| Chain sequence(s) |
A: DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPWTFGGGTKLEIKVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSFGVSWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTAYMELRSLTSEDSAVFFCVRATYDGGDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[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 (00:04:10)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/3451c9213337147/tmp/folded.pdb (00:04:10)
[INFO] Main: Simulation completed successfully. (00:06:13)
|
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 | -1.4438 | |
| 2 | V | A | 0.0000 | |
| 3 | V | A | 0.6993 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.3697 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | -0.0266 | |
| 8 | P | A | 0.5294 | |
| 9 | L | A | 1.3474 | |
| 10 | S | A | 0.5593 | |
| 11 | L | A | 0.3283 | |
| 12 | P | A | -0.2773 | |
| 13 | V | A | -0.8194 | |
| 14 | S | A | -1.2825 | |
| 15 | L | A | -1.2701 | |
| 16 | G | A | -2.4388 | |
| 17 | D | A | -3.2382 | |
| 18 | Q | A | -3.0457 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.7770 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8012 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.3097 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -1.0008 | |
| 27 | Q | A | -1.5333 | |
| 28 | S | A | -0.9256 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.1293 | |
| 31 | H | A | -0.7854 | |
| 32 | S | A | -1.0113 | |
| 33 | N | A | -1.6952 | |
| 34 | G | A | -1.2128 | |
| 35 | N | A | -0.8741 | |
| 36 | T | A | -0.2871 | |
| 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 | -0.9212 | |
| 44 | K | A | -1.4960 | |
| 45 | P | A | -1.4218 | |
| 46 | G | A | -1.5663 | |
| 47 | Q | A | -1.9905 | |
| 48 | S | A | -1.3122 | |
| 49 | P | A | 0.0000 | |
| 50 | K | A | -1.2139 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.2244 | |
| 55 | R | A | -0.5520 | |
| 56 | V | A | -0.5865 | |
| 57 | S | A | -0.7902 | |
| 58 | N | A | -1.1070 | |
| 59 | R | A | -1.5860 | |
| 60 | F | A | -0.6471 | |
| 61 | S | A | -0.5642 | |
| 62 | G | A | -0.7915 | |
| 63 | V | A | -0.9769 | |
| 64 | P | A | -1.2916 | |
| 65 | D | A | -2.2498 | |
| 66 | R | A | -2.2193 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.1700 | |
| 69 | G | A | -0.7200 | |
| 70 | S | A | -0.7291 | |
| 71 | G | A | -1.0646 | |
| 72 | S | A | -0.7481 | |
| 73 | G | A | -0.8184 | |
| 74 | T | A | -1.5121 | |
| 75 | D | A | -2.1443 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -0.9150 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -1.3287 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.6721 | |
| 82 | R | A | -3.4195 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.4793 | |
| 85 | A | A | 0.0000 | |
| 86 | E | A | -2.0996 | |
| 87 | D | A | 0.0000 | |
| 88 | L | A | 0.0000 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | 0.2265 | |
| 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 | 0.4334 | |
| 97 | T | A | 0.2217 | |
| 98 | H | A | 0.0838 | |
| 99 | V | A | 1.2120 | |
| 100 | P | A | 0.1397 | |
| 101 | W | A | 0.0000 | |
| 102 | T | A | 0.1906 | |
| 103 | F | A | 0.2081 | |
| 104 | G | A | 0.0000 | |
| 105 | G | A | -0.2460 | |
| 106 | G | A | -0.0843 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | 0.0701 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -0.3591 | |
| 111 | I | A | -0.1775 | |
| 112 | K | A | -0.2471 | |
| 113 | V | A | 0.8962 | |
| 114 | A | A | 0.1641 | |
| 115 | A | A | 0.0571 | |
| 116 | P | A | 0.0000 | |
| 117 | S | A | -0.1896 | |
| 118 | V | A | 0.0000 | |
| 119 | F | A | 0.0000 | |
| 120 | I | A | 0.0000 | |
| 121 | F | A | 0.0000 | |
| 122 | P | A | -0.9387 | |
| 123 | P | A | 0.0000 | |
| 124 | S | A | 0.0000 | |
| 125 | D | A | -2.8048 | |
| 126 | E | A | -2.7176 | |
| 127 | Q | A | 0.0000 | |
| 128 | L | A | -2.1370 | |
| 129 | K | A | -2.7535 | |
| 130 | S | A | -1.7175 | |
| 131 | G | A | -1.1777 | |
| 132 | T | A | -1.2017 | |
| 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 | -0.6897 | |
| 142 | F | A | 0.0000 | |
