| Chain sequence(s) |
A: DIQMTQTPSSLSASLGDRVTINCRASQDIENHLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISNLEQEDIATYFCQQGNTLPATFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: DVQLQESGPGLVKSSQSLSLTCSVTGYSITSGYFWNWIRQFPGNKLEWMGEMTYDGSNNYNPSLKNRISITRDTSKNQFFLKLNSVTAEDTATYYCARDGHLPFDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:09:37)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/88c4df8077ecb3e/tmp/folded.pdb (00:09:37)
[INFO] Main: Simulation completed successfully. (00:15:03)
|
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 | -2.0462 | |
| 2 | I | A | -1.7675 | |
| 3 | Q | A | -2.1947 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.4338 | |
| 6 | Q | A | -1.0218 | |
| 7 | T | A | -0.7758 | |
| 8 | P | A | -0.6067 | |
| 9 | S | A | -0.7818 | |
| 10 | S | A | -0.7865 | |
| 11 | L | A | -0.5792 | |
| 12 | S | A | -0.8709 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.2748 | |
| 15 | L | A | -0.7931 | |
| 16 | G | A | -1.6228 | |
| 17 | D | A | -2.2015 | |
| 18 | R | A | -2.6945 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6189 | |
| 21 | I | A | 0.0000 | |
| 22 | N | A | -1.3844 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -3.1673 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.3300 | |
| 27 | Q | A | -3.1957 | |
| 28 | D | A | -3.5156 | |
| 29 | I | A | 0.0000 | |
| 30 | E | A | -2.7926 | |
| 31 | N | A | -1.7592 | |
| 32 | H | A | -1.0357 | |
| 33 | L | A | 0.0000 | |
| 34 | N | 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 | -2.1565 | |
| 40 | P | A | -2.0262 | |
| 41 | D | A | -2.5006 | |
| 42 | G | A | -1.5918 | |
| 43 | T | A | -1.3371 | |
| 44 | V | A | -0.8770 | |
| 45 | K | A | -0.8881 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.1706 | |
| 50 | Y | A | -0.2316 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -0.8617 | |
| 53 | R | A | -1.3093 | |
| 54 | L | A | -0.3748 | |
| 55 | H | A | -0.6358 | |
| 56 | S | A | -0.6166 | |
| 57 | G | A | -0.5623 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.3628 | |
| 60 | S | A | -0.5454 | |
| 61 | R | A | -1.0948 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.5747 | |
| 64 | G | A | -0.5405 | |
| 65 | S | A | -0.9029 | |
| 66 | G | A | -1.2264 | |
| 67 | S | A | -1.7765 | |
| 68 | G | A | -2.4315 | |
| 69 | T | A | -2.7142 | |
| 70 | D | A | -2.6767 | |
| 71 | F | A | 0.0000 | |
| 72 | S | A | -1.0370 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.8269 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.9749 | |
| 77 | N | A | -2.5234 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.2029 | |
| 80 | Q | A | -2.2519 | |
| 81 | E | A | -2.8878 | |
| 82 | D | A | 0.0000 | |
| 83 | I | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -1.0038 | |
| 86 | Y | A | 0.0000 | |
| 87 | F | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | G | A | -0.2356 | |
| 92 | N | A | -0.9915 | |
| 93 | T | A | -0.0450 | |
| 94 | L | A | 0.4945 | |
| 95 | P | A | -0.0180 | |
| 96 | A | A | 0.0000 | |
