| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRASQSVSYMNWYKQKPGLAPRLLIYDTSNLAYGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQGLWMGYINPSRGYTNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
B: MQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMGSADDAKKDAAKKDDAKKDDAKKDGSDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARV 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. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:14:34)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/55554687f7c9c68/tmp/folded.pdb (00:14:34)
[INFO] Main: Simulation completed successfully. (00:25:20)
|
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 | -1.8398 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.8621 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.2303 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.4471 | |
| 8 | P | A | -0.2915 | |
| 9 | A | A | -0.4293 | |
| 10 | T | A | -0.6022 | |
| 11 | L | A | -0.4611 | |
| 12 | S | A | -0.9211 | |
| 13 | L | A | -1.0324 | |
| 14 | S | A | -1.5183 | |
| 15 | P | A | -1.9496 | |
| 16 | G | A | -2.3293 | |
| 17 | E | A | -2.7434 | |
| 18 | R | A | -3.1732 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.5375 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.6879 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -1.4568 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -0.8765 | |
| 27 | Q | A | -1.6672 | |
| 28 | S | A | -1.3398 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.3281 | |
| 31 | Y | A | 0.0000 | |
| 32 | M | A | 0.0000 | |
| 33 | N | A | 0.0000 | |
| 34 | W | A | 0.0000 | |
| 35 | Y | A | 0.0000 | |
| 36 | K | A | -0.3885 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.8826 | |
| 39 | P | A | -0.4743 | |
| 40 | G | A | -0.5049 | |
| 41 | L | A | -0.1786 | |
| 42 | A | A | -0.3316 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.5023 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.2160 | |
| 49 | D | A | -0.7345 | |
| 50 | T | A | -0.5572 | |
| 51 | S | A | -0.6867 | |
| 52 | N | A | -0.6077 | |
| 53 | L | A | 0.0343 | |
| 54 | A | A | 0.0000 | |
| 55 | Y | A | 1.1333 | |
| 56 | G | A | -0.0728 | |
| 57 | I | A | -0.0621 | |
| 58 | P | A | -0.7706 | |
| 59 | D | A | -1.8837 | |
| 60 | R | A | -1.9004 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.7626 | |
| 63 | G | A | -0.4718 | |
| 64 | S | A | -0.8848 | |
| 65 | G | A | -1.1391 | |
| 66 | S | A | -0.8250 | |
| 67 | G | A | -1.0381 | |
| 68 | T | A | -1.7651 | |
| 69 | D | A | -2.4791 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7705 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8059 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.3668 | |
| 76 | R | A | -3.3279 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.6275 | |
| 79 | P | A | -1.7856 | |
| 80 | E | A | -2.6229 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -1.0308 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.5783 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | W | A | 0.0000 | |
| 91 | S | A | -0.6379 | |
| 92 | S | A | -1.2392 | |
| 93 | N | A | -1.8382 | |
| 94 | P | A | -1.4714 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.1882 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -1.0873 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -1.2953 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.3714 | |
| 105 | I | A | -0.8041 | |
| 106 | K | A | -1.8758 | |
| 107 | G | A | -1.5044 | |
| 108 | G | A | -1.3575 | |
| 109 | G | A | -1.1727 | |
| 110 | G | A | -1.2938 | |
| 111 | S | A | -1.0559 | |
| 112 | G | A | -1.4939 | |
| 113 | G | A | -1.5637 | |
| 114 | G | A | -1.5292 | |
| 115 | G | A | -1.6269 | |
| 116 | S | A | -1.2202 | |
| 117 | G | A | -1.4791 | |
| 118 | G | A | -1.2243 | |
| 119 | G | A | -1.1750 | |
| 120 | G | A | -1.4780 | |
| 121 | S | A | -1.2360 | |
| 122 | Q | A | -1.8054 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.5674 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.1732 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5779 | |
| 129 | G | A | -0.5945 | |
| 130 | A | A | -0.0103 | |
| 131 | E | A | -0.0838 | |
| 132 | V | A | 0.9348 | |
| 133 | Q | A | -0.8354 | |
| 134 | K | A | -2.0458 | |
| 135 | P | A | -2.0063 | |
| 136 | G | A | -1.4145 | |
| 137 | A | A | -1.1611 | |
