| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR
B: EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 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 |
| Mutated residues | SK50A,SR85B,SR21B |
| Energy difference between WT (input) and mutated protein (by FoldX) | -3.51527 kcal/mol |
| 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] FoldX: Building mutant model (00:01:52)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:02:12)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/86b9144e8f3a3ee/tmp/folded.pdb (00:02:12)
[INFO] Main: Simulation completed successfully. (00:03:59)
|
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 | -2.2951 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.3193 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.3444 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.6486 | |
| 8 | P | A | -0.4365 | |
| 9 | S | A | -0.6849 | |
| 10 | S | A | -0.5616 | |
| 11 | L | A | -0.3154 | |
| 12 | S | A | -0.6775 | |
| 13 | A | A | -0.8852 | |
| 14 | S | A | -0.8163 | |
| 15 | V | A | 0.0297 | |
| 16 | G | A | -0.9087 | |
| 17 | D | A | -2.1194 | |
| 18 | R | A | -2.4837 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6611 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.7715 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.8558 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.3512 | |
| 27 | Q | A | -2.9780 | |
| 28 | D | A | -2.7251 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.9099 | |
| 31 | T | A | -0.5535 | |
| 32 | A | A | -0.0168 | |
| 33 | V | A | 0.0000 | |
| 34 | A | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | -0.9930 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -1.8099 | |
| 40 | P | A | -1.5492 | |
| 41 | G | A | -1.6688 | |
| 42 | K | A | -2.6894 | |
| 43 | A | A | -1.6849 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -1.6658 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | K | A | 0.0162 | mutated: SK50A |
| 51 | A | A | 0.0000 | |
| 52 | S | A | 0.4116 | |
| 53 | F | A | 1.7580 | |
| 54 | L | A | 1.0723 | |
| 55 | Y | A | 0.3846 | |
| 56 | S | A | -0.0053 | |
| 57 | G | A | -0.5037 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.4016 | |
| 60 | S | A | -0.4755 | |
| 61 | R | A | -0.7962 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | 0.0621 | |
| 64 | G | A | 0.0284 | |
| 65 | S | A | -0.4595 | |
| 66 | G | A | -1.0979 | |
| 67 | S | A | -1.3833 | |
| 68 | G | A | -1.8758 | |
| 69 | T | A | -2.3003 | |
| 70 | D | A | -2.3035 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7012 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6293 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.4965 | |
| 77 | S | A | -1.1978 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -0.6771 | |
| 80 | P | A | -1.3079 | |
| 81 | E | A | -1.8745 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.7586 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -0.7294 | |
| 86 | Y | A | 0.0000 | |
| 87 | Y | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | S | A | 0.8058 | |
| 92 | Y | A | 1.2181 | |
| 93 | T | A | 0.5598 | |
| 94 | T | A | 0.0203 | |
| 95 | P | A | -0.1464 | |
| 96 | P | A | 0.0000 | |
| 97 | T | A | -0.7440 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | Q | A | -1.4478 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.1059 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.1847 | |
| 108 | R | A | -0.7700 | |
| 109 | T | A | -0.1411 | |
| 110 | V | A | 0.2471 | |
| 111 | A | A | -0.0695 | |
| 112 | A | A | -0.1647 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.1939 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0211 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.7861 | |
| 120 | P | A | -1.0083 | |
| 121 | S | A | 0.0000 | |
| 122 | D | A | -3.2249 | |
| 123 | E | A | -3.2836 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.3178 | |
| 126 | K | A | -2.9571 | |
| 127 | S | A | -1.8627 | |
| 128 | G | A | -1.3455 | |
| 129 | T | A | -1.1481 | |
| 130 | A | A | 0.0000 | |
| 131 | S | A | 0.0000 | |
| 132 | V | A | 0.0000 | |
| 133 | V | A | 0.0000 | |
| 134 | C | A | 0.0000 | |
| 135 | L | A | 0.0000 | |
| 136 | L | A | 0.0000 | |
| 137 | N | A | 0.0000 | |
