| Chain sequence(s) |
A: DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSFGVSWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTAYMELRSLTSEDSAVFFCVRATYDGGDYWGQGTTLTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 (00:05:26)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/4e8331870f06808/tmp/folded.pdb (00:05:26)
[INFO] Main: Simulation completed successfully. (00:07:16)
|
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 | -1.4184 | |
| 2 | V | A | 0.0000 | |
| 3 | V | A | 0.6959 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.3780 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0669 | |
| 8 | P | A | 0.4467 | |
| 9 | L | A | 1.2362 | |
| 10 | S | A | 0.4419 | |
| 11 | L | A | 0.0395 | |
| 12 | P | A | 0.0000 | |
| 13 | V | A | 0.0000 | |
| 14 | S | A | -1.0209 | |
| 15 | L | A | -0.4355 | |
| 16 | G | A | -1.9818 | |
| 17 | D | A | -2.9351 | |
| 18 | Q | A | -2.8206 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.6883 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8087 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.3567 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -1.0239 | |
| 27 | Q | A | -1.5537 | |
| 28 | S | A | -0.9289 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.1844 | |
| 31 | H | A | -0.6235 | |
| 32 | S | A | -0.9347 | |
| 33 | N | A | -1.6479 | |
| 34 | G | A | -1.1751 | |
| 35 | N | A | -0.9365 | |
| 36 | T | A | -0.3794 | |
| 37 | Y | A | 0.0000 | |
| 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 | -1.0460 | |
| 44 | K | A | -1.4687 | |
| 45 | P | A | -0.9664 | |
| 46 | G | A | -1.4583 | |
| 47 | Q | A | -2.1302 | |
| 48 | S | A | -1.4575 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.4235 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.4170 | |
| 55 | R | A | -0.8759 | |
| 56 | V | A | 0.0000 | |
| 57 | S | A | -0.8258 | |
| 58 | N | A | -1.1210 | |
| 59 | R | A | -1.5846 | |
| 60 | F | A | -0.6022 | |
| 61 | S | A | -0.5571 | |
| 62 | G | A | -0.8066 | |
| 63 | V | A | -0.9921 | |
| 64 | P | A | -1.2733 | |
| 65 | D | A | -2.2121 | |
| 66 | R | A | -2.0252 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.1158 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.7543 | |
| 71 | G | A | -1.1131 | |
| 72 | S | A | -0.8184 | |
| 73 | G | A | -0.8581 | |
| 74 | T | A | -1.5910 | |
| 75 | D | A | -2.2797 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -0.9286 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -1.2010 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.5019 | |
| 82 | R | A | -3.2078 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.2800 | |
| 85 | A | A | -1.1712 | |
| 86 | E | A | -2.0765 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | -0.4904 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | 0.0878 | |
| 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 | S | A | 0.0000 | |
| 97 | T | A | 0.2500 | |
| 98 | H | A | 0.1621 | |
| 99 | V | A | 1.2745 | |
| 100 | P | A | 0.2428 | |
| 101 | W | A | 0.5131 | |
| 102 | T | A | 0.2532 | |