| 138 | S | A | -1.3643 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -2.1272 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.6335 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9123 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.8633 | |
| 147 | G | A | -0.9662 | |
| 148 | Y | A | -0.7047 | |
| 149 | T | A | -0.7728 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -2.1437 | |
| 152 | R | A | -2.5386 | |
| 153 | Y | A | -0.8840 | |
| 154 | T | A | 0.0000 | |
| 155 | M | A | 0.0000 | |
| 156 | H | A | 0.0000 | |
| 157 | W | A | 0.0000 | |
| 158 | V | A | 0.0000 | |
| 159 | R | A | 0.0000 | |
| 160 | Q | A | -0.4735 | |
| 161 | A | A | -0.8614 | |
| 162 | P | A | -0.9121 | |
| 163 | G | A | -1.4732 | |
| 164 | Q | A | -1.6948 | |
| 165 | G | A | -0.7790 | |
| 166 | L | A | -0.3988 | |
| 167 | W | A | 0.0000 | |
| 168 | M | A | 0.0000 | |
| 169 | G | A | 0.0000 | |
| 170 | Y | A | 0.0000 | |
| 171 | I | A | 0.0000 | |
| 172 | N | A | 0.0000 | |
| 173 | P | A | 0.0000 | |
| 174 | S | A | -1.6949 | |
| 175 | R | A | -1.5097 | |
| 176 | G | A | -0.7426 | |
| 177 | Y | A | -0.2759 | |
| 178 | T | A | -0.0520 | |
| 179 | N | A | -0.4947 | |
| 180 | Y | A | -1.3658 | |
| 181 | A | A | -1.8503 | |
| 182 | Q | A | -2.9014 | |
| 183 | K | A | -3.0246 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.5221 | |
| 186 | D | A | -3.2596 | |
| 187 | R | A | -2.2949 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -1.1519 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.5298 | |
| 192 | R | A | -1.1709 | |
| 193 | D | A | -1.1652 | |
| 194 | T | A | -0.8366 | |
| 195 | S | A | -0.5686 | |
| 196 | T | A | -0.6858 | |
| 197 | S | A | -0.8695 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7588 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.6590 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.3021 | |
| 205 | S | A | -1.2155 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.4896 | |
| 208 | S | A | -2.1159 | |
| 209 | E | A | -2.3434 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.7846 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.1332 | |
| 214 | Y | A | 0.0000 | |
| 215 | Y | A | 0.0000 | |
| 216 | C | A | 0.0000 | |
| 217 | A | A | 0.0000 | |
| 218 | R | A | 0.0000 | |
| 219 | Y | A | 0.0000 | |
| 220 | Y | A | -0.5264 | |
| 221 | D | A | -1.1820 | |
| 222 | D | A | -2.0352 | |
| 223 | H | A | -1.0736 | |
| 224 | Y | A | -0.5300 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1934 | |
| 229 | W | A | -0.1784 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.9407 | |
| 232 | G | A | -0.3464 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0450 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2638 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8039 | |
| 239 | S | A | -0.9503 | |
| 1 | M | B | 0.6930 | |
| 2 | Q | B | -0.5479 | |
| 3 | S | B | -0.2903 | |
| 4 | I | B | 0.3103 | |
| 5 | K | B | -1.7416 | |
| 6 | G | B | -1.8733 | |
| 7 | N | B | -2.4342 | |
| 8 | H | B | -1.8202 | |
| 9 | L | B | -1.6703 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.7753 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.9591 | |
| 14 | D | B | 0.4651 | |
| 15 | Y | B | 0.3609 | |
| 16 | Q | B | -1.4322 | |
| 17 | E | B | -2.7618 | |
| 18 | D | B | -2.8071 | |
| 19 | G | B | -1.5975 | |
| 20 | S | B | 0.0000 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.3746 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3831 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.7788 | |
| 27 | A | B | 0.0000 | |
| 28 | E | B | -3.3263 | |
| 29 | A | B | -3.0398 | |
| 30 | K | B | -3.7352 | |
| 31 | N | B | -2.5791 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.0000 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | 0.0000 | |
| 36 | K | B | -1.3291 | |
| 37 | D | B | -1.8142 | |
| 38 | G | B | -1.3220 | |
| 39 | K | B | -1.5328 | |
| 40 | M | B | 0.4250 | |
| 41 | I | B | 0.8199 | |
| 42 | G | B | 1.3110 | |
| 43 | F | B | 1.5576 | |
| 44 | L | B | -1.0415 | |
| 45 | T | B | -2.6334 | |
| 46 | E | B | -4.6410 | |
| 47 | D | B | -4.2996 | |
| 48 | K | B | -4.1667 | |
| 49 | K | B | -4.2050 | |
| 50 | K | B | -2.8926 | |
| 51 | W | B | -0.9583 | |
| 52 | N | B | -1.4967 | |
| 53 | L | B | -0.9016 | |
| 54 | G | B | -1.0961 | |
| 55 | S | B | -1.3860 | |
| 56 | N | B | -1.1457 | |
| 57 | A | B | -1.0648 | |
| 58 | K | B | -2.2269 | |
| 59 | D | B | -1.5834 | |
| 60 | P | B | -1.0268 | |
