| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCRASHHVHTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYDPATFGQGTKVEIKRTASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGHSTYYADSVHGRFTISADHSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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 (00:04:39)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/7870dfd3caefbf2/tmp/folded.pdb (00:04:39)
[INFO] Main: Simulation completed successfully. (00:07:34)
|
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 | -2.4614 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.2955 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.4491 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.8225 | |
| 8 | P | A | -0.4342 | |
| 9 | S | A | -0.7224 | |
| 10 | S | A | -0.5452 | |
| 11 | L | A | -0.3147 | |
| 12 | S | A | -0.5015 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -0.8607 | |
| 15 | V | A | -0.2574 | |
| 16 | G | A | -0.7853 | |
| 17 | D | A | -1.7164 | |
| 18 | R | A | -2.2814 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6273 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.8184 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.7765 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.0787 | |
| 27 | H | A | -2.4442 | |
| 28 | H | A | -2.0623 | |
| 29 | V | A | 0.0000 | |
| 30 | H | A | -1.5180 | |
| 31 | T | A | -0.7851 | |
| 32 | A | A | -0.0669 | |
| 33 | V | A | 0.0000 | |
| 34 | A | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -1.5598 | |
| 40 | P | A | -1.1541 | |
| 41 | G | A | -1.6448 | |
| 42 | K | A | -2.5921 | |
| 43 | A | A | -1.6091 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -1.4597 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.9844 | |
| 50 | S | A | 0.4750 | |
| 51 | A | A | 0.0000 | |
| 52 | S | A | 0.8071 | |
| 53 | F | A | 2.1828 | |
| 54 | L | A | 1.4849 | |
| 55 | Y | A | 0.6416 | |
| 56 | S | A | 0.0166 | |
| 57 | G | A | -0.4728 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.3457 | |
| 60 | S | A | -0.4081 | |
| 61 | R | A | -0.7368 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | 0.0747 | |
| 64 | G | A | 0.2076 | |
| 65 | S | A | -0.3004 | |
| 66 | G | A | -1.0503 | |
| 67 | S | A | -1.1040 | |
| 68 | G | A | 0.0000 | |
| 69 | T | A | -1.9956 | |
| 70 | D | A | -2.1699 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7075 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6078 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3241 | |
| 77 | S | A | -1.1340 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -0.8238 | |
| 80 | P | A | -0.9366 | |
| 81 | E | A | -1.7325 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.2915 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -0.5221 | |
| 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 | Y | A | 0.5632 | |
| 92 | L | A | 0.7517 | |
| 93 | Y | A | 0.7623 | |
| 94 | D | A | -0.6290 | |
| 95 | P | A | -0.8891 | |
| 96 | A | A | 0.0000 | |
| 97 | T | A | -0.7293 | |
| 98 | F | A | -0.4615 | |
| 99 | G | A | 0.0000 | |
