| Chain sequence(s) |
A: DIVMTQSPSSLSVSAGEKVTMSCKSSQSLLNSGNQKNYLAWYQQKPGQPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHSYPYTFGGGTKLEIKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS
B: QVQLQQSGAELARPGASVKLSCKASGYTFTSYGISWVKQRTGQGLEWIGEIYPRSGNTYYNEKFKGKATLTADKSSSTAYMELRSLTSEDSAVYFCARRASTVVAPYAMDYWGQGTSVTVVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:09:34)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/880cf1d29bab9f/tmp/folded.pdb (00:09:34)
[INFO] Main: Simulation completed successfully. (00:17:00)
|
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 | -1.5519 | |
| 2 | I | A | -0.2928 | |
| 3 | V | A | 0.9350 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2979 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.6180 | |
| 8 | P | A | -0.4970 | |
| 9 | S | A | -0.6258 | |
| 10 | S | A | -0.6407 | |
| 11 | L | A | -0.4754 | |
| 12 | S | A | -0.8591 | |
| 13 | V | A | 0.0000 | |
| 14 | S | A | -1.6860 | |
| 15 | A | A | -1.6773 | |
| 16 | G | A | -1.7957 | |
| 17 | E | A | -2.6216 | |
| 18 | K | A | -2.7239 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.4628 | |
| 21 | M | A | 0.0000 | |
| 22 | S | A | -0.7452 | |
| 23 | C | A | 0.0000 | |
| 24 | K | A | -1.6152 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.8038 | |
| 27 | Q | A | -1.4782 | |
| 28 | S | A | -1.0509 | |
| 29 | L | A | 0.0000 | |
| 30 | L | A | -0.6764 | |
| 31 | N | A | -0.9918 | |
| 32 | S | A | -1.1979 | |
| 33 | G | A | -1.0114 | |
| 34 | N | A | -1.2008 | |
| 35 | Q | A | -2.0269 | |
| 36 | K | A | -1.5505 | |
| 37 | N | A | -0.9338 | |
| 38 | Y | A | 0.0000 | |
| 39 | L | A | 0.0000 | |
| 40 | A | A | 0.0000 | |
| 41 | W | A | 0.0000 | |
| 42 | Y | A | 0.0000 | |
| 43 | Q | A | 0.0000 | |
| 44 | Q | A | 0.0000 | |
| 45 | K | A | -1.5524 | |
| 46 | P | A | -1.1644 | |
| 47 | G | A | -1.4290 | |
| 48 | Q | A | -2.0179 | |
| 49 | P | A | -1.3574 | |
| 50 | P | A | 0.0000 | |
| 51 | K | A | -1.4954 | |
| 52 | L | A | 0.0000 | |
| 53 | L | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | Y | A | -0.0588 | |
| 56 | G | A | -0.4584 | |
| 57 | A | A | 0.0000 | |
| 58 | S | A | -0.6186 | |
| 59 | T | A | -0.4952 | |
| 60 | R | A | -1.1924 | |
| 61 | E | A | -1.2512 | |
| 62 | S | A | -0.7940 | |
| 63 | G | A | -0.9516 | |
| 64 | V | A | -1.0850 | |
| 65 | P | A | -1.2953 | |
| 66 | D | A | -2.1955 | |
| 67 | R | A | -1.5712 | |
| 68 | F | A | 0.0000 | |
| 69 | T | A | -0.7565 | |
| 70 | G | A | 0.0000 | |
| 71 | S | A | -0.6778 | |
| 72 | G | A | -1.1028 | |
| 73 | S | A | -1.1503 | |
| 74 | G | A | -1.0482 | |
| 75 | T | A | -1.5577 | |
| 76 | D | A | -2.3062 | |
| 77 | F | A | 0.0000 | |
| 78 | T | A | -0.7217 | |
| 79 | L | A | 0.0000 | |
| 80 | T | A | -0.5401 | |
| 81 | I | A | 0.0000 | |
| 82 | S | A | -1.7717 | |
| 83 | S | A | -1.9164 | |
| 84 | V | A | 0.0000 | |
| 85 | Q | A | -1.7246 | |
| 86 | A | A | -1.3584 | |
| 87 | E | A | -1.6377 | |
| 88 | D | A | 0.0000 | |
| 89 | L | A | 0.0000 | |
| 90 | A | A | 0.0000 | |
| 91 | V | A | -0.3535 | |
| 92 | Y | A | 0.0000 | |
| 93 | Y | A | 0.0000 | |
| 94 | C | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | N | A | 0.0000 | |
| 97 | D | A | 0.0000 | |
| 98 | H | A | -0.1497 | |
| 99 | S | A | -0.1097 | |
