| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH 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] (00:00:08)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:08)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:08)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:08)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:10)
[INFO] FoldX: Starting FoldX energy minimization (00:00:10)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:10:05)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/fe35a92ae6e8eb2/tmp/folded.pdb (00:10:05)
[INFO] Main: Simulation completed successfully. (00:18:39)
|
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 | -2.3348 | |
| 2 | I | A | -1.5804 | |
| 3 | Q | A | -2.1555 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.4468 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.7068 | |
| 8 | P | A | -0.4302 | |
| 9 | S | A | -0.7662 | |
| 10 | S | A | -0.5509 | |
| 11 | L | A | -0.3249 | |
| 12 | S | A | -0.7217 | |
| 13 | A | A | -0.8972 | |
| 14 | S | A | -0.8419 | |
| 15 | V | A | 0.0041 | |
| 16 | G | A | -0.8450 | |
| 17 | D | A | -1.8051 | |
| 18 | R | A | -2.3586 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6507 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.8457 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.9514 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.2469 | |
| 27 | Q | A | -2.8131 | |
| 28 | D | A | -2.6719 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.8975 | |
| 31 | T | A | -0.4586 | |
| 32 | A | A | 0.1423 | |
| 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 | -1.8917 | |
| 40 | P | A | -1.5457 | |
| 41 | G | A | -1.6080 | |
| 42 | K | A | -2.5893 | |
| 43 | A | A | -1.6126 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -1.4552 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.9214 | |
| 50 | S | A | 0.5524 | |
| 51 | A | A | 0.0000 | |
| 52 | S | A | 0.7830 | |
| 53 | F | A | 2.1725 | |
| 54 | L | A | 1.4473 | |
| 55 | Y | A | 0.6501 | |
| 56 | S | A | 0.0311 | |
| 57 | G | A | -0.4624 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.3349 | |
| 60 | S | A | -0.3807 | |
| 61 | R | A | -0.7506 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | 0.0719 | |
| 64 | G | A | 0.1876 | |
| 65 | S | A | -0.3910 | |
| 66 | G | A | -1.0336 | |
| 67 | S | A | -1.0703 | |
| 68 | G | A | -1.8048 | |
| 69 | T | A | -2.3088 | |
| 70 | D | A | -2.4280 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7634 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6195 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3884 | |
| 77 | S | A | -1.2312 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -0.8160 | |
| 80 | P | A | -1.3437 | |
| 81 | E | A | -1.7594 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -0.7521 | |
| 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 | 0.7385 | |
| 92 | L | A | 0.9429 | |
| 93 | Y | A | 0.3323 | |
| 94 | H | A | -0.2253 | |
| 95 | P | A | -0.6070 | |
| 96 | A | A | 0.0000 | |
| 97 | T | A | -0.5867 | |
| 98 | F | A | -0.4366 | |
| 99 | G | A | 0.0000 | |
| 100 | Q | A | -1.8370 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.1650 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | 0.0000 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.2970 | |
| 108 | R | A | -0.9742 | |
| 109 | T | A | -0.1950 | |
| 110 | V | A | 0.3026 | |
| 111 | A | A | -0.0353 | |
| 112 | A | A | -0.1140 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.2166 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.5281 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | -1.8843 | |
| 122 | D | A | -3.1960 | |
| 123 | E | A | -3.1579 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.2935 | |
| 126 | K | A | -2.8794 | |
| 127 | S | A | -1.7625 | |
| 128 | G | A | -1.2137 | |
| 129 | T | A | -0.9549 | |
| 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 | -0.8488 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.5942 | |
| 142 | R | A | -2.5298 | |
| 143 | E | A | -3.0188 | |
| 144 | A | A | -2.2460 | |
| 145 | K | A | -2.4325 | |
| 146 | V | A | 0.0000 | |
| 147 | Q | A | -0.7054 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.4943 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -1.8268 | |