| 138 | N | A | -0.8504 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.5580 | |
| 142 | R | A | -2.4482 | |
| 143 | E | A | -2.9678 | |
| 144 | A | A | -2.2725 | |
| 145 | K | A | -2.2838 | |
| 146 | V | A | -1.3003 | |
| 147 | Q | A | -0.6439 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.6983 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -2.2457 | |
| 152 | N | A | -1.6957 | |
| 153 | A | A | -0.3557 | |
| 154 | L | A | 0.6265 | |
| 155 | Q | A | -0.3874 | |
| 156 | S | A | -0.6692 | |
| 157 | G | A | -1.2857 | |
| 158 | N | A | -1.5883 | |
| 159 | S | A | -1.4358 | |
| 160 | Q | A | -1.4161 | |
| 161 | E | A | -1.6525 | |
| 162 | S | A | -0.8918 | |
| 163 | V | A | -0.8991 | |
| 164 | T | A | -1.0904 | |
| 165 | E | A | -2.0960 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -2.0836 | |
| 168 | S | A | -2.1430 | |
| 169 | K | A | -2.5034 | |
| 170 | D | A | -1.7704 | |
| 171 | S | A | 0.0000 | |
| 172 | T | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | L | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | T | A | -0.7148 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.6611 | |
| 181 | L | A | -0.7473 | |
| 182 | S | A | -1.2925 | |
| 183 | K | A | -2.4165 | |
| 184 | A | A | -2.1798 | |
| 185 | D | A | -2.9618 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.8147 | |
| 188 | K | A | -3.7148 | |
| 189 | H | A | -3.5380 | |
| 190 | K | A | -3.6364 | |
| 191 | V | A | -1.9641 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.6805 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.2572 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.7530 | |
| 200 | G | A | -0.5585 | |
| 201 | L | A | -0.3242 | |
| 202 | S | A | -0.5058 | |
| 203 | S | A | -0.4386 | |
| 204 | P | A | -0.5878 | |
| 205 | V | A | -0.0397 | |
| 206 | T | A | -0.4614 | |
| 207 | K | A | -0.6993 | |
| 208 | S | A | -0.8301 | |
| 209 | F | A | -1.2736 | |
| 210 | N | A | -2.5781 | |
| 211 | R | A | -3.1671 | |
| 1 | E | B | -1.9317 | |
| 2 | V | B | -0.8740 | |
| 3 | Q | B | -0.7397 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.3111 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.8317 | |
| 8 | G | B | -1.2518 | |
| 9 | G | B | -0.5468 | |
| 10 | G | B | -0.1901 | |
| 11 | L | B | 0.0540 | |
| 12 | V | B | -0.4914 | |
| 13 | Q | B | -1.6828 | |
| 14 | P | B | -1.9094 | |
| 15 | G | B | -1.9066 | |
| 16 | G | B | -1.4298 | |
| 17 | S | B | -1.4372 | |
| 18 | L | B | -1.1861 | |
| 19 | R | B | -2.4220 | |
| 20 | L | B | 0.0000 | |
| 21 | R | B | -1.8241 | mutated: SR21B |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.5988 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -0.8488 | |
| 26 | G | B | -1.0616 | |
| 27 | F | B | -0.6294 | |
| 28 | T | B | -0.8022 | |
| 29 | I | B | 0.0000 | |
| 30 | S | B | -1.1481 | |
| 31 | D | B | -1.7569 | |
| 32 | Y | B | -0.2633 | |
| 33 | W | B | 0.1044 | |
| 34 | I | B | 0.0000 | |
| 35 | H | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.7618 | |
| 40 | A | B | -1.1284 | |
| 41 | P | B | -0.9539 | |
| 42 | G | B | -1.4659 | |
| 43 | K | B | -2.3345 | |
| 44 | G | B | -1.5756 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.1939 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | A | B | 0.0000 | |
| 50 | G | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | T | B | 0.0140 | |
| 53 | P | B | -0.6445 | |
| 54 | A | B | -0.5939 | |
| 55 | G | B | -0.5880 | |
| 56 | G | B | -0.0574 | |
| 57 | Y | B | 1.0330 | |
| 58 | T | B | 0.7272 | |
| 59 | Y | B | 0.4690 | |
| 60 | Y | B | -0.5424 | |
| 61 | A | B | -1.4487 | |
| 62 | D | B | -2.3669 | |
| 63 | S | B | -1.6349 | |
| 64 | V | B | 0.0000 | |
| 65 | K | B | -2.4220 | |
| 66 | G | B | -1.8015 | |
| 67 | R | B | 0.0000 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.6997 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.4325 | |
| 72 | A | B | -1.0088 | |
| 73 | D | B | -1.4802 | |
| 74 | T | B | -1.2630 | |
| 75 | S | B | -1.3715 | |
| 76 | K | B | -2.1906 | |
| 77 | N | B | -1.3827 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | 0.0000 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.4041 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.9559 | |