| 103 | F | A | 0.2519 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.3356 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.2656 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -0.4028 | |
| 111 | I | A | -0.6918 | |
| 112 | K | A | -1.1773 | |
| 113 | A | A | -0.5904 | |
| 114 | S | A | -0.5797 | |
| 115 | T | A | -1.1476 | |
| 116 | K | A | -1.4294 | |
| 117 | G | A | -1.4681 | |
| 118 | P | A | 0.0000 | |
| 119 | S | A | -0.5786 | |
| 120 | V | A | 0.0000 | |
| 121 | F | A | 0.0000 | |
| 122 | P | A | -1.1958 | |
| 123 | L | A | 0.0000 | |
| 124 | A | A | -1.2483 | |
| 125 | P | A | 0.0000 | |
| 126 | S | A | -0.8961 | |
| 127 | S | A | -0.6978 | |
| 128 | K | A | -0.9232 | |
| 129 | S | A | 0.0000 | |
| 130 | T | A | -0.6505 | |
| 131 | S | A | -0.6925 | |
| 132 | G | A | -0.8081 | |
| 133 | G | A | -0.8756 | |
| 134 | T | A | -0.5937 | |
| 135 | A | A | 0.0000 | |
| 136 | A | A | 0.0000 | |
| 137 | L | A | 0.0000 | |
| 138 | G | A | 0.0000 | |
| 139 | C | A | 0.0000 | |
| 140 | L | A | 0.0000 | |
| 141 | V | A | 0.0000 | |
| 142 | K | A | 0.0000 | |
| 143 | D | A | -0.6252 | |
| 144 | Y | A | 0.0000 | |
| 145 | F | A | -0.0413 | |
| 146 | P | A | -0.5241 | |
| 147 | E | A | -0.7063 | |
| 148 | P | A | -0.8016 | |
| 149 | V | A | -0.6430 | |
| 150 | T | A | -0.6638 | |
| 151 | V | A | -0.4305 | |
| 152 | S | A | -0.4352 | |
| 153 | W | A | 0.0000 | |
| 154 | N | A | -0.7524 | |
| 155 | S | A | -0.6737 | |
| 156 | G | A | -0.5242 | |
| 157 | A | A | -0.2558 | |
| 158 | L | A | -0.0248 | |
| 159 | T | A | -0.2017 | |
| 160 | S | A | -0.2268 | |
| 161 | G | A | -0.3078 | |
| 162 | V | A | 0.1292 | |
| 163 | H | A | -0.3213 | |
| 164 | T | A | -0.1434 | |
| 165 | F | A | 0.0000 | |
| 166 | P | A | -0.3039 | |
| 167 | A | A | 0.2465 | |
| 168 | V | A | 0.5166 | |
| 169 | L | A | 1.1529 | |
| 170 | Q | A | 0.2137 | |
| 171 | S | A | -0.2162 | |
| 172 | S | A | -0.3107 | |
| 173 | G | A | 0.0169 | |
| 174 | L | A | 0.1113 | |
| 175 | Y | A | 0.4002 | |
| 176 | S | A | 0.0000 | |
| 177 | L | A | 0.0000 | |
| 178 | S | A | 0.0000 | |
| 179 | S | A | 0.0000 | |
| 180 | V | A | 0.0000 | |
| 181 | V | A | 0.0000 | |
| 182 | T | A | -0.1655 | |
| 183 | V | A | 0.0000 | |
| 184 | P | A | -0.6213 | |
| 185 | S | A | -0.5761 | |
| 186 | S | A | -0.5852 | |
| 187 | S | A | -0.5715 | |
| 188 | L | A | -0.7639 | |
| 189 | G | A | -0.9434 | |
| 190 | T | A | -0.6884 | |
| 191 | Q | A | -1.1405 | |
| 192 | T | A | -1.0592 | |
| 193 | Y | A | 0.0000 | |
| 194 | I | A | -1.2206 | |
| 195 | C | A | 0.0000 | |
| 196 | N | A | -1.5339 | |
| 197 | V | A | 0.0000 | |
| 198 | N | A | -2.0994 | |
| 199 | H | A | 0.0000 | |
| 200 | K | A | -2.4177 | |
| 201 | P | A | -1.7382 | |
| 202 | S | A | -1.8445 | |
| 203 | N | A | -2.4818 | |
| 204 | T | A | -2.0749 | |
| 205 | K | A | -2.7131 | |
| 206 | V | A | -1.6822 | |
| 207 | D | A | -2.5320 | |
| 208 | K | A | -2.1002 | |
| 209 | K | A | -2.4842 | |
| 210 | V | A | 0.0000 | |
| 211 | E | A | -2.7936 | |
| 212 | P | A | -1.7831 | |
| 213 | K | A | -2.1631 | |
| 214 | S | A | -1.2337 | |
| 1 | Q | B | -1.4059 | |