| 143 | Y | A | -0.6654 | |
| 144 | P | A | -1.2797 | |
| 145 | R | A | -2.6544 | |
| 146 | E | A | -3.1595 | |
| 147 | A | A | -2.2980 | |
| 148 | K | A | -2.4975 | |
| 149 | V | A | -1.2055 | |
| 150 | Q | A | -0.7857 | |
| 151 | W | A | 0.0000 | |
| 152 | K | A | -0.5778 | |
| 153 | V | A | 0.0000 | |
| 154 | D | A | -1.9482 | |
| 155 | N | A | -1.5287 | |
| 156 | A | A | -0.2919 | |
| 157 | L | A | 0.6183 | |
| 158 | Q | A | -0.3763 | |
| 159 | S | A | -0.6893 | |
| 160 | G | A | -1.2665 | |
| 161 | N | A | -1.5516 | |
| 162 | S | A | -1.4213 | |
| 163 | Q | A | -1.3648 | |
| 164 | E | A | -1.5067 | |
| 165 | S | A | -0.7445 | |
| 166 | V | A | -0.5619 | |
| 167 | T | A | -1.1223 | |
| 168 | E | A | -2.2110 | |
| 169 | Q | A | 0.0000 | |
| 170 | D | A | -2.0978 | |
| 171 | S | A | -2.1513 | |
| 172 | K | A | -2.6534 | |
| 173 | D | A | -2.0550 | |
| 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 | -0.6766 | |
| 182 | L | A | 0.0000 | |
| 183 | T | A | -0.6736 | |
| 184 | L | A | -0.9378 | |
| 185 | S | A | -1.1671 | |
| 186 | K | A | -2.1256 | |
| 187 | A | A | -2.0615 | |
| 188 | D | A | -2.9673 | |
| 189 | Y | A | 0.0000 | |
| 190 | E | A | -3.6671 | |
| 191 | K | A | -3.8045 | |
| 192 | H | A | -3.2342 | |
| 193 | K | A | -3.3878 | |
| 194 | V | A | -1.7491 | |
| 195 | Y | A | 0.0000 | |
| 196 | A | A | 0.0000 | |
| 197 | C | A | 0.0000 | |
| 198 | E | A | -0.9915 | |
| 199 | V | A | 0.0000 | |
| 200 | T | A | -1.2968 | |
| 201 | H | A | 0.0000 | |
| 202 | Q | A | -1.4907 | |
| 203 | G | A | -0.3327 | |
| 204 | L | A | -0.3561 | |
| 205 | S | A | -0.4652 | |
| 206 | S | A | -0.4606 | |
| 207 | P | A | -0.6312 | |
| 208 | V | A | -0.1071 | |
| 209 | T | A | -0.5069 | |
| 210 | K | A | -0.7481 | |
| 211 | S | A | -0.6843 | |
| 212 | F | A | 0.0000 | |
| 213 | N | A | -1.9798 | |
| 214 | R | A | -2.5436 | |
| 215 | G | A | -1.8360 | |
| 216 | E | A | -1.8243 | |
| 217 | C | A | -0.6130 | |
| 1 | Q | B | -1.5342 | |
| 2 | V | B | -1.1244 | |
| 3 | Q | B | -1.9219 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.1480 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.0672 | |
| 8 | G | B | -1.2449 | |
| 9 | A | B | -0.9260 | |
| 10 | E | B | -1.1495 | |
| 11 | L | B | -0.7089 | |
| 12 | A | B | -1.1171 | |
| 13 | R | B | -2.1186 | |
| 14 | P | B | -1.5446 | |
| 15 | G | B | -1.4755 | |
| 16 | A | B | -1.3446 | |
| 17 | S | B | -1.6857 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -1.9256 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.8390 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.6679 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.2579 | |
| 26 | G | B | -1.0928 | |
| 27 | Y | B | -0.3952 | |
| 28 | T | B | -0.0507 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.1222 | |
| 31 | S | B | -0.3036 | |
| 32 | F | B | 0.3842 | |
| 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 | -0.8407 | |
| 39 | Q | B | -1.3669 | |
| 40 | R | B | -2.2787 | |
| 41 | T | B | -1.3530 | |
| 42 | G | B | -1.5038 | |
| 43 | Q | B | -2.1935 | |
| 44 | G | B | -1.4804 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.1326 | |
| 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 | -0.5505 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.4644 | |
| 55 | S | B | -1.6026 | |
| 56 | G | B | -1.8059 | |
| 57 | N | B | -1.5274 | |
| 58 | T | B | -0.1798 | |
| 59 | Y | B | 0.6696 | |
| 60 | Y | B | -0.2944 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.0945 | |
| 63 | K | B | -3.1857 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9188 | |
| 66 | G | B | -2.2260 | |
| 67 | K | B | -2.2112 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -0.9914 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.5675 | |
| 72 | A | B | -1.3234 | |
| 73 | D | B | -2.0033 | |
| 74 | K | B | -2.5829 | |
| 75 | S | B | -1.3244 | |
| 76 | S | B | -1.1362 | |
| 77 | S | B | -1.2718 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5159 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.4562 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -2.3661 | |