| 100 | Y | A | -0.0094 | |
| 101 | P | A | -0.5865 | |
| 102 | Y | A | 0.0000 | |
| 103 | T | A | 0.0200 | |
| 104 | F | A | 0.2143 | |
| 105 | G | A | 0.0000 | |
| 106 | G | A | -0.5746 | |
| 107 | G | A | 0.0000 | |
| 108 | T | A | 0.0000 | |
| 109 | K | A | -1.0042 | |
| 110 | L | A | 0.0000 | |
| 111 | E | A | -1.0109 | |
| 112 | I | A | 0.0000 | |
| 113 | K | A | -1.7042 | |
| 114 | A | A | -1.0688 | |
| 115 | S | A | -0.8212 | |
| 116 | T | A | -1.0644 | |
| 117 | K | A | -1.2636 | |
| 118 | G | A | -1.4664 | |
| 119 | P | A | 0.0000 | |
| 120 | S | A | -0.1104 | |
| 121 | V | A | 0.0000 | |
| 122 | F | A | 0.7846 | |
| 123 | P | A | 0.0918 | |
| 124 | L | A | 0.2040 | |
| 125 | A | A | -0.9191 | |
| 126 | P | A | 0.0000 | |
| 127 | S | A | -1.4042 | |
| 128 | S | A | -1.3562 | |
| 129 | K | A | -1.8926 | |
| 130 | S | A | -0.9958 | |
| 131 | T | A | -1.0305 | |
| 132 | S | A | -0.9684 | |
| 133 | G | A | -0.8580 | |
| 134 | G | A | -0.9168 | |
| 135 | T | A | -0.6525 | |
| 136 | A | A | 0.0000 | |
| 137 | A | A | -0.1949 | |
| 138 | L | A | 0.0000 | |
| 139 | G | A | 0.0000 | |
| 140 | C | A | 0.0000 | |
| 141 | L | A | 0.7172 | |
| 142 | V | A | 0.0000 | |
| 143 | K | A | -0.1568 | |
| 144 | D | A | -0.7005 | |
| 145 | Y | A | 0.0000 | |
| 146 | F | A | 0.0000 | |
| 147 | P | A | -1.1498 | |
| 148 | E | A | -1.1001 | |
| 149 | P | A | -1.0317 | |
| 150 | V | A | -0.8312 | |
| 151 | T | A | -0.6450 | |
| 152 | V | A | -0.4738 | |
| 153 | S | A | -0.4762 | |
| 154 | W | A | 0.0000 | |
| 155 | N | A | -0.7316 | |
| 156 | S | A | -0.6610 | |
| 157 | G | A | -0.4866 | |
| 158 | A | A | -0.2527 | |
| 159 | L | A | -0.0210 | |
| 160 | T | A | -0.3425 | |
| 161 | S | A | -0.4618 | |
| 162 | G | A | -0.4957 | |
| 163 | V | A | -0.1321 | |
| 164 | H | A | -0.5468 | |
| 165 | T | A | 0.1808 | |
| 166 | F | A | 1.0915 | |
| 167 | P | A | 0.6486 | |
| 168 | A | A | 0.9553 | |
| 169 | V | A | 1.9448 | |
| 170 | L | A | 0.8251 | |
| 171 | Q | A | -0.0084 | |
| 172 | S | A | -0.7013 | |
| 173 | S | A | -0.8251 | |
| 174 | G | A | 0.0000 | |
| 175 | L | A | -0.3398 | |
| 176 | Y | A | 0.2556 | |
| 177 | S | A | 0.0000 | |
| 178 | L | A | 0.0000 | |
| 179 | S | A | 0.6937 | |
| 180 | S | A | 0.0000 | |
| 181 | V | A | 0.4021 | |
| 182 | V | A | 0.0000 | |
| 183 | T | A | -0.2468 | |
| 184 | V | A | 0.0000 | |
| 185 | P | A | -0.5573 | |
| 186 | S | A | -0.6106 | |
| 187 | S | A | -0.6305 | |
| 188 | S | A | -0.6799 | |
| 189 | L | A | -0.9035 | |
| 190 | G | A | -1.0556 | |
| 191 | T | A | -0.8612 | |
| 192 | Q | A | -1.4575 | |
| 193 | T | A | -1.1976 | |
| 194 | Y | A | 0.0000 | |
| 195 | I | A | -1.1502 | |
| 196 | C | A | 0.0000 | |
| 197 | N | A | -1.4883 | |
| 198 | V | A | 0.0000 | |
| 199 | N | A | -1.9840 | |
| 200 | H | A | 0.0000 | |
| 201 | K | A | -2.8006 | |
| 202 | P | A | -1.7209 | |
| 203 | S | A | -1.8681 | |
| 204 | N | A | -2.6163 | |
| 205 | T | A | -2.1009 | |
| 206 | K | A | -2.7410 | |
| 207 | V | A | -1.6820 | |
| 208 | D | A | -2.5699 | |
| 209 | K | A | -2.0926 | |
| 210 | K | A | -2.2007 | |
| 211 | V | A | 0.0000 | |
| 212 | E | A | -2.7957 | |
| 213 | P | A | -1.9375 | |
| 214 | K | A | -2.3106 | |
| 215 | S | A | -1.3128 | |
| 1 | Q | B | -1.6830 | |
| 2 | V | B | 0.0000 | |
