| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGPGTDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVKLVESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSSISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
B: AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALPDPPAASALP 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 (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:45)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/b56f7d854b69ae0/tmp/folded.pdb (00:04:45)
[INFO] Main: Simulation completed successfully. (00:11:48)
|
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 | E | A | -1.7809 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.6952 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.7104 | |
| 6 | Q | A | -0.6695 | |
| 7 | S | A | -0.7282 | |
| 8 | P | A | -0.3239 | |
| 9 | A | A | -0.3217 | |
| 10 | T | A | -0.4323 | |
| 11 | L | A | -0.4120 | |
| 12 | S | A | -0.7887 | |
| 13 | L | A | -1.1385 | |
| 14 | S | A | -1.7469 | |
| 15 | P | A | -2.0006 | |
| 16 | G | A | -1.8851 | |
| 17 | E | A | -2.4585 | |
| 18 | R | A | -2.7773 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6633 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -1.0799 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.7122 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.3454 | |
| 27 | Q | A | -2.3892 | |
| 28 | N | A | -2.5836 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.1465 | |
| 31 | S | A | -0.9215 | |
| 32 | N | A | -0.9288 | |
| 33 | L | 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 | -1.3983 | |
| 40 | P | A | -0.9238 | |
| 41 | G | A | -1.3568 | |
| 42 | Q | A | -1.9657 | |
| 43 | A | A | -1.4572 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.7492 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | D | A | -1.1519 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.2063 | |
| 53 | N | A | -1.5783 | |
| 54 | R | A | -1.6110 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.8403 | |
| 57 | G | A | -0.7076 | |
| 58 | I | A | -0.6734 | |
| 59 | P | A | -0.4049 | |
| 60 | A | A | -0.4020 | |
| 61 | R | A | -0.9103 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6894 | |
| 64 | G | A | -0.8005 | |
| 65 | S | A | -0.9738 | |
| 66 | G | A | -1.1972 | |
| 67 | P | A | -1.3241 | |
| 68 | G | A | -1.8402 | |
| 69 | T | A | -2.4338 | |
| 70 | D | A | -3.0452 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.9702 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6455 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.5612 | |
| 77 | S | A | -1.8679 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.3185 | |
| 80 | P | A | -2.1477 | |
| 81 | E | A | -2.3858 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.7136 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.1262 | |
| 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 | R | A | 0.0000 | |
| 92 | R | A | -1.1475 | |
| 93 | N | A | -1.3297 | |
| 94 | W | A | -0.9263 | |
| 95 | P | A | -0.9013 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.1745 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7540 | |
| 101 | G | A | -0.6871 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.7946 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.1052 | |
| 106 | I | A | -1.7794 | |
| 107 | K | A | -2.1836 | |
| 108 | G | A | -1.7929 | |
| 109 | G | A | -1.8308 | |
| 110 | G | A | -1.4332 | |
| 111 | G | A | -1.2106 | |
| 112 | S | A | -1.1515 | |
| 113 | G | A | -1.4505 | |
| 114 | G | A | -1.5708 | |
| 115 | G | A | -1.2386 | |
| 116 | G | A | -1.6061 | |
| 117 | S | A | -1.1051 | |
| 118 | G | A | -1.2300 | |
| 119 | G | A | -1.2981 | |
| 120 | G | A | -1.4416 | |
| 121 | G | A | -1.6796 | |
| 122 | S | A | -1.6686 | |
| 123 | E | A | -2.4506 | |
| 124 | V | A | -1.6012 | |
| 125 | K | A | -1.8117 | |
| 126 | L | A | 0.0000 | |
| 127 | V | A | 0.1010 | |
| 128 | E | A | 0.0000 | |