| 97 | T | A | -0.5766 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.5595 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.5000 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.4066 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.4445 | |
| 108 | R | A | -1.0986 | |
| 109 | T | A | -0.2055 | |
| 110 | V | A | 0.2294 | |
| 111 | A | A | -0.1119 | |
| 112 | A | A | -0.1349 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.2744 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.4366 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | -1.6790 | |
| 122 | D | A | -3.0429 | |
| 123 | E | A | -3.1908 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.3163 | |
| 126 | K | A | -2.9029 | |
| 127 | S | A | -1.8219 | |
| 128 | G | A | -1.2477 | |
| 129 | T | A | -1.0824 | |
| 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 | -1.0130 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.7869 | |
| 142 | R | A | -2.9778 | |
| 143 | E | A | -3.2216 | |
| 144 | A | A | -2.3470 | |
| 145 | K | A | -2.4987 | |
| 146 | V | A | -1.1901 | |
| 147 | Q | A | -0.7994 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.7082 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -1.9590 | |
| 152 | N | A | -1.5986 | |
| 153 | A | A | -0.4129 | |
| 154 | L | A | 0.4034 | |
| 155 | Q | A | -0.4500 | |
| 156 | S | A | -0.7196 | |
| 157 | G | A | -1.2730 | |
| 158 | N | A | -1.5955 | |
| 159 | S | A | -1.3982 | |
| 160 | Q | A | -1.2913 | |
| 161 | E | A | -1.4056 | |
| 162 | S | A | -0.7405 | |
| 163 | V | A | -0.6419 | |
| 164 | T | A | -1.0007 | |
| 165 | E | A | -2.1375 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -2.0989 | |
| 168 | S | A | -2.5300 | |
| 169 | K | A | -2.7556 | |
| 170 | D | A | -1.9810 | |
| 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 | -0.6709 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.6831 | |
| 181 | L | A | -0.9561 | |
| 182 | S | A | -1.1789 | |
| 183 | K | A | -2.1570 | |
| 184 | A | A | -2.0951 | |
| 185 | D | A | -2.9704 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.8133 | |
| 188 | K | A | -3.8241 | |
| 189 | H | A | -3.0827 | |
| 190 | K | A | -3.2171 | |
| 191 | V | A | -1.6348 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.9645 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.2852 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.7522 | |
| 200 | G | A | -0.4153 | |
| 201 | L | A | -0.2139 | |
| 202 | S | A | -0.4473 | |
| 203 | S | A | -0.4470 | |
| 204 | P | A | -0.6186 | |
| 205 | V | A | -0.1021 | |
| 206 | T | A | -0.5113 | |
| 207 | K | A | -0.8481 | |
| 208 | S | A | -0.7144 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -1.7885 | |
| 211 | R | A | -2.3966 | |
| 212 | G | A | -1.9610 | |
| 213 | E | A | -2.1795 | |
| 214 | C | A | -1.0478 | |
| 1 | D | B | -2.1018 | |
| 2 | V | B | 0.0000 | |
| 3 | Q | B | -1.9504 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -1.4970 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.7635 | |