| 100 | Q | A | -1.6965 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.9799 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.4893 | |
| 108 | R | A | -2.0956 | |
| 109 | T | A | -1.2153 | |
| 110 | A | A | -0.9745 | |
| 111 | S | A | -0.8520 | |
| 112 | T | A | -0.8882 | |
| 113 | K | A | -1.1407 | |
| 114 | G | A | -1.4219 | |
| 115 | P | A | 0.0000 | |
| 116 | S | A | -0.4090 | |
| 117 | V | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -1.0778 | |
| 120 | L | A | 0.0000 | |
| 121 | A | A | -1.1564 | |
| 122 | P | A | 0.0000 | |
| 123 | S | A | -0.9558 | |
| 124 | S | A | -0.7696 | |
| 125 | K | A | -1.0835 | |
| 126 | S | A | 0.0000 | |
| 127 | T | A | -0.6620 | |
| 128 | S | A | -0.6817 | |
| 129 | G | A | -0.8037 | |
| 130 | G | A | -0.8743 | |
| 131 | T | A | -0.6053 | |
| 132 | A | A | 0.0000 | |
| 133 | A | A | 0.0000 | |
| 134 | L | A | 0.0000 | |
| 135 | G | A | 0.0000 | |
| 136 | C | A | 0.0000 | |
| 137 | L | A | 0.0000 | |
| 138 | V | A | 0.0000 | |
| 139 | K | A | 0.0000 | |
| 140 | D | A | -0.4276 | |
| 141 | Y | A | 0.0000 | |
| 142 | F | A | 0.0000 | |
| 143 | P | A | 0.0000 | |
| 144 | E | A | -0.6545 | |
| 145 | P | A | -0.7789 | |
| 146 | V | A | -0.7755 | |
| 147 | T | A | -0.7552 | |
| 148 | V | A | -0.4960 | |
| 149 | S | A | -0.4719 | |
| 150 | W | A | 0.0000 | |
| 151 | N | A | -0.7149 | |
| 152 | S | A | -0.6750 | |
| 153 | G | A | -0.5119 | |
| 154 | A | A | -0.2380 | |
| 155 | L | A | 0.0351 | |
| 156 | T | A | -0.1532 | |
| 157 | S | A | -0.1578 | |
| 158 | G | A | -0.1855 | |
| 159 | V | A | 0.1846 | |
| 160 | H | A | -0.2758 | |
| 161 | T | A | 0.0237 | |
| 162 | F | A | 0.0000 | |
| 163 | P | A | -0.3235 | |
| 164 | A | A | 0.1596 | |
| 165 | V | A | 0.3320 | |
| 166 | L | A | 0.7168 | |
| 167 | Q | A | 0.0631 | |
| 168 | S | A | -0.1616 | |
| 169 | S | A | -0.2732 | |
| 170 | G | A | -0.3581 | |
| 171 | L | A | -0.1973 | |
| 172 | Y | A | 0.2323 | |
| 173 | S | A | 0.0000 | |
| 174 | L | A | 0.0000 | |
| 175 | S | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | V | A | 0.0000 | |
| 178 | V | A | 0.0000 | |
| 179 | T | A | -0.1120 | |
| 180 | V | A | 0.0000 | |
| 181 | P | A | -0.6237 | |
| 182 | S | A | -0.5768 | |
| 183 | S | A | -0.5897 | |
| 184 | S | A | -0.6285 | |
| 185 | L | A | -0.8037 | |
| 186 | G | A | -0.9686 | |
| 187 | T | A | -0.7050 | |
| 188 | Q | A | -1.1793 | |
| 189 | T | A | -1.0304 | |
| 190 | Y | A | 0.0000 | |
| 191 | I | A | -1.0818 | |
| 192 | C | A | 0.0000 | |
| 193 | N | A | -1.5808 | |
| 194 | V | A | 0.0000 | |
| 195 | N | A | -2.4694 | |
| 196 | H | A | 0.0000 | |
| 197 | K | A | -2.8834 | |
| 198 | P | A | -1.6501 | |
| 199 | S | A | -1.9157 | |
| 200 | N | A | -2.7167 | |
| 201 | T | A | -2.2263 | |
| 202 | K | A | -2.8924 | |
| 203 | V | A | -1.6812 | |
| 204 | D | A | -2.4987 | |
| 205 | K | A | -1.9620 | |
| 206 | K | A | -2.1690 | |
| 207 | V | A | 0.0000 | |
| 208 | E | A | -2.6679 | |
| 209 | P | A | -1.7007 | |
| 210 | K | A | -1.9827 | |
| 211 | S | A | -1.2246 | |
| 1 | E | B | -2.2959 | |
| 2 | V | B | 0.0000 | |
| 3 | Q | B | -1.4536 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.9386 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.3265 | |
