| Chain sequence(s) |
A: DVVVTQIPLSLPVSLGDQASISCRSSQSLVHSFGITYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVAAEDLGVYFCSQTTHVPYTFGGGTKLEIKVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSYGISWVSQRTGQGLEWIGEIYPRTANTYYNEKFKGKATLTADKSSNTAYMELRSLTSEDSAIYFCARKSTDGVDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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 (00:05:48)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/a81d1d66583d643/tmp/folded.pdb (00:05:48)
[INFO] Main: Simulation completed successfully. (00:08:08)
|
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 | -1.5371 | |
| 2 | V | A | 0.0000 | |
| 3 | V | A | 0.7624 | |
| 4 | V | A | 0.0000 | |
| 5 | T | A | 0.0934 | |
| 6 | Q | A | 0.0000 | |
| 7 | I | A | 1.3995 | |
| 8 | P | A | 1.2375 | |
| 9 | L | A | 1.6521 | |
| 10 | S | A | 0.4675 | |
| 11 | L | A | 0.2504 | |
| 12 | P | A | -0.4609 | |
| 13 | V | A | -0.6749 | |
| 14 | S | A | -0.9663 | |
| 15 | L | A | -0.5504 | |
| 16 | G | A | -1.8066 | |
| 17 | D | A | -2.9260 | |
| 18 | Q | A | -3.0294 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8486 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.3203 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -1.7637 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9185 | |
| 27 | Q | A | -1.5105 | |
| 28 | S | A | -0.9141 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.9038 | |
| 31 | H | A | 0.7274 | |
| 32 | S | A | 0.7740 | |
| 33 | F | A | 1.8510 | |
| 34 | G | A | 0.8552 | |
| 35 | I | A | 0.9017 | |
| 36 | T | A | 0.4110 | |
| 37 | Y | A | -0.0202 | |
| 38 | L | A | 0.0000 | |
| 39 | H | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -1.0081 | |
| 44 | K | A | -1.5373 | |
| 45 | P | A | -1.2051 | |
| 46 | G | A | -1.5110 | |
| 47 | Q | A | -2.0339 | |
| 48 | S | A | -1.3558 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.3066 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.6154 | |
| 55 | R | A | -0.9592 | |
| 56 | V | A | 0.0000 | |
| 57 | S | A | -0.9951 | |
| 58 | N | A | -1.2955 | |
| 59 | R | A | -1.7282 | |
| 60 | F | A | -0.7053 | |
| 61 | S | A | -0.5615 | |
| 62 | G | A | -0.8014 | |
| 63 | V | A | -0.9887 | |
| 64 | P | A | -1.2719 | |
| 65 | D | A | -2.4167 | |
| 66 | R | A | -2.2415 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.5076 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -1.0486 | |
| 71 | G | A | -1.0919 | |
| 72 | S | A | -0.7970 | |
| 73 | G | A | -0.8157 | |
| 74 | T | A | -1.4615 | |
| 75 | D | A | -2.1074 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -0.9599 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1848 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.7571 | |
| 82 | R | A | -3.3244 | |
| 83 | V | A | 0.0000 | |
| 84 | A | A | -1.4352 | |
| 85 | A | A | -1.5318 | |
| 86 | E | A | -2.2934 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | 0.0000 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0372 | |
| 91 | Y | A | 0.0000 | |
| 92 | F | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | S | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | T | A | 0.0221 | |
| 97 | T | A | 0.0475 | |
| 98 | H | A | -0.1300 | |
| 99 | V | A | 0.6877 | |
| 100 | P | A | -0.1860 | |