| 3 | Q | B | -2.1996 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -2.3092 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -1.1682 | |
| 8 | G | B | -0.9213 | |
| 9 | A | B | -0.1493 | |
| 10 | E | B | -0.1898 | |
| 11 | L | B | 0.8697 | |
| 12 | A | B | -0.4028 | |
| 13 | R | B | -1.8624 | |
| 14 | P | B | -1.4508 | |
| 15 | G | B | -1.3515 | |
| 16 | A | B | -1.2176 | |
| 17 | S | B | -1.5902 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -2.2289 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.9878 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -2.0078 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.5200 | |
| 26 | G | B | -1.2577 | |
| 27 | Y | B | -0.5060 | |
| 28 | T | B | -0.2716 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -1.1955 | |
| 31 | S | B | -0.3539 | |
| 32 | Y | B | -0.0840 | |
| 33 | G | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | 0.0000 | |
| 39 | Q | B | -0.5790 | |
| 40 | R | B | -0.8717 | |
| 41 | T | B | -0.6311 | |
| 42 | G | B | -1.1892 | |
| 43 | Q | B | -1.2545 | |
| 44 | G | B | -0.8570 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.9419 | |
| 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 | -0.8563 | |
| 53 | P | B | 0.0000 | |
| 54 | R | B | -2.5803 | |
| 55 | S | B | -1.6880 | |
| 56 | G | B | -1.8820 | |
| 57 | N | B | -1.5647 | |
| 58 | T | B | -0.1500 | |
| 59 | Y | B | 0.5949 | |
| 60 | Y | B | -0.4156 | |
| 61 | N | B | 0.0000 | |
| 62 | E | B | -3.2531 | |
| 63 | K | B | -3.2035 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9248 | |
| 66 | G | B | -2.0797 | |
| 67 | K | B | -1.9860 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -1.0035 | |
| 70 | L | B | 0.0000 | |
| 71 | T | B | -0.6423 | |
| 72 | A | B | -1.4036 | |
| 73 | D | B | -2.0591 | |
| 74 | K | B | -2.6163 | |
| 75 | S | B | -1.3687 | |
| 76 | S | B | -1.3063 | |
| 77 | S | B | -1.4358 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.6261 | |
| 81 | M | B | 0.0000 | |
| 82 | E | B | -1.7587 | |
| 83 | L | B | 0.0000 | |
| 84 | R | B | -1.8044 | |
| 85 | S | B | -1.2786 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.0285 | |
| 88 | S | B | -1.0685 | |
| 89 | E | B | -1.4957 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | 0.0000 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.0950 | |
| 94 | Y | B | 0.0000 | |
| 95 | F | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | R | B | 0.0000 | |
| 100 | A | B | 0.0000 | |
| 101 | S | B | 0.3946 | |
| 102 | T | B | 1.4602 | |
| 103 | V | B | 2.6270 | |
| 104 | V | B | 2.4152 | |
| 105 | A | B | 1.0084 | |
| 106 | P | B | 0.0000 | |
| 107 | Y | B | 0.9020 | |
| 108 | A | B | 0.0000 | |
| 109 | M | B | 0.0000 | |
| 110 | D | B | -0.2306 | |
| 111 | Y | B | -0.1757 | |
| 112 | W | B | -0.7228 | |
| 113 | G | B | 0.0000 | |
| 114 | Q | B | -1.8612 | |
| 115 | G | B | -0.9953 | |
| 116 | T | B | 0.0000 | |
| 117 | S | B | -0.0983 | |
| 118 | V | B | 0.0000 | |
| 119 | T | B | 0.1102 | |
| 120 | V | B | 0.0000 | |
| 121 | V | B | -0.5644 | |
| 122 | A | B | -0.8012 | |
| 123 | A | B | -0.5578 | |
| 124 | P | B | 0.0000 | |
| 125 | S | B | -0.0097 | |
| 126 | V | B | 0.4334 | |
| 127 | F | B | 1.3023 | |
| 128 | I | B | 1.2847 | |
| 129 | F | B | 1.5671 | |