| 8 | G | B | -0.8339 | |
| 9 | P | B | -0.7053 | |
| 10 | G | B | -0.6611 | |
| 11 | L | B | -0.5383 | |
| 12 | V | B | 0.0000 | |
| 13 | K | B | -1.6644 | |
| 14 | S | B | -1.4918 | |
| 15 | S | B | -1.3806 | |
| 16 | Q | B | -1.9468 | |
| 17 | S | B | -1.5170 | |
| 18 | L | B | 0.0000 | |
| 19 | S | B | -0.8669 | |
| 20 | L | B | 0.0000 | |
| 21 | T | B | -0.4896 | |
| 22 | C | B | 0.0000 | |
| 23 | S | B | -1.0275 | |
| 24 | V | B | 0.0000 | |
| 25 | T | B | -1.2099 | |
| 26 | G | B | -1.0892 | |
| 27 | Y | B | -0.2311 | |
| 28 | S | B | -0.1787 | |
| 29 | I | B | 0.0000 | |
| 30 | T | B | -0.3317 | |
| 31 | S | B | -0.1962 | |
| 32 | G | B | -0.3768 | |
| 33 | Y | B | 0.1891 | |
| 34 | F | B | 0.2788 | |
| 35 | W | B | 0.0000 | |
| 36 | N | B | 0.0000 | |
| 37 | W | B | 0.0000 | |
| 38 | I | B | 0.0000 | |
| 39 | R | B | 0.0000 | |
| 40 | Q | B | 0.0000 | |
| 41 | F | B | -1.2643 | |
| 42 | P | B | -1.2976 | |
| 43 | G | B | -1.6456 | |
| 44 | N | B | -2.3583 | |
| 45 | K | B | -2.5651 | |
| 46 | L | B | 0.0000 | |
| 47 | E | B | -0.7308 | |
| 48 | W | B | 0.0000 | |
| 49 | M | B | 0.0000 | |
| 50 | G | B | 0.0000 | |
| 51 | E | B | 0.0000 | |
| 52 | M | B | 0.0000 | |
| 53 | T | B | 0.0000 | |
| 54 | Y | B | -0.1576 | |
| 55 | D | B | -1.5735 | |
| 56 | G | B | -1.0663 | |
| 57 | S | B | -0.8835 | |
| 58 | N | B | -0.8642 | |
| 59 | N | B | -0.8197 | |
| 60 | Y | B | -0.8774 | |
| 61 | N | B | 0.0000 | |
| 62 | P | B | -1.3204 | |
| 63 | S | B | -1.2268 | |
| 64 | L | B | 0.0000 | |
| 65 | K | B | -2.6219 | |
| 66 | N | B | -2.4408 | |
| 67 | R | B | -1.9671 | |
| 68 | I | B | 0.0000 | |
| 69 | S | B | -1.1080 | |
| 70 | I | B | 0.0000 | |
| 71 | T | B | -0.5888 | |
| 72 | R | B | -1.0461 | |
| 73 | D | B | -1.3541 | |
| 74 | T | B | -1.2324 | |
| 75 | S | B | -1.3649 | |
| 76 | K | B | -2.2198 | |
| 77 | N | B | -1.4665 | |
| 78 | Q | B | -1.2687 | |
| 79 | F | B | 0.0000 | |
| 80 | F | B | -0.2091 | |
| 81 | L | B | 0.0000 | |
| 82 | K | B | -1.1526 | |
| 83 | L | B | 0.0000 | |
| 84 | N | B | -1.6285 | |
| 85 | S | B | -1.3716 | |
| 86 | V | B | 0.0000 | |
| 87 | T | B | -1.2345 | |
| 88 | A | B | -1.0732 | |
| 89 | E | B | -1.8100 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.5550 | |
| 92 | A | B | 0.0000 | |
| 93 | T | B | -0.2908 | |
| 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 | D | B | -0.1736 | |
| 100 | G | B | -0.4634 | |
| 101 | H | B | -0.8349 | |
| 102 | L | B | -0.2380 | |
| 103 | P | B | 0.0000 | |
| 104 | F | B | 0.0000 | |
| 105 | D | B | -0.4061 | |
| 106 | Y | B | -0.5253 | |
| 107 | W | B | -0.5756 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.7251 | |
| 110 | G | B | 0.0000 | |
| 111 | T | B | -0.5866 | |
| 112 | T | B | -0.1993 | |
| 113 | L | B | 0.0000 | |
| 114 | T | B | -0.4965 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.7490 | |
| 117 | S | B | -0.6680 | |
| 118 | A | B | -0.4941 | |
| 119 | S | B | -0.6390 | |
| 120 | T | B | -0.7850 | |
| 121 | K | B | -1.2479 | |