| 61 | R | B | -1.0849 | |
| 62 | G | B | -0.8066 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | 0.0000 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.9056 | |
| 68 | G | B | -2.6037 | |
| 69 | S | B | -2.0832 | |
| 70 | Q | B | -2.5083 | |
| 71 | N | B | -2.6880 | |
| 72 | K | B | -2.2930 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.5805 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.3658 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | 0.0000 | |
| 82 | M | B | -0.8733 | |
| 83 | G | B | -1.4456 | |
| 84 | S | B | -1.3390 | |
| 85 | A | B | -1.9983 | |
| 86 | D | B | -3.7229 | |
| 87 | D | B | -4.3665 | |
| 88 | A | B | -3.3262 | |
| 89 | K | B | -4.2910 | |
| 90 | K | B | -4.8224 | |
| 91 | D | B | -4.7014 | |
| 92 | A | B | -3.5536 | |
| 93 | A | B | -3.5903 | |
| 94 | K | B | -4.9417 | |
| 95 | K | B | -4.8301 | |
| 96 | D | B | -4.9125 | |
| 97 | D | B | -4.8616 | |
| 98 | A | B | -4.2384 | |
| 99 | K | B | -4.9213 | |
| 100 | K | B | -4.5639 | |
| 101 | D | B | -4.4227 | |
| 102 | D | B | -4.1656 | |
| 103 | A | B | -3.4443 | |
| 104 | K | B | -3.9420 | |
| 105 | K | B | -3.8241 | |
| 106 | D | B | -3.6128 | |
| 107 | G | B | -2.7729 | |
| 108 | S | B | -2.3840 | |
| 109 | D | B | -3.1232 | |
| 110 | G | B | -2.8293 | |
| 111 | N | B | -3.3786 | |
| 112 | E | B | -3.4895 | |
| 113 | E | B | -2.8787 | |
| 114 | M | B | -1.2228 | |
| 115 | G | B | -0.9257 | |
| 116 | G | B | -0.8821 | |
| 117 | I | B | -0.3827 | |
| 118 | T | B | -0.4624 | |
| 119 | Q | B | -0.8564 | |
| 120 | T | B | -0.7755 | |
| 121 | P | B | -0.8603 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.5431 | |
| 124 | V | B | -0.4605 | |
| 125 | S | B | -0.1380 | |
| 126 | I | B | 0.1533 | |
| 127 | S | B | -0.2121 | |
| 128 | G | B | -0.6728 | |
| 129 | T | B | -1.1661 | |
| 130 | T | B | -1.0676 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1798 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | 0.0000 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.4117 | |
| 138 | Y | B | -0.7207 | |
| 139 | P | B | -0.9987 | |
| 140 | G | B | -1.0747 | |
| 141 | S | B | -0.9983 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.7023 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.9049 | |
| 147 | H | B | -1.7961 | |
| 148 | N | B | -2.1908 | |
| 149 | D | B | -3.2737 | |
| 150 | K | B | -3.3525 | |
| 151 | N | B | -2.9112 | |
| 152 | I | B | -1.6904 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.4494 | |
| 155 | D | B | -3.4780 | |
| 156 | E | B | -4.2850 | |
| 157 | D | B | -3.9598 | |
| 158 | D | B | -3.4886 | |
| 159 | K | B | -3.4717 | |
| 160 | N | B | -2.7467 | |
| 161 | I | B | -2.0497 | |
| 162 | G | B | -2.0277 | |
| 163 | S | B | -1.8044 | |
| 164 | D | B | -3.0968 | |
| 165 | E | B | -2.9743 | |
| 166 | D | B | -2.0877 | |
| 167 | H | B | -1.7800 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8908 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.7310 | |
| 172 | E | B | -2.5452 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1173 | |
| 175 | E | B | -0.6462 | |
| 176 | L | B | 0.2379 | |
| 177 | E | B | -1.2287 | |
| 178 | Q | B | -0.9712 | |
| 179 | S | B | -0.6170 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | -0.6467 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.5254 | |
| 187 | R | B | -0.3919 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | -0.7464 | |
| 190 | K | B | 0.0000 | |
| 191 | P | B | 0.0000 | |
| 192 | E | B | -2.1654 | |
| 193 | D | B | -2.3769 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.6854 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | -0.2898 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.4456 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.0658 | |
| 204 | V | B | -0.0695 |
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 | -0.9257 | 3.7472 | View | CSV | PDB |
| 4.5 | -1.0068 | 3.7176 | View | CSV | PDB |
| 5.0 | -1.1019 | 3.6828 | View | CSV | PDB |
| 5.5 | -1.1943 | 3.659 | View | CSV | PDB |
| 6.0 | -1.2657 | 3.6662 | View | CSV | PDB |
| 6.5 | -1.3021 | 3.7156 | View | CSV | PDB |
| 7.0 | -1.3048 | 3.8013 | View | CSV | PDB |
| 7.5 | -1.2853 | 3.9076 | View | CSV | PDB |
| 8.0 | -1.2526 | 4.0224 | View | CSV | PDB |
| 8.5 | -1.2081 | 4.1398 | View | CSV | PDB |
| 9.0 | -1.1492 | 4.2566 | 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