| 8 | G | B | -0.6702 | |
| 9 | G | B | -0.0670 | |
| 10 | G | B | 0.4565 | |
| 11 | L | B | 1.1184 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.2512 | |
| 14 | P | B | -1.5280 | |
| 15 | G | B | -1.3645 | |
| 16 | G | B | -0.9370 | |
| 17 | S | B | -1.2721 | |
| 18 | L | B | -0.9580 | |
| 19 | R | B | -2.1974 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.3710 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.1996 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.2198 | |
| 26 | G | B | -1.4822 | |
| 27 | F | B | -0.8936 | |
| 28 | T | B | -0.7357 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.8301 | |
| 31 | D | B | -1.5458 | |
| 32 | S | B | 0.0000 | |
| 33 | W | B | 0.1580 | |
| 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 | -0.6333 | |
| 40 | A | B | -1.3075 | |
| 41 | P | B | -1.3365 | |
| 42 | G | B | -1.9783 | |
| 43 | K | B | -2.5482 | |
| 44 | G | B | -1.5654 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.0658 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | A | B | 0.0000 | |
| 50 | W | B | 0.2397 | |
| 51 | I | B | 0.0000 | |
| 52 | S | B | -0.0368 | |
| 53 | P | B | -0.1574 | |
| 54 | Y | B | 0.4931 | |
| 55 | G | B | -0.1889 | |
| 56 | H | B | -0.7875 | |
| 57 | S | B | -0.3414 | |
| 58 | T | B | 0.0714 | |
| 59 | Y | B | 0.2117 | |
| 60 | Y | B | -0.5233 | |
| 61 | A | B | 0.0000 | |
| 62 | D | B | -2.3431 | |
| 63 | S | B | -1.5834 | |
| 64 | V | B | 0.0000 | |
| 65 | H | B | -1.8035 | |
| 66 | G | B | -1.4199 | |
| 67 | R | B | -1.3249 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.7334 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.2878 | |
| 72 | A | B | -0.5795 | |
| 73 | D | B | -1.1462 | |
| 74 | H | B | -1.1626 | |
| 75 | S | B | -1.4792 | |
| 76 | K | B | -2.3271 | |
| 77 | N | B | -1.7371 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5572 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.4955 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.3769 | |
| 85 | S | B | -1.1691 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.4723 | |
| 88 | A | B | -2.5111 | |
| 89 | E | B | -2.9137 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.6133 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | R | B | -0.0583 | |
| 100 | H | B | 0.0526 | |
| 101 | W | B | 0.4041 | |
| 102 | P | B | 0.1996 | |
| 103 | G | B | 0.0000 | |
| 104 | G | B | 0.0000 | |
| 105 | F | B | 0.0000 | |
| 106 | D | B | 0.0000 | |
| 107 | Y | B | -0.2475 | |
| 108 | W | B | -0.4176 | |
| 109 | G | B | 0.0000 | |
| 110 | Q | B | -1.3213 | |
| 111 | G | B | -0.4234 | |
| 112 | T | B | 0.3139 | |
| 113 | L | B | 1.1852 | |
| 114 | V | B | 0.0000 | |
| 115 | T | B | 0.0000 | |
| 116 | V | B | 0.0000 | |
| 117 | S | B | 0.0000 | |
| 118 | S | B | 0.0881 | |
| 119 | V | B | 0.4822 | |
| 120 | A | B | -0.0488 | |
| 121 | A | B | -0.1286 | |
| 122 | P | B | 0.0000 | |
| 123 | S | B | -0.2300 | |
| 124 | V | B | 0.0000 | |
| 125 | F | B | 0.0000 | |
| 126 | I | B | 0.0000 | |
| 127 | F | B | 0.0000 | |
| 128 | P | B | -0.7136 | |
| 129 | P | B | -0.7693 | |
| 130 | S | B | 0.0000 | |