| 85 | S | B | -1.5934 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.4645 | |
| 88 | S | B | -1.4469 | |
| 89 | E | B | -2.1337 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.9762 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.2198 | |
| 94 | F | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | V | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | A | B | 0.0000 | |
| 100 | T | B | 0.6235 | |
| 101 | Y | B | 1.1599 | |
| 102 | D | B | 0.2827 | |
| 103 | G | B | 0.0000 | |
| 104 | G | B | 0.0000 | |
| 105 | D | B | 0.0340 | |
| 106 | Y | B | -0.0722 | |
| 107 | W | B | -0.6495 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.7865 | |
| 110 | G | B | -0.9542 | |
| 111 | T | B | 0.0000 | |
| 112 | T | B | -0.4759 | |
| 113 | L | B | 0.0000 | |
| 114 | T | B | -0.6682 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.8517 | |
| 117 | S | B | -0.9732 | |
| 118 | A | B | -0.5772 | |
| 119 | S | B | -0.6524 | |
| 120 | T | B | -0.8774 | |
| 121 | K | B | -1.2003 | |
| 122 | G | B | -1.3413 | |
| 123 | P | B | 0.0000 | |
| 124 | S | B | -0.4221 | |
| 125 | V | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -1.0757 | |
| 128 | L | B | 0.0000 | |
| 129 | A | B | -1.3304 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -1.0426 | |
| 132 | S | B | -0.6985 | |
| 133 | K | B | -0.7861 | |
| 134 | S | B | 0.0000 | |
| 135 | T | B | -0.5821 | |
| 136 | S | B | -0.6600 | |
| 137 | G | B | -0.8070 | |
| 138 | G | B | -0.8744 | |
| 139 | T | B | -0.5857 | |
| 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 | -0.3305 | |
| 149 | Y | B | 0.0000 | |
| 150 | F | B | -0.1628 | |
| 151 | P | B | 0.0000 | |
| 152 | E | B | -0.4639 | |
| 153 | P | B | -0.6890 | |
| 154 | V | B | -0.5664 | |
| 155 | T | B | -0.5225 | |
| 156 | V | B | -0.3208 | |
| 157 | S | B | -0.3838 | |
| 158 | W | B | 0.0000 | |
| 159 | N | B | -0.8830 | |
| 160 | S | B | -0.7323 | |
| 161 | G | B | -0.6169 | |
| 162 | A | B | -0.2887 | |
| 163 | L | B | -0.0207 | |
| 164 | T | B | -0.1926 | |
| 165 | S | B | -0.1977 | |
| 166 | G | B | -0.2527 | |
| 167 | V | B | 0.1528 | |
| 168 | H | B | -0.3036 | |
| 169 | T | B | 0.0397 | |
| 170 | F | B | 0.0000 | |
| 171 | P | B | -0.2699 | |
| 172 | A | B | 0.3024 | |
| 173 | V | B | 0.5631 | |
| 174 | L | B | 1.2850 | |
| 175 | Q | B | 0.3233 | |
| 176 | S | B | -0.0675 | |
| 177 | S | B | -0.2284 | |
| 178 | G | B | 0.0390 | |
| 179 | L | B | 0.2221 | |
| 180 | Y | B | 0.5311 | |
| 181 | S | B | 0.0000 | |
| 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 | -0.1496 | |
| 188 | V | B | 0.0000 | |
| 189 | P | B | -0.5162 | |
| 190 | S | B | -0.5583 | |
| 191 | S | B | -0.5946 | |
| 192 | S | B | 0.0000 | |
| 193 | L | B | -0.8298 | |
| 194 | G | B | -0.9892 | |
| 195 | T | B | -0.8110 | |
| 196 | Q | B | -1.3807 | |
| 197 | T | B | -1.2163 | |
| 198 | Y | B | 0.0000 | |
| 199 | I | B | -1.2189 | |
| 200 | C | B | 0.0000 | |
| 201 | N | B | -1.4712 | |
| 202 | V | B | 0.0000 | |
| 203 | N | B | -1.7860 | |
| 204 | H | B | 0.0000 | |
| 205 | K | B | -2.8019 | |
| 206 | P | B | -1.6943 | |
| 207 | S | B | -1.8019 | |
| 208 | N | B | -2.5589 | |
| 209 | T | B | -2.0417 | |
| 210 | K | B | -2.6462 | |
| 211 | V | B | -1.6197 | |
| 212 | D | B | -2.5361 | |
| 213 | K | B | -2.1927 | |
| 214 | K | B | -2.4630 | |
| 215 | V | B | 0.0000 | |
| 216 | E | B | -2.8657 | |
| 217 | P | B | -1.9427 | |
| 218 | K | B | -2.1797 | |
| 219 | S | B | -1.2170 |
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 | -0.8238 | 1.7653 | View | CSV | PDB |
| 4.5 | -0.8665 | 1.7656 | View | CSV | PDB |
| 5.0 | -0.9157 | 1.7663 | View | CSV | PDB |
| 5.5 | -0.9607 | 1.7686 | View | CSV | PDB |
| 6.0 | -0.9904 | 1.7744 | View | CSV | PDB |
| 6.5 | -0.9966 | 1.7861 | View | CSV | PDB |
| 7.0 | -0.9806 | 1.8036 | View | CSV | PDB |
| 7.5 | -0.95 | 1.8245 | View | CSV | PDB |
| 8.0 | -0.9113 | 1.8466 | View | CSV | PDB |
| 8.5 | -0.8663 | 1.8693 | View | CSV | PDB |
| 9.0 | -0.8155 | 1.8919 | 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