| 122 | G | B | -1.4013 | |
| 123 | P | B | -0.6344 | |
| 124 | S | B | -0.4410 | |
| 125 | V | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -1.1165 | |
| 128 | L | B | 0.0000 | |
| 129 | A | B | -1.3494 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -1.2126 | |
| 132 | S | B | -0.8924 | |
| 133 | K | B | -1.2126 | |
| 134 | S | B | 0.0000 | |
| 135 | T | B | -0.6864 | |
| 136 | S | B | -0.7165 | |
| 137 | G | B | -0.8118 | |
| 138 | G | B | -0.8742 | |
| 139 | T | B | -0.6109 | |
| 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 | -0.4148 | |
| 149 | Y | B | 0.0000 | |
| 150 | F | B | 0.0000 | |
| 151 | P | B | 0.0000 | |
| 152 | E | B | -0.3658 | |
| 153 | P | B | -0.6267 | |
| 154 | V | B | -0.6496 | |
| 155 | T | B | -0.5878 | |
| 156 | V | B | -0.3535 | |
| 157 | S | B | -0.3801 | |
| 158 | W | B | 0.0000 | |
| 159 | N | B | -0.6872 | |
| 160 | S | B | -0.6365 | |
| 161 | G | B | -0.5858 | |
| 162 | A | B | -0.2613 | |
| 163 | L | B | -0.0168 | |
| 164 | T | B | -0.1881 | |
| 165 | S | B | -0.1945 | |
| 166 | G | B | -0.2399 | |
| 167 | V | B | 0.1573 | |
| 168 | H | B | -0.2932 | |
| 169 | T | B | 0.0094 | |
| 170 | F | B | 0.0000 | |
| 171 | P | B | -0.2692 | |
| 172 | A | B | 0.2887 | |
| 173 | V | B | 0.6001 | |
| 174 | L | B | 1.2851 | |
| 175 | Q | B | 0.3334 | |
| 176 | S | B | -0.1629 | |
| 177 | S | B | -0.2155 | |
| 178 | G | B | 0.0348 | |
| 179 | L | B | 0.1787 | |
| 180 | Y | B | 0.5057 | |
| 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 | -0.1389 | |
| 188 | V | B | 0.0000 | |
| 189 | P | B | -0.5321 | |
| 190 | S | B | -0.5778 | |
| 191 | S | B | -0.5906 | |
| 192 | S | B | -0.5898 | |
| 193 | L | B | -0.9865 | |
| 194 | G | B | -0.9832 | |
| 195 | T | B | -0.7255 | |
| 196 | Q | B | -1.1917 | |
| 197 | T | B | -1.0524 | |
| 198 | Y | B | 0.0000 | |
| 199 | I | B | -0.9965 | |
| 200 | C | B | 0.0000 | |
| 201 | N | B | -1.3442 | |
| 202 | V | B | 0.0000 | |
| 203 | N | B | -1.9853 | |
| 204 | H | B | 0.0000 | |
| 205 | K | B | -2.7934 | |
| 206 | P | B | -1.6537 | |
| 207 | S | B | -1.8536 | |
| 208 | N | B | -2.5938 | |
| 209 | T | B | -2.0938 | |
| 210 | K | B | -2.6506 | |
| 211 | V | B | -1.4549 | |
| 212 | D | B | -2.1733 | |
| 213 | K | B | -1.8683 | |
| 214 | K | B | -2.2094 | |
| 215 | V | B | 0.0000 | |
| 216 | E | B | -2.7716 | |
| 217 | P | B | -1.9896 | |
| 218 | K | B | -2.2877 | |
| 219 | S | B | -1.2703 |
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 | -0.8177 | 1.7014 | View | CSV | PDB |
| 4.5 | -0.8646 | 1.6556 | View | CSV | PDB |
| 5.0 | -0.9182 | 1.5868 | View | CSV | PDB |
| 5.5 | -0.9686 | 1.5399 | View | CSV | PDB |
| 6.0 | -1.0042 | 1.5176 | View | CSV | PDB |
| 6.5 | -1.0167 | 1.4978 | View | CSV | PDB |
| 7.0 | -1.0063 | 1.4812 | View | CSV | PDB |
| 7.5 | -0.9799 | 1.467 | View | CSV | PDB |
| 8.0 | -0.9434 | 1.4547 | View | CSV | PDB |
| 8.5 | -0.8988 | 1.4445 | View | CSV | PDB |
| 9.0 | -0.8466 | 1.4376 | 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