| 131 | D | B | -2.9714 | |
| 132 | E | B | -3.0787 | |
| 133 | Q | B | 0.0000 | |
| 134 | L | B | -2.1864 | |
| 135 | K | B | -2.8293 | |
| 136 | S | B | -1.7578 | |
| 137 | G | B | -1.3752 | |
| 138 | T | B | -1.0170 | |
| 139 | A | B | 0.0000 | |
| 140 | S | B | 0.0000 | |
| 141 | V | B | 0.0000 | |
| 142 | V | B | 0.0000 | |
| 143 | C | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | N | B | 0.0000 | |
| 147 | N | B | -1.0061 | |
| 148 | F | B | 0.0000 | |
| 149 | Y | B | 0.0000 | |
| 150 | P | B | -1.3211 | |
| 151 | R | B | -3.0123 | |
| 152 | E | B | -3.1985 | |
| 153 | A | B | -2.2720 | |
| 154 | K | B | -2.2080 | |
| 155 | V | B | -0.9216 | |
| 156 | Q | B | -0.3838 | |
| 157 | W | B | 0.0000 | |
| 158 | K | B | -0.4412 | |
| 159 | V | B | 0.0000 | |
| 160 | D | B | -1.8119 | |
| 161 | N | B | -1.4621 | |
| 162 | A | B | -0.2061 | |
| 163 | L | B | 0.8242 | |
| 164 | Q | B | -0.2127 | |
| 165 | S | B | -0.6239 | |
| 166 | G | B | -1.3122 | |
| 167 | N | B | -1.6586 | |
| 168 | S | B | -1.4284 | |
| 169 | Q | B | -1.4870 | |
| 170 | E | B | -1.5805 | |
| 171 | S | B | -0.8462 | |
| 172 | V | B | -0.7002 | |
| 173 | T | B | 0.0000 | |
| 174 | E | B | -2.2804 | |
| 175 | Q | B | 0.0000 | |
| 176 | D | B | -2.2267 | |
| 177 | S | B | -2.5653 | |
| 178 | K | B | -2.9997 | |
| 179 | D | B | -2.4408 | |
| 180 | S | B | 0.0000 | |
| 181 | T | B | 0.0000 | |
| 182 | Y | B | -1.3638 | |
| 183 | S | B | 0.0000 | |
| 184 | L | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | T | B | -0.7351 | |
| 188 | L | B | 0.0000 | |
| 189 | T | B | -0.6709 | |
| 190 | L | B | -0.7492 | |
| 191 | S | B | -0.9268 | |
| 192 | K | B | -1.7752 | |
| 193 | A | B | -1.5988 | |
| 194 | D | B | -2.3700 | |
| 195 | Y | B | 0.0000 | |
| 196 | E | B | -2.7144 | |
| 197 | K | B | -3.2530 | |
| 198 | H | B | -2.7504 | |
| 199 | K | B | -3.1011 | |
| 200 | V | B | -1.4031 | |
| 201 | Y | B | 0.0000 | |
| 202 | A | B | 0.0000 | |
| 203 | C | B | 0.0000 | |
| 204 | E | B | -0.8230 | |
| 205 | V | B | 0.0000 | |
| 206 | T | B | -1.1511 | |
| 207 | H | B | 0.0000 | |
| 208 | Q | B | -1.7375 | |
| 209 | G | B | -0.4280 | |
| 210 | L | B | -0.3388 | |
| 211 | S | B | -0.4442 | |
| 212 | S | B | -0.4433 | |
| 213 | P | B | -0.5849 | |
| 214 | V | B | -0.0784 | |
| 215 | T | B | -0.4445 | |
| 216 | K | B | -0.7950 | |
| 217 | S | B | -0.6711 | |
| 218 | F | B | 0.0000 | |
| 219 | N | B | -1.9217 | |
| 220 | R | B | -2.3936 | |
| 221 | G | B | -1.9782 | |
| 222 | E | B | -2.5333 | |
| 223 | C | B | -1.4323 |
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 | -0.704 | 4.0838 | View | CSV | PDB |
| 4.5 | -0.7447 | 4.0838 | View | CSV | PDB |
| 5.0 | -0.7897 | 4.0838 | View | CSV | PDB |
| 5.5 | -0.8294 | 4.0838 | View | CSV | PDB |
| 6.0 | -0.8544 | 4.0838 | View | CSV | PDB |
| 6.5 | -0.8592 | 4.0838 | View | CSV | PDB |
| 7.0 | -0.846 | 4.0838 | View | CSV | PDB |
| 7.5 | -0.8221 | 4.0838 | View | CSV | PDB |
| 8.0 | -0.7921 | 4.0838 | View | CSV | PDB |
| 8.5 | -0.7565 | 4.0837 | View | CSV | PDB |
| 9.0 | -0.7153 | 4.0833 | 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