| 101 | Y | A | 0.0000 | |
| 102 | T | A | 0.1685 | |
| 103 | F | A | 0.2730 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.0762 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4098 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -0.7686 | |
| 111 | I | A | -0.0897 | |
| 112 | K | A | -0.2065 | |
| 113 | V | A | 0.9781 | |
| 114 | A | A | 0.1439 | |
| 115 | A | A | -0.0256 | |
| 116 | P | A | 0.0000 | |
| 117 | S | A | -0.2274 | |
| 118 | V | A | 0.0000 | |
| 119 | F | A | 0.0000 | |
| 120 | I | A | 0.0000 | |
| 121 | F | A | 0.0000 | |
| 122 | P | A | -0.7509 | |
| 123 | P | A | 0.0000 | |
| 124 | S | A | -1.6465 | |
| 125 | D | A | -2.8366 | |
| 126 | E | A | -2.7758 | |
| 127 | Q | A | 0.0000 | |
| 128 | L | A | -2.1610 | |
| 129 | K | A | -2.7863 | |
| 130 | S | A | -1.7423 | |
| 131 | G | A | -1.2506 | |
| 132 | T | A | -1.2482 | |
| 133 | A | A | 0.0000 | |
| 134 | S | A | 0.0000 | |
| 135 | V | A | 0.0000 | |
| 136 | V | A | 0.0000 | |
| 137 | C | A | 0.0000 | |
| 138 | L | A | 0.0000 | |
| 139 | L | A | 0.0000 | |
| 140 | N | A | 0.0000 | |
| 141 | N | A | -0.7429 | |
| 142 | F | A | 0.0000 | |
| 143 | Y | A | 0.0000 | |
| 144 | P | A | -1.3975 | |
| 145 | R | A | -3.0358 | |
| 146 | E | A | -3.2845 | |
| 147 | A | A | -2.3804 | |
| 148 | K | A | -2.5249 | |
| 149 | V | A | -1.2932 | |
| 150 | Q | A | -0.7831 | |
| 151 | W | A | 0.0000 | |
| 152 | K | A | -0.5417 | |
| 153 | V | A | 0.0000 | |
| 154 | D | A | -1.9150 | |
| 155 | N | A | -1.5020 | |
| 156 | A | A | -0.2379 | |
| 157 | L | A | 0.7259 | |
| 158 | Q | A | -0.2850 | |
| 159 | S | A | -0.7648 | |
| 160 | G | A | -1.3255 | |
| 161 | N | A | -1.6282 | |
| 162 | S | A | -1.7622 | |
| 163 | Q | A | -2.1334 | |
| 164 | E | A | -2.2338 | |
| 165 | S | A | 0.0000 | |
| 166 | V | A | -0.7262 | |
| 167 | T | A | -0.8674 | |
| 168 | E | A | -1.5040 | |
| 169 | Q | A | 0.0000 | |
| 170 | D | A | -1.8595 | |
| 171 | S | A | -2.0932 | |
| 172 | K | A | -2.6432 | |
| 173 | D | A | -1.9177 | |
| 174 | S | A | 0.0000 | |
| 175 | T | A | 0.0000 | |
| 176 | Y | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | L | A | 0.0000 | |
| 179 | S | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | T | A | -0.9419 | |
| 182 | L | A | 0.0000 | |
| 183 | T | A | -0.7449 | |
| 184 | L | A | -0.8716 | |
| 185 | S | A | -1.1394 | |
| 186 | K | A | -2.1174 | |
| 187 | A | A | -1.9564 | |
| 188 | D | A | -2.8202 | |
| 189 | Y | A | 0.0000 | |
| 190 | E | A | -3.3032 | |
| 191 | K | A | -3.6004 | |
| 192 | H | A | -3.0169 | |
| 193 | K | A | -3.3059 | |
| 194 | V | A | -1.5689 | |
| 195 | Y | A | 0.0000 | |
| 196 | A | A | 0.0000 | |
| 197 | C | A | 0.0000 | |
| 198 | E | A | -0.9854 | |
| 199 | V | A | 0.0000 | |
| 200 | T | A | -1.3020 | |
| 201 | H | A | 0.0000 | |
| 202 | Q | A | -1.7634 | |
| 203 | G | A | -0.4331 | |
| 204 | L | A | -0.3711 | |
| 205 | S | A | -0.4582 | |
| 206 | S | A | -0.4531 | |
| 207 | P | A | -0.6224 | |
| 208 | V | A | -0.0931 | |
| 209 | T | A | -0.4790 | |
| 210 | K | A | -0.7175 | |
| 211 | S | A | -0.6394 | |
| 212 | F | A | 0.0000 | |
| 213 | N | A | -2.0064 | |
| 214 | R | A | -2.5414 | |
| 215 | G | A | -2.0184 | |
| 216 | E | A | -2.2330 | |
| 217 | C | A | -0.7091 | |
