 | |
| 211 | R | B | -2.9672 | |
| 212 | G | B | -2.7805 | |
| 213 | E | B | -3.1329 | |
| 214 | C | B | -2.0932 |
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 | -0.7839 | 3.9951 | View | CSV | PDB |
| 4.5 | -0.8288 | 3.9951 | View | CSV | PDB |
| 5.0 | -0.8811 | 3.9951 | View | CSV | PDB |
| 5.5 | -0.9298 | 3.9951 | View | CSV | PDB |
| 6.0 | -0.9629 | 3.9951 | View | CSV | PDB |
| 6.5 | -0.9716 | 3.9951 | View | CSV | PDB |
| 7.0 | -0.9572 | 3.995 | View | CSV | PDB |
| 7.5 | -0.9285 | 3.995 | View | CSV | PDB |
| 8.0 | -0.8922 | 3.9949 | View | CSV | PDB |
| 8.5 | -0.8503 | 3.9947 | View | CSV | PDB |
| 9.0 | -0.8022 | 3.9938 | 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