| 152 | N | A | -1.4776 | |
| 153 | A | A | -0.2181 | |
| 154 | L | A | 0.7171 | |
| 155 | Q | A | -0.3398 | |
| 156 | S | A | -0.6860 | |
| 157 | G | A | -1.2953 | |
| 158 | N | A | -1.6289 | |
| 159 | S | A | -1.4280 | |
| 160 | Q | A | -1.2740 | |
| 161 | E | A | -1.3072 | |
| 162 | S | A | -0.5213 | |
| 163 | V | A | -0.1639 | |
| 164 | T | A | -0.8476 | |
| 165 | E | A | -1.9992 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -2.0326 | |
| 168 | S | A | -2.0286 | |
| 169 | K | A | -2.4194 | |
| 170 | D | A | -1.6884 | |
| 171 | S | A | -1.8656 | |
| 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 | -0.6406 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.6094 | |
| 181 | L | A | -0.7165 | |
| 182 | S | A | -0.8987 | |
| 183 | K | A | -1.9113 | |
| 184 | A | A | -1.6893 | |
| 185 | D | A | -2.1717 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.4085 | |
| 188 | K | A | -3.4959 | |
| 189 | H | A | -2.8930 | |
| 190 | K | A | -3.2236 | |
| 191 | V | A | -1.3809 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.5493 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.2022 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.7064 | |
| 200 | G | A | -0.4192 | |
| 201 | L | A | -0.2097 | |
| 202 | S | A | -0.4364 | |
| 203 | S | A | -0.3880 | |
| 204 | P | A | -0.4678 | |
| 205 | V | A | 0.2367 | |
| 206 | T | A | -0.2196 | |
| 207 | K | A | -0.5067 | |
| 208 | S | A | -0.5124 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -1.7133 | |
| 211 | R | A | -2.3647 | |
| 212 | G | A | -1.8774 | |
| 213 | E | A | -2.0642 | |
| 214 | C | A | -0.9801 | |
| 1 | E | B | -2.1451 | |
| 2 | V | B | -1.3388 | |
| 3 | Q | B | -1.2871 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.7294 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.4431 | |
| 8 | G | B | -0.9334 | |
| 9 | G | B | -0.4876 | |
| 10 | G | B | -0.2741 | |
| 11 | L | B | -0.0183 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.6496 | |
| 14 | P | B | -1.7523 | |
| 15 | G | B | -1.4555 | |
| 16 | G | B | -1.1359 | |
| 17 | S | B | -1.3154 | |
| 18 | L | B | -1.1796 | |
| 19 | R | B | -2.1030 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.4113 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.2190 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.1030 | |
| 26 | G | B | -1.3160 | |
| 27 | F | B | -0.7763 | |
| 28 | T | B | -0.6702 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.6558 | |
| 31 | D | B | -1.5265 | |
| 32 | S | B | 0.0000 | |
| 33 | W | B | -0.2728 | |
| 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 | -0.7679 | |
| 40 | A | B | -1.1511 | |
| 41 | P | B | -0.9406 | |
| 42 | G | B | -1.4657 | |
| 43 | K | B | -2.3888 | |
| 44 | G | B | -1.6511 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.0753 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | A | B | 0.0000 | |
| 50 | W | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | S | B | -0.2102 | |
| 53 | P | B | -0.1905 | |
| 54 | Y | B | 0.4646 | |
| 55 | G | B | -0.3248 | |
| 56 | G | B | -0.4760 | |
| 57 | S | B | -0.2287 | |
| 58 | T | B | 0.0686 | |
| 59 | Y | B | 0.1743 | |
| 60 | Y | B | -0.6575 | |
| 61 | A | B | 0.0000 | |
| 62 | D | B | -2.6166 | |
| 63 | S | B | -1.7451 | |
| 64 | V | B | 0.0000 | |
| 65 | K | B | -2.5163 | |
| 66 | G | B | -1.7385 | |
| 67 | R | B | -1.4743 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.7585 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.3178 | |
| 72 | A | B | -0.4741 | |
| 73 | D | B | -1.0424 | |
| 74 | T | B | -0.8761 | |
| 75 | S | B | -1.3307 | |
| 76 | K | B | -2.2003 | |
| 77 | N | B | -1.5857 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.5101 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.2398 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.4816 | |
| 85 | S | B | -1.2796 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.2904 | |
| 88 | A | B | -1.7111 | |
| 89 | E | B | -2.2166 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.6891 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.2609 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | -0.5125 | |