| 1 | Q | B | -1.5649 | |
| 2 | V | B | -1.0595 | |
| 3 | Q | B | -2.0731 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.2374 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.2234 | |
| 8 | G | B | -1.2682 | |
| 9 | A | B | -0.8766 | |
| 10 | E | B | -1.2071 | |
| 11 | L | B | -0.7727 | |
| 12 | A | B | 0.0000 | |
| 13 | R | B | -2.1984 | |
| 14 | P | B | -1.7141 | |
| 15 | G | B | -1.5732 | |
| 16 | A | B | -1.4541 | |
| 17 | S | B | -2.0352 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.4805 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -1.0019 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -2.0503 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.3792 | |
| 26 | G | B | -1.1008 | |
| 27 | Y | B | -0.4620 | |
| 28 | T | B | -0.1321 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.1430 | |
| 31 | S | B | -0.3864 | |
| 32 | Y | B | 0.0403 | |
| 33 | G | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | S | B | 0.0000 | |
| 39 | Q | B | -0.6737 | |
| 40 | R | B | -1.3401 | |
| 41 | T | B | -1.0637 | |
| 42 | G | B | -1.2664 | |
| 43 | Q | B | -1.8435 | |
| 44 | G | B | -1.1826 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.7306 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | E | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | Y | B | -0.4941 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.2869 | |
| 55 | T | B | -1.2464 | |
| 56 | A | B | -1.2721 | |
| 57 | N | B | -1.2618 | |
| 58 | T | B | -0.0149 | |
| 59 | Y | B | 0.6644 | |
| 60 | Y | B | -0.4021 | |
| 61 | N | B | -1.6026 | |
| 62 | E | B | -3.2127 | |
| 63 | K | B | -3.2231 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9552 | |
| 66 | G | B | -2.3151 | |
| 67 | K | B | -2.3005 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.2632 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.5763 | |
| 72 | A | B | -1.3183 | |
| 73 | D | B | -2.0390 | |
| 74 | K | B | -2.5881 | |
| 75 | S | B | -1.4300 | |
| 76 | S | B | -1.4322 | |
| 77 | N | B | -1.8468 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.7281 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -2.2563 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.7399 | |
| 85 | S | B | -1.6543 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.5468 | |
| 88 | S | B | -1.4990 | |
| 89 | E | B | -2.0452 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.7803 | |
| 92 | A | B | 0.0000 | |
| 93 | I | B | 0.2819 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | K | B | -0.1102 | |
| 100 | S | B | -0.1577 | |
| 101 | T | B | -0.2271 | |
| 102 | D | B | -0.5461 | |
| 103 | G | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | D | B | 0.0000 | |
| 106 | Y | B | -0.2127 | |
| 107 | W | B | -0.6387 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.8435 | |
| 110 | G | B | -0.8576 | |
| 111 | T | B | 0.0000 | |
| 112 | S | B | -0.2981 | |
| 113 | V | B | 0.0000 | |
| 114 | T | B | -0.7166 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.9316 | |
| 117 | S | B | -1.0170 | |
| 118 | A | B | -0.5843 | |
| 119 | S | B | -0.6588 | |
| 120 | T | B | -0.9591 | |
| 121 | K | B | -1.2205 | |
| 122 | G | B | -1.3064 | |
| 123 | P | B | 0.0000 | |
| 124 | S | B | -0.2983 | |