| 2 | V | B | -0.9100 | |
| 3 | Q | B | -1.6327 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.0709 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.1014 | |
| 8 | G | B | -0.7225 | |
| 9 | A | B | -0.0682 | |
| 10 | E | B | -0.0258 | |
| 11 | L | B | 0.8584 | |
| 12 | A | B | -0.3923 | |
| 13 | R | B | -1.6337 | |
| 14 | P | B | -1.4055 | |
| 15 | G | B | -1.2788 | |
| 16 | A | B | -1.1139 | |
| 17 | S | B | -1.4417 | |
| 18 | V | B | -1.2541 | |
| 19 | K | B | -2.1320 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.9532 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.5857 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.0718 | |
| 26 | G | B | -0.8892 | |
| 27 | Y | B | -0.2836 | |
| 28 | T | B | -0.0275 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.1223 | |
| 31 | S | B | -0.3273 | |
| 32 | F | B | 0.3265 | |
| 33 | G | B | 0.0000 | |
| 34 | V | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | 0.0000 | |
| 39 | Q | B | -0.7362 | |
| 40 | R | B | -1.3531 | |
| 41 | T | B | -1.3281 | |
| 42 | G | B | -1.5941 | |
| 43 | Q | B | -1.7939 | |
| 44 | G | B | -1.1359 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.9320 | |
| 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 | -0.5684 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.4513 | |
| 55 | S | B | -1.5625 | |
| 56 | G | B | -1.7681 | |
| 57 | N | B | -1.5074 | |
| 58 | T | B | -0.1590 | |
| 59 | Y | B | 0.6920 | |
| 60 | Y | B | -0.2854 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.1170 | |
| 63 | K | B | -3.1973 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9334 | |
| 66 | G | B | -2.0638 | |
| 67 | K | B | -1.9733 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.0064 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.6377 | |
| 72 | A | B | -1.3119 | |
| 73 | D | B | -1.9637 | |
| 74 | K | B | -2.5661 | |
| 75 | S | B | -1.3123 | |
| 76 | S | B | -1.1250 | |
| 77 | S | B | -1.2488 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.6475 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.7202 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -1.6614 | |
| 85 | S | B | -1.1741 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.4171 | |
| 88 | S | B | -1.8194 | |
| 89 | E | B | -2.0518 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.0674 | |
| 94 | F | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | V | B | 0.0000 | |
| 98 | R | B | -0.0134 | |
| 99 | A | B | 0.0000 | |
| 100 | T | B | 0.5411 | |
| 101 | Y | B | 1.0117 | |
| 102 | D | B | -0.0628 | |
| 103 | G | B | 0.0000 | |
| 104 | G | B | 0.0000 | |
| 105 | D | B | -0.1096 | |
| 106 | Y | B | -0.1411 | |
| 107 | W | B | -0.7116 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.8459 | |
| 110 | G | B | -0.9762 | |
| 111 | T | B | 0.0000 | |
| 112 | T | B | -0.0506 | |
| 113 | L | B | 0.0000 | |
| 114 | T | B | 0.0000 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.4653 | |
| 117 | S | B | -0.0758 | |
| 118 | V | B | 0.5144 | |
| 119 | A | B | -0.0232 | |
| 120 | A | B | -0.1038 | |
| 121 | P | B | 0.0000 | |