| 130 | P | B | 0.1365 | |
| 131 | P | B | -0.5313 | |
| 132 | S | B | -1.6969 | |
| 133 | D | B | -3.2357 | |
| 134 | E | B | -3.4684 | |
| 135 | Q | B | -2.5469 | |
| 136 | L | B | -2.5683 | |
| 137 | K | B | -3.0588 | |
| 138 | S | B | -1.9514 | |
| 139 | G | B | -1.4976 | |
| 140 | T | B | -1.2002 | |
| 141 | A | B | 0.0000 | |
| 142 | S | B | 0.0647 | |
| 143 | V | B | 0.0000 | |
| 144 | V | B | 0.7320 | |
| 145 | C | B | 0.0000 | |
| 146 | L | B | 0.5406 | |
| 147 | L | B | 0.0000 | |
| 148 | N | B | -0.5340 | |
| 149 | N | B | -1.1294 | |
| 150 | F | B | 0.0000 | |
| 151 | Y | B | -1.2025 | |
| 152 | P | B | -1.5060 | |
| 153 | R | B | -2.8341 | |
| 154 | E | B | -2.9920 | |
| 155 | A | B | -2.1831 | |
| 156 | K | B | -2.2250 | |
| 157 | V | B | -0.8920 | |
| 158 | Q | B | -0.4563 | |
| 159 | W | B | 0.0000 | |
| 160 | K | B | -0.5942 | |
| 161 | V | B | 0.0000 | |
| 162 | D | B | -1.8266 | |
| 163 | N | B | -1.3694 | |
| 164 | A | B | -0.3495 | |
| 165 | L | B | 0.5062 | |
| 166 | Q | B | -0.3912 | |
| 167 | S | B | -0.8478 | |
| 168 | G | B | -1.4950 | |
| 169 | N | B | -1.7976 | |
| 170 | S | B | -1.8086 | |
| 171 | Q | B | -2.4970 | |
| 172 | E | B | -2.2615 | |
| 173 | S | B | -1.2086 | |
| 174 | V | B | -0.7179 | |
| 175 | T | B | -1.0942 | |
| 176 | E | B | -2.1975 | |
| 177 | Q | B | -2.0972 | |
| 178 | D | B | -2.1620 | |
| 179 | S | B | -2.0354 | |
| 180 | K | B | -2.4227 | |
| 181 | D | B | -1.9792 | |
| 182 | S | B | 0.0000 | |
| 183 | T | B | 0.0000 | |
| 184 | Y | B | 0.0000 | |
| 185 | S | B | -0.8562 | |
| 186 | L | B | 0.0000 | |
| 187 | S | B | -0.4601 | |
| 188 | S | B | 0.0000 | |
| 189 | T | B | -0.7676 | |
| 190 | L | B | 0.0000 | |
| 191 | T | B | -0.7263 | |
| 192 | L | B | -0.8428 | |
| 193 | S | B | -1.0694 | |
| 194 | K | B | -2.1201 | |
| 195 | A | B | -1.8655 | |
| 196 | D | B | -2.5815 | |
| 197 | Y | B | 0.0000 | |
| 198 | E | B | -3.4556 | |
| 199 | K | B | -3.6124 | |
| 200 | H | B | -2.9344 | |
| 201 | K | B | -2.8588 | |
| 202 | V | B | -1.2003 | |
| 203 | Y | B | 0.0000 | |
| 204 | A | B | 0.0000 | |
| 205 | C | B | 0.0000 | |
| 206 | E | B | -0.5717 | |
| 207 | V | B | 0.0000 | |
| 208 | T | B | -1.1307 | |
| 209 | H | B | 0.0000 | |
| 210 | Q | B | -2.0050 | |
| 211 | G | B | -0.9377 | |
| 212 | L | B | -0.3528 | |
| 213 | S | B | -0.4530 | |
| 214 | S | B | -0.4357 | |
| 215 | P | B | -0.5119 | |
| 216 | V | B | 0.0239 | |
| 217 | T | B | -0.2755 | |
| 218 | K | B | -0.2678 | |
| 219 | S | B | -0.2370 | |
| 220 | F | B | 0.0000 | |
| 221 | N | B | -1.5534 | |
| 222 | R | B | -2.1785 | |
| 223 | G | B | -1.8290 | |
| 224 | E | B | -2.0968 | |
| 225 | C | B | -0.3547 |
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 | -0.7731 | 3.3731 | View | CSV | PDB |
| 4.5 | -0.8184 | 3.3748 | View | CSV | PDB |
| 5.0 | -0.8705 | 3.3798 | View | CSV | PDB |
| 5.5 | -0.9182 | 3.3924 | View | CSV | PDB |
| 6.0 | -0.9477 | 3.4162 | View | CSV | PDB |
| 6.5 | -0.9487 | 3.4457 | View | CSV | PDB |
| 7.0 | -0.9221 | 3.4688 | View | CSV | PDB |
| 7.5 | -0.8783 | 3.4809 | View | CSV | PDB |
| 8.0 | -0.8254 | 3.4856 | View | CSV | PDB |
| 8.5 | -0.7662 | 3.4872 | View | CSV | PDB |
| 9.0 | -0.701 | 3.4876 | 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