| 129 | S | A | -0.3738 | |
| 130 | G | A | -0.6901 | |
| 131 | G | A | 0.0805 | |
| 132 | G | A | 0.5802 | |
| 133 | L | A | 1.2926 | |
| 134 | V | A | 0.0000 | |
| 135 | Q | A | -1.4228 | |
| 136 | P | A | -1.6151 | |
| 137 | G | A | -1.3905 | |
| 138 | G | A | -0.9592 | |
| 139 | S | A | -1.2108 | |
| 140 | L | A | -0.7374 | |
| 141 | R | A | -1.7475 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.4462 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.3590 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -0.9053 | |
| 148 | G | A | -1.2495 | |
| 149 | F | A | -0.9705 | |
| 150 | T | A | -0.6413 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.5169 | |
| 153 | R | A | -2.0736 | |
| 154 | Y | A | 0.0000 | |
| 155 | A | A | 0.0000 | |
| 156 | M | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | R | A | 0.0000 | |
| 161 | Q | A | -0.6766 | |
| 162 | A | A | -1.0671 | |
| 163 | P | A | -0.8557 | |
| 164 | G | A | -1.4472 | |
| 165 | K | A | -2.2695 | |
| 166 | G | A | -1.3674 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9587 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | S | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.7466 | |
| 177 | G | A | -0.3982 | |
| 178 | A | A | -0.1072 | |
| 179 | T | A | 0.0000 | |
| 180 | T | A | 0.0769 | |
| 181 | Y | A | -0.0946 | |
| 182 | Y | A | -0.7411 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.6287 | |
| 185 | P | A | -1.8330 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.5836 | |
| 188 | G | A | -1.7461 | |
| 189 | R | A | -1.3482 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.7942 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4032 | |
| 194 | R | A | -0.9827 | |
| 195 | D | A | -1.6189 | |
| 196 | N | A | -1.8580 | |
| 197 | S | A | -1.5981 | |
| 198 | K | A | -2.3864 | |
| 199 | N | A | -1.7287 | |
| 200 | T | A | -1.0901 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.4870 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.1892 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.3672 | |
| 207 | S | A | -1.1898 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.3070 | |
| 210 | A | A | -1.7475 | |
| 211 | E | A | -2.2474 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.4497 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.5964 | |
| 216 | Y | A | 0.0000 | |
| 217 | Y | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | K | A | 0.0000 | |
| 221 | D | A | 0.0000 | |
| 222 | Q | A | 0.0000 | |
| 223 | D | A | -1.9764 | |
| 224 | F | A | -1.0054 | |
| 225 | D | A | -1.6545 | |
| 226 | I | A | 0.5939 | |
| 227 | L | A | 0.0000 | |
| 228 | T | A | -0.5538 | |
| 229 | G | A | 0.0000 | |
| 230 | Y | A | 0.0000 | |
| 231 | L | A | 0.0000 | |
| 232 | N | A | 0.0000 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -0.9987 | |
| 236 | P | A | -1.2240 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.4564 | |
| 240 | G | A | -0.3194 | |
| 241 | T | A | 0.3108 | |
| 242 | L | A | 1.3430 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.1978 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.7483 | |
| 247 | S | A | -0.7120 | |
| 1 | A | B | -0.7376 | |
| 2 | Q | B | -1.7024 | |
| 3 | E | B | -2.3435 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.9341 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9809 | |
| 8 | P | B | -0.9158 | |
| 9 | H | B | -0.8184 | |
| 10 | C | B | -0.6311 | |
| 11 | T | B | -0.6472 | |
| 12 | T | B | -0.0942 | |
| 13 | V | B | -0.3158 | |
| 14 | P | B | -0.9470 | |
| 15 | V | B | -0.6317 | |
| 16 | G | B | -0.8797 | |
| 17 | A | B | -0.5846 | |
| 18 | S | B | -0.9950 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.4022 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -1.1076 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7943 | |
| 25 | T | B | -1.8170 | |
| 26 | S | B | -1.7027 | |
| 27 | G | B | -1.2985 | |
| 28 | G | B | -1.4927 | |