| 122 | S | B | -0.2334 | |
| 123 | V | B | 0.0000 | |
| 124 | F | B | 0.0000 | |
| 125 | I | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -0.7201 | |
| 128 | P | B | -0.8752 | |
| 129 | S | B | -1.9075 | |
| 130 | D | B | -3.1122 | |
| 131 | E | B | -3.3008 | |
| 132 | Q | B | 0.0000 | |
| 133 | L | B | -2.3912 | |
| 134 | K | B | -2.9825 | |
| 135 | S | B | -1.8815 | |
| 136 | G | B | -1.3571 | |
| 137 | T | B | -1.3503 | |
| 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 | 0.0000 | |
| 146 | N | B | -1.0635 | |
| 147 | F | B | 0.0000 | |
| 148 | Y | B | 0.0000 | |
| 149 | P | B | -1.4146 | |
| 150 | R | B | -2.9208 | |
| 151 | E | B | -3.2070 | |
| 152 | A | B | -2.3401 | |
| 153 | K | B | -2.5170 | |
| 154 | V | B | -1.2204 | |
| 155 | Q | B | -0.9165 | |
| 156 | W | B | 0.0000 | |
| 157 | K | B | -0.8370 | |
| 158 | V | B | 0.0000 | |
| 159 | D | B | -1.9584 | |
| 160 | N | B | -1.4856 | |
| 161 | A | B | -0.4990 | |
| 162 | L | B | 0.2271 | |
| 163 | Q | B | -0.5584 | |
| 164 | S | B | -0.8461 | |
| 165 | G | B | -1.2725 | |
| 166 | N | B | -1.6022 | |
| 167 | S | B | -1.3846 | |
| 168 | Q | B | -1.2563 | |
| 169 | E | B | -1.2944 | |
| 170 | S | B | -0.6342 | |
| 171 | V | B | -0.4764 | |
| 172 | T | B | 0.0000 | |
| 173 | E | B | -2.1592 | |
| 174 | Q | B | 0.0000 | |
| 175 | D | B | -2.1673 | |
| 176 | S | B | -2.2431 | |
| 177 | K | B | -2.7222 | |
| 178 | D | B | -2.2503 | |
| 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 | -0.6558 | |
| 187 | L | B | 0.0000 | |
| 188 | T | B | -0.6901 | |
| 189 | L | B | -0.9160 | |
| 190 | S | B | -1.1492 | |
| 191 | K | B | -2.1399 | |
| 192 | A | B | -1.9438 | |
| 193 | D | B | -2.7323 | |
| 194 | Y | B | 0.0000 | |
| 195 | E | B | -3.2798 | |
| 196 | K | B | -3.5599 | |
| 197 | H | B | -2.8763 | |
| 198 | K | B | -2.9003 | |
| 199 | V | B | -1.2549 | |
| 200 | Y | B | 0.0000 | |
| 201 | A | B | 0.0000 | |
| 202 | C | B | 0.0000 | |
| 203 | E | B | -0.9752 | |
| 204 | V | B | 0.0000 | |
| 205 | T | B | -1.3025 | |
| 206 | H | B | 0.0000 | |
| 207 | Q | B | -1.7137 | |
| 208 | G | B | -0.3801 | |
| 209 | L | B | -0.2203 | |
| 210 | S | B | -0.4520 | |
| 211 | S | B | -0.4588 | |
| 212 | P | B | -0.6236 | |
| 213 | V | B | -0.0870 | |
| 214 | T | B | -0.4793 | |
| 215 | K | B | -0.7390 | |
| 216 | S | B | -0.5633 | |
| 217 | F | B | 0.0000 | |
| 218 | N | B | -1.6938 | |
| 219 | R | B | -2.2612 | |
| 220 | G | B | -1.8871 | |
| 221 | E | B | -2.3394 | |
| 222 | C | B | -1.0225 |
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 | -0.76 | 1.5984 | View | CSV | PDB |
| 4.5 | -0.8068 | 1.5728 | View | CSV | PDB |
| 5.0 | -0.8612 | 1.5747 | View | CSV | PDB |
| 5.5 | -0.9126 | 1.5802 | View | CSV | PDB |
| 6.0 | -0.9487 | 1.5947 | View | CSV | PDB |
| 6.5 | -0.9599 | 1.6244 | View | CSV | PDB |
| 7.0 | -0.9461 | 1.6699 | View | CSV | PDB |
| 7.5 | -0.9158 | 1.7248 | View | CSV | PDB |
| 8.0 | -0.8762 | 1.7836 | View | CSV | PDB |
| 8.5 | -0.8299 | 1.8437 | View | CSV | PDB |
| 9.0 | -0.7772 | 1.9039 | 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