| 99 | R | B | -0.7563 | |
| 100 | H | B | -0.6007 | |
| 101 | W | B | 0.4804 | |
| 102 | P | B | 0.3159 | |
| 103 | G | B | 0.1326 | |
| 104 | G | B | 0.0000 | |
| 105 | F | B | 0.0000 | |
| 106 | D | B | -0.4312 | |
| 107 | Y | B | -0.4724 | |
| 108 | W | B | -0.5296 | |
| 109 | G | B | 0.0000 | |
| 110 | Q | B | -1.3936 | |
| 111 | G | B | -0.5619 | |
| 112 | T | B | -0.0064 | |
| 113 | L | B | 0.2974 | |
| 114 | V | B | 0.0000 | |
| 115 | T | B | 0.0000 | |
| 116 | V | B | 0.0000 | |
| 117 | S | B | -0.9902 | |
| 118 | S | B | -0.7275 | |
| 119 | A | B | -0.4786 | |
| 120 | S | B | -0.6009 | |
| 121 | T | B | -0.7946 | |
| 122 | K | B | -1.3129 | |
| 123 | G | B | -1.3569 | |
| 124 | P | B | 0.0000 | |
| 125 | S | B | -0.4302 | |
| 126 | V | B | 0.0000 | |
| 127 | F | B | 0.0000 | |
| 128 | P | B | -1.3350 | |
| 129 | L | B | 0.0000 | |
| 130 | A | B | -1.3198 | |
| 131 | P | B | 0.0000 | |
| 132 | S | B | -0.9363 | |
| 133 | S | B | -0.5458 | |
| 134 | K | B | -0.9155 | |
| 135 | S | B | 0.0000 | |
| 136 | T | B | -0.6594 | |
| 137 | S | B | -0.6824 | |
| 138 | G | B | -0.7973 | |
| 139 | G | B | -0.8653 | |
| 140 | T | B | -0.6066 | |
| 141 | A | B | 0.0000 | |
| 142 | A | B | 0.0000 | |
| 143 | L | B | 0.0000 | |
| 144 | G | B | 0.0000 | |
| 145 | C | B | 0.0000 | |
| 146 | L | B | 0.0000 | |
| 147 | V | B | 0.0000 | |
| 148 | K | B | 0.0000 | |
| 149 | D | B | -0.3669 | |
| 150 | Y | B | 0.0000 | |
| 151 | F | B | 0.0000 | |
| 152 | P | B | 0.0000 | |
| 153 | E | B | -0.3937 | |
| 154 | P | B | -0.6596 | |
| 155 | V | B | -0.5842 | |
| 156 | T | B | -0.4938 | |
| 157 | V | B | -0.0923 | |
| 158 | S | B | -0.3516 | |
| 159 | W | B | 0.0000 | |
| 160 | N | B | -0.7371 | |
| 161 | S | B | -0.6410 | |
| 162 | G | B | -0.4738 | |
| 163 | A | B | -0.2119 | |
| 164 | L | B | 0.0233 | |
| 165 | T | B | -0.1564 | |
| 166 | S | B | -0.1777 | |
| 167 | G | B | -0.2144 | |
| 168 | V | B | 0.1694 | |
| 169 | H | B | -0.2635 | |
| 170 | T | B | 0.0783 | |
| 171 | F | B | 0.0000 | |
| 172 | P | B | -0.1939 | |
| 173 | A | B | 0.3265 | |
| 174 | V | B | 0.5854 | |
| 175 | L | B | 1.2471 | |
| 176 | Q | B | 0.3306 | |
| 177 | S | B | -0.0457 | |
| 178 | S | B | -0.1908 | |
| 179 | G | B | 0.0696 | |
| 180 | L | B | 0.1532 | |
| 181 | Y | B | 0.4954 | |
| 182 | S | B | 0.0000 | |
| 183 | L | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | V | B | 0.0000 | |
| 188 | T | B | -0.1357 | |
| 189 | V | B | 0.0000 | |
| 190 | P | B | -0.6093 | |
| 191 | S | B | -0.5674 | |
| 192 | S | B | -0.5772 | |
| 193 | S | B | -0.5591 | |
| 194 | L | B | -0.7621 | |
| 195 | G | B | -0.9359 | |
| 196 | T | B | -0.6772 | |
| 197 | Q | B | -1.1504 | |
| 198 | T | B | -1.0856 | |
| 199 | Y | B | 0.0000 | |
| 200 | I | B | -1.2835 | |
| 201 | C | B | 0.0000 | |
| 202 | N | B | -1.3946 | |
| 203 | V | B | 0.0000 | |
| 204 | N | B | -1.7823 | |
| 205 | H | B | 0.0000 | |
| 206 | K | B | -2.7158 | |
| 207 | P | B | -1.5977 | |
| 208 | S | B | -1.8653 | |
| 209 | N | B | -2.5848 | |
| 210 | T | B | -2.0286 | |
| 211 | K | B | -2.6082 | |
| 212 | V | B | -1.4988 | |
| 213 | D | B | -2.4108 | |
| 214 | K | B | -2.0812 | |
| 215 | K | B | -2.4616 | |
| 216 | V | B | 0.0000 | |
| 217 | E | B | -2.8702 | |
| 218 | P | B | -1.8433 | |
| 219 | K | B | -2.5226 | |
| 220 | S | B | -1.7780 | |
| 221 | C | B | -1.5778 | |
| 222 | D | B | -2.7646 | |
| 223 | K | B | -2.9708 | |
| 224 | T | B | -2.3286 | |
| 225 | H | B | -2.7973 | |
| 226 | H | B | -2.6877 | |
| 227 | H | B | -2.7395 | |
| 228 | H | B | -2.7080 | |
| 229 | H | B | -2.4147 | |
| 230 | H | B | -1.9105 |
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 | -0.7517 | 3.8067 | View | CSV | PDB |
| 4.5 | -0.7965 | 3.8067 | View | CSV | PDB |
| 5.0 | -0.8463 | 3.8067 | View | CSV | PDB |
| 5.5 | -0.8901 | 3.8067 | View | CSV | PDB |
| 6.0 | -0.9158 | 3.8067 | View | CSV | PDB |
| 6.5 | -0.9169 | 3.8067 | View | CSV | PDB |
| 7.0 | -0.8982 | 3.8067 | View | CSV | PDB |
| 7.5 | -0.8694 | 3.8067 | View | CSV | PDB |
| 8.0 | -0.8352 | 3.8067 | View | CSV | PDB |
| 8.5 | -0.7952 | 3.8066 | View | CSV | PDB |
| 9.0 | -0.7479 | 3.8063 | 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