| 85 | R | B | -2.7019 | mutated: SR85B |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.6232 | |
| 88 | A | B | -1.8874 | |
| 89 | E | B | -2.2286 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.6631 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.3253 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | -0.0921 | |
| 99 | F | B | 0.9488 | |
| 100 | V | B | 0.0000 | |
| 101 | F | B | 3.6045 | |
| 102 | F | B | 3.7453 | |
| 103 | L | B | 2.9149 | |
| 104 | P | B | 2.0077 | |
| 105 | Y | B | 2.1785 | |
| 106 | A | B | 0.0000 | |
| 107 | M | B | 0.0000 | |
| 108 | D | B | -0.1808 | |
| 109 | Y | B | -0.0341 | |
| 110 | W | B | 0.0000 | |
| 111 | G | B | 0.0000 | |
| 112 | Q | B | -1.4182 | |
| 113 | G | B | -0.6780 | |
| 114 | T | B | -0.1416 | |
| 115 | L | B | 0.3827 | |
| 116 | V | B | 0.0000 | |
| 117 | T | B | -0.3652 | |
| 118 | V | B | 0.0000 | |
| 119 | S | B | -0.9026 | |
| 120 | S | B | -0.6773 | |
| 121 | A | B | -0.4351 | |
| 122 | S | B | -0.5454 | |
| 123 | T | B | -0.7320 | |
| 124 | K | B | -1.2471 | |
| 125 | G | B | -1.3089 | |
| 126 | P | B | 0.0000 | |
| 127 | S | B | -0.5100 | |
| 128 | V | B | 0.0000 | |
| 129 | F | B | 0.0000 | |
| 130 | P | B | -1.0907 | |
| 131 | L | B | 0.0000 | |
| 132 | A | B | -1.0540 | |
| 133 | P | B | 0.0000 | |
| 134 | S | B | -0.6014 | |
| 135 | S | B | -0.2183 | |
| 141 | G | B | -0.6319 | |
| 142 | T | B | -0.4769 | |
| 143 | A | B | -0.2487 | |
| 144 | A | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | G | B | 0.0000 | |
| 147 | C | B | 0.0000 | |
| 148 | L | B | 0.0000 | |
| 149 | V | B | 0.0000 | |
| 150 | K | B | 0.0000 | |
| 151 | D | B | -0.4160 | |
| 152 | Y | B | 0.0000 | |
| 153 | F | B | 0.0000 | |
| 154 | P | B | 0.0000 | |
| 155 | E | B | -0.7803 | |
| 156 | P | B | -0.7826 | |
| 157 | V | B | -0.5039 | |
| 158 | T | B | -0.5843 | |
| 159 | V | B | -0.1063 | |
| 160 | S | B | -0.3299 | |
| 161 | W | B | 0.0000 | |
| 162 | N | B | -0.7968 | |
| 163 | S | B | -0.6484 | |
| 164 | G | B | -0.5837 | |
| 165 | A | B | -0.2812 | |
| 166 | L | B | -0.0769 | |
| 167 | T | B | -0.2134 | |
| 168 | S | B | -0.2014 | |
| 169 | G | B | -0.2355 | |
| 170 | V | B | 0.1380 | |
| 171 | H | B | -0.3344 | |
| 172 | T | B | -0.1925 | |
| 173 | F | B | 0.0000 | |
| 174 | P | B | -0.3649 | |
| 175 | A | B | 0.2037 | |
| 176 | V | B | 0.5548 | |
| 177 | L | B | 1.2004 | |
| 178 | Q | B | 0.3093 | |
| 179 | S | B | -0.1542 | |
| 180 | S | B | -0.1861 | |
| 181 | G | B | 0.1115 | |
| 182 | L | B | 0.1526 | |
| 183 | Y | B | 0.4009 | |
| 184 | S | B | 0.0000 | |
| 185 | L | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | S | B | 0.0000 | |
| 188 | V | B | 0.0000 | |
| 189 | V | B | 0.0000 | |
| 190 | T | B | -0.1346 | |
| 191 | V | B | 0.0000 | |
| 192 | P | B | -0.4729 | |
| 193 | S | B | -0.4780 | |
| 194 | S | B | -0.5481 | |
| 195 | S | B | -0.5543 | |
| 196 | L | B | -0.6423 | |
| 197 | G | B | -0.9577 | |
| 198 | T | B | -0.7331 | |
| 199 | Q | B | -1.2645 | |
| 200 | T | B | -1.2120 | |
| 201 | Y | B | 0.0000 | |
| 202 | I | B | -1.2117 | |
| 203 | C | B | 0.0000 | |
| 204 | N | B | -1.3421 | |
| 205 | V | B | 0.0000 | |
| 206 | N | B | -1.8256 | |
| 207 | H | B | 0.0000 | |
| 208 | K | B | -2.6926 | |
| 209 | P | B | -1.5877 | |
| 210 | S | B | -1.8411 | |
| 211 | N | B | -2.5424 | |
| 212 | T | B | -2.0792 | |
| 213 | K | B | -2.6148 | |
| 214 | V | B | -1.3294 | |
| 215 | D | B | -2.1939 | |
| 216 | K | B | -1.8824 | |
| 217 | K | B | -2.4383 | |
| 218 | V | B | 0.0000 | |
| 219 | E | B | -2.4828 | |
| 220 | P | B | -1.6193 | |
| 221 | K | B | -2.2419 | |
| 222 | S | B | -0.8559 | |
| 223 | C | B | 0.1127 |
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 | -0.6334 | 7.3529 | View | CSV | PDB |
| 4.5 | -0.6773 | 7.3529 | View | CSV | PDB |
| 5.0 | -0.7274 | 7.3529 | View | CSV | PDB |
| 5.5 | -0.774 | 7.3529 | View | CSV | PDB |
| 6.0 | -0.8069 | 7.3529 | View | CSV | PDB |
| 6.5 | -0.8181 | 7.3529 | View | CSV | PDB |
| 7.0 | -0.8074 | 7.3529 | View | CSV | PDB |
| 7.5 | -0.7823 | 7.3529 | View | CSV | PDB |
| 8.0 | -0.7491 | 7.3529 | View | CSV | PDB |
| 8.5 | -0.7095 | 7.3528 | View | CSV | PDB |
| 9.0 | -0.6628 | 7.3525 | 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