| 29 | L | B | -1.8287 | |
| 30 | R | B | -2.5614 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0144 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.7629 | |
| 36 | Q | B | -0.9212 | |
| 37 | L | B | -0.3017 | |
| 38 | G | B | -1.1155 | |
| 39 | P | B | -1.1525 | |
| 40 | Q | B | -1.6942 | |
| 41 | P | B | -1.4459 | |
| 42 | Q | B | -1.6650 | |
| 43 | D | B | -1.4276 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.0725 | |
| 47 | Y | B | -0.5576 | |
| 48 | E | B | -1.6777 | |
| 49 | D | B | -2.5161 | |
| 50 | G | B | -1.4606 | |
| 51 | V | B | -0.8777 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -0.3820 | |
| 55 | T | B | 0.0000 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -2.4229 | |
| 58 | R | B | -2.1394 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -1.5984 | |
| 61 | G | B | -1.5115 | |
| 62 | R | B | -1.5613 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | 0.0000 | |
| 66 | S | B | -0.8157 | |
| 67 | G | B | -1.2198 | |
| 68 | S | B | -1.5513 | |
| 69 | Q | B | -1.9474 | |
| 70 | D | B | -2.2997 | |
| 71 | N | B | -2.1979 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0333 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6789 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.4611 | |
| 78 | R | B | -2.0937 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.8632 | |
| 81 | L | B | 0.3781 | |
| 82 | S | B | -0.0044 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.2517 | |
| 85 | G | B | 0.1740 | |
| 86 | T | B | 0.0944 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.5971 | |
| 93 | T | B | 0.0000 | |
| 94 | E | B | -1.4927 | |
| 95 | V | B | 0.3893 | |
| 96 | N | B | -0.5404 | |
| 97 | V | B | -0.3275 | |
| 98 | Y | B | -0.0443 | |
| 99 | G | B | -0.5323 | |
| 100 | S | B | -0.6766 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.4113 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.7893 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.1709 | |
| 108 | E | B | -2.7208 | |
| 109 | E | B | -3.3817 | |
| 110 | Q | B | -2.7694 | |
| 111 | S | B | -2.2188 | |
| 112 | Q | B | -2.0482 | |
| 113 | G | B | -1.8973 | |
| 114 | W | B | -1.6849 | |
| 115 | H | B | -2.0405 | |
| 116 | R | B | -2.5623 | |
| 117 | C | B | -1.5198 | |
| 118 | S | B | -1.7380 | |
| 119 | D | B | -2.2796 | |
| 120 | A | B | -1.3174 | |
| 121 | P | B | -1.2779 | |
| 122 | P | B | -1.3282 | |
| 123 | R | B | -1.9558 | |
| 124 | A | B | -0.6838 | |
| 125 | S | B | -0.3407 | |
| 126 | A | B | 0.3776 | |
| 127 | L | B | 1.4569 | |
| 128 | P | B | 0.3910 | |
| 129 | A | B | 0.1706 | |
| 130 | P | B | -0.2636 | |
| 131 | P | B | -0.6197 | |
| 132 | T | B | -0.5362 | |
| 133 | G | B | -0.4445 | |
| 134 | S | B | -0.0890 | |
| 135 | A | B | 0.1925 | |
| 136 | L | B | 0.7919 | |
| 137 | P | B | -0.6810 | |
| 138 | D | B | -1.9763 | |
| 139 | P | B | -1.5261 | |
| 140 | Q | B | -1.9446 | |
| 141 | T | B | -1.0259 | |
| 142 | A | B | -0.2009 | |
| 143 | S | B | 0.0177 | |
| 144 | A | B | 0.3506 | |
| 145 | L | B | 0.8925 | |
| 146 | P | B | -0.5044 | |
| 147 | D | B | -1.6829 | |
| 148 | P | B | -1.0422 | |
| 149 | P | B | -0.8986 | |
| 150 | A | B | -0.4563 | |
| 151 | A | B | 0.1310 | |
| 152 | S | B | 0.2302 | |
| 153 | A | B | 0.6678 | |
| 154 | L | B | 1.4016 | |
| 155 | P | B | 0.4781 |
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 | -0.3952 | 3.8724 | View | CSV | PDB |
| 4.5 | -0.4418 | 3.8724 | View | CSV | PDB |
| 5.0 | -0.4982 | 3.8724 | View | CSV | PDB |
| 5.5 | -0.5569 | 3.8724 | View | CSV | PDB |
| 6.0 | -0.6105 | 3.8724 | View | CSV | PDB |
| 6.5 | -0.6529 | 3.8724 | View | CSV | PDB |
| 7.0 | -0.6821 | 3.8724 | View | CSV | PDB |
| 7.5 | -0.7007 | 3.8724 | View | CSV | PDB |
| 8.0 | -0.7118 | 3.8724 | View | CSV | PDB |
| 8.5 | -0.7155 | 3.8724 | View | CSV | PDB |
| 9.0 | -0.7109 | 3.8724 | 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