| 125 | V | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -1.0639 | |
| 128 | L | B | 0.0000 | |
| 129 | A | B | -1.1283 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -0.8796 | |
| 132 | S | B | -0.6611 | |
| 133 | K | B | -0.8948 | |
| 134 | S | B | 0.0000 | |
| 135 | T | B | -0.6178 | |
| 136 | S | B | -0.6872 | |
| 137 | G | B | -0.8102 | |
| 138 | G | B | -0.8676 | |
| 139 | T | B | -0.5794 | |
| 140 | A | B | 0.0000 | |
| 141 | A | B | 0.0000 | |
| 142 | L | B | 0.0000 | |
| 143 | G | B | 0.0000 | |
| 144 | C | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | V | B | 0.0000 | |
| 147 | K | B | 0.0000 | |
| 148 | D | B | -0.3938 | |
| 149 | Y | B | 0.0000 | |
| 150 | F | B | -0.2279 | |
| 151 | P | B | 0.0000 | |
| 152 | E | B | -0.5837 | |
| 153 | P | B | -0.7372 | |
| 154 | V | B | -0.5931 | |
| 155 | T | B | -0.5306 | |
| 156 | V | B | -0.3277 | |
| 157 | S | B | -0.4155 | |
| 158 | W | B | 0.0000 | |
| 159 | N | B | -0.8711 | |
| 160 | S | B | -0.7389 | |
| 161 | G | B | -0.6244 | |
| 162 | A | B | -0.3019 | |
| 163 | L | B | -0.0652 | |
| 164 | T | B | -0.2205 | |
| 165 | S | B | -0.2229 | |
| 166 | G | B | -0.2917 | |
| 167 | V | B | 0.1304 | |
| 168 | H | B | -0.2494 | |
| 169 | T | B | 0.0161 | |
| 170 | F | B | 0.0000 | |
| 171 | P | B | -0.3616 | |
| 172 | A | B | 0.1223 | |
| 173 | V | B | 0.2295 | |
| 174 | L | B | 1.0036 | |
| 175 | Q | B | 0.0841 | |
| 176 | S | B | -0.1435 | |
| 177 | S | B | -0.2809 | |
| 178 | G | B | -0.0338 | |
| 179 | L | B | 0.1009 | |
| 180 | Y | B | 0.3975 | |
| 181 | S | B | 0.1398 | |
| 182 | L | B | 0.0000 | |
| 183 | S | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | V | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | T | B | -0.1558 | |
| 188 | V | B | 0.0000 | |
| 189 | P | B | -0.6056 | |
| 190 | S | B | -0.5540 | |
| 191 | S | B | -0.5805 | |
| 192 | S | B | -0.6054 | |
| 193 | L | B | -0.8616 | |
| 194 | G | B | -1.0432 | |
| 195 | T | B | -0.7926 | |
| 196 | Q | B | -1.3717 | |
| 197 | T | B | -1.1763 | |
| 198 | Y | B | 0.0000 | |
| 199 | I | B | -1.1752 | |
| 200 | C | B | 0.0000 | |
| 201 | N | B | -1.4342 | |
| 202 | V | B | 0.0000 | |
| 203 | N | B | -1.7826 | |
| 204 | H | B | 0.0000 | |
| 205 | K | B | -2.7235 | |
| 206 | P | B | -1.6813 | |
| 207 | S | B | -1.7859 | |
| 208 | N | B | -2.5513 | |
| 209 | T | B | -2.0149 | |
| 210 | K | B | -2.6154 | |
| 211 | V | B | -1.5470 | |
| 212 | D | B | -2.4587 | |
| 213 | K | B | -2.0538 | |
| 214 | K | B | -2.3176 | |
| 215 | V | B | 0.0000 | |
| 216 | E | B | -2.6989 | |
| 217 | P | B | -1.7078 | |
| 218 | K | B | -1.7957 | |
| 219 | S | B | -1.0109 |
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 | -0.7868 | 3.8005 | View | CSV | PDB |
| 4.5 | -0.8311 | 3.8019 | View | CSV | PDB |
| 5.0 | -0.8823 | 3.8059 | View | CSV | PDB |
| 5.5 | -0.9304 | 3.8162 | View | CSV | PDB |
| 6.0 | -0.9638 | 3.8357 | View | CSV | PDB |
| 6.5 | -0.9727 | 3.8604 | View | CSV | PDB |
| 7.0 | -0.9575 | 3.8801 | View | CSV | PDB |
| 7.5 | -0.9263 | 3.8905 | View | CSV | PDB |
| 8.0 | -0.8864 | 3.8946 | View | CSV | PDB |
| 8.5 | -0.8396 | 3.8961 | View | CSV | PDB |
| 9.0 | -0.7862 | 3.8965 | 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