| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRASQSVSYMNWYKQKPGLAPRLLIYDTSNLATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQWSSNPFTFGQGTKLEIKGGGGSGGGGSGGGGSQVQLVQSGAEVQKPGASVKVSCKASGYTFNRYTMHWVRQAPGQGLWMGYINPSRGYYNYAQKFKDRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARYYDDHYCLDYWGQGTTVTVSS
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. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:11:08)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/42fce0f780a4a94/tmp/folded.pdb (00:11:08)
[INFO] Main: Simulation completed successfully. (00:20:45)
|
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 | -1.7140 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.6640 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6125 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.6905 | |
| 8 | P | A | -0.2795 | |
| 9 | A | A | -0.2988 | |
| 10 | T | A | -0.4005 | |
| 11 | L | A | -0.2570 | |
| 12 | S | A | -0.7868 | |
| 13 | L | A | -1.1556 | |
| 14 | S | A | -1.9440 | |
| 15 | P | A | -2.2012 | |
| 16 | G | A | -2.3573 | |
| 17 | E | A | -2.9291 | |
| 18 | R | A | -3.2944 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6804 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.8974 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.3421 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -1.0428 | |
| 27 | Q | A | -1.7365 | |
| 28 | S | A | -1.3572 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -0.7414 | |
| 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 | -0.2253 | |
| 37 | Q | A | 0.0000 | |
| 38 | K | A | -0.3185 | |
| 39 | P | A | -0.0936 | |
| 40 | G | A | -0.1203 | |
| 41 | L | A | 0.5859 | |
| 42 | A | A | 0.0045 | |
| 43 | P | A | 0.0000 | |
| 44 | R | A | -0.4127 | |
| 45 | L | A | 0.0000 | |
| 46 | L | A | 0.0000 | |
| 47 | I | A | 0.0000 | |
| 48 | Y | A | -0.5432 | |
| 49 | D | A | -0.8999 | |
| 50 | T | A | -0.6377 | |
| 51 | S | A | -0.8110 | |
| 52 | N | A | -1.0364 | |
| 53 | L | A | -0.3961 | |
| 54 | A | A | 0.0000 | |
| 55 | T | A | -0.2956 | |
| 56 | G | A | -0.8533 | |
| 57 | I | A | -0.5265 | |
| 58 | P | A | -0.9612 | |
| 59 | D | A | -1.8966 | |
| 60 | R | A | -1.9514 | |
| 61 | F | A | 0.0000 | |
| 62 | S | A | -0.8118 | |
| 63 | G | A | -0.5329 | |
| 64 | S | A | -0.8516 | |
| 65 | G | A | -1.1088 | |
| 66 | S | A | -1.0281 | |
| 67 | G | A | -1.1989 | |
| 68 | T | A | -1.7628 | |
| 69 | D | A | -2.1923 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.8129 | |
| 72 | L | A | 0.0000 | |
| 73 | T | A | -0.8319 | |
| 74 | I | A | 0.0000 | |
| 75 | S | A | -2.4459 | |
| 76 | R | A | -3.3892 | |
| 77 | L | A | 0.0000 | |
| 78 | E | A | -2.4792 | |
| 79 | P | A | -1.9578 | |
| 80 | E | A | -1.9256 | |
| 81 | D | A | 0.0000 | |
| 82 | F | A | -0.7192 | |
| 83 | A | A | 0.0000 | |
| 84 | V | A | -0.2196 | |
| 85 | Y | A | 0.0000 | |
| 86 | Y | A | -0.1440 | |
| 87 | C | A | 0.0000 | |
| 88 | Q | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | W | A | 0.0000 | |
| 91 | S | A | -0.5630 | |
| 92 | S | A | -0.9935 | |
| 93 | N | A | -1.2583 | |
| 94 | P | A | -1.1967 | |
| 95 | F | A | 0.0000 | |
| 96 | T | A | 0.0000 | |
| 97 | F | A | 0.2693 | |
| 98 | G | A | 0.0000 | |
| 99 | Q | A | -0.9177 | |
| 100 | G | A | 0.0000 | |
| 101 | T | A | 0.0000 | |
| 102 | K | A | -0.7888 | |
| 103 | L | A | 0.0000 | |
| 104 | E | A | -1.3189 | |
| 105 | I | A | -1.7626 | |
| 106 | K | A | -2.2670 | |
| 107 | G | A | -1.7964 | |
| 108 | G | A | -1.9732 | |
| 109 | G | A | -1.3918 | |
| 110 | G | A | -1.3117 | |
| 111 | S | A | -1.0811 | |
| 112 | G | A | -1.4027 | |
| 113 | G | A | -1.2115 | |
| 114 | G | A | -1.2672 | |
| 115 | G | A | -1.2534 | |
| 116 | S | A | -1.0283 | |
| 117 | G | A | -1.2551 | |
| 118 | G | A | -1.4446 | |
| 119 | G | A | -1.3896 | |
| 120 | G | A | -1.3487 | |
| 121 | S | A | -1.3293 | |
| 122 | Q | A | -1.8334 | |
| 123 | V | A | 0.0000 | |
| 124 | Q | A | -1.4385 | |
| 125 | L | A | 0.0000 | |
| 126 | V | A | 0.3913 | |
| 127 | Q | A | 0.0000 | |
| 128 | S | A | -0.5451 | |
| 129 | G | A | -0.5969 | |
| 130 | A | A | -0.0613 | |
| 131 | E | A | -0.1385 | |
| 132 | V | A | 0.9241 | |
| 133 | Q | A | -0.7844 | |
| 134 | K | A | -2.0441 | |
| 135 | P | A | -2.0872 | |
| 136 | G | A | -1.3991 | |
| 137 | A | A | -1.1365 | |
| 138 | S | A | -1.2936 | |
| 139 | V | A | 0.0000 | |
| 140 | K | A | -1.9119 | |
| 141 | V | A | 0.0000 | |
| 142 | S | A | -0.5895 | |
| 143 | C | A | 0.0000 | |
| 144 | K | A | -0.9326 | |
| 145 | A | A | 0.0000 | |
| 146 | S | A | -0.7806 | |
| 147 | G | A | -0.9053 | |
| 148 | Y | A | -0.6490 | |
| 149 | T | A | -0.6651 | |
| 150 | F | A | 0.0000 | |
| 151 | N | A | -1.6991 | |
| 152 | R | A | -2.4680 | |
| 153 | Y | A | -0.9399 | |
| 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 | -0.3179 | |
| 161 | A | A | -0.7158 | |
| 162 | P | A | -0.6947 | |
| 163 | G | A | -1.2031 | |
| 164 | Q | A | -1.2369 | |
| 165 | G | A | -0.5682 | |
| 166 | L | A | -0.2797 | |
| 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 | -1.2443 | |
| 175 | R | A | -0.7896 | |
| 176 | G | A | -0.0361 | |
| 177 | Y | A | 0.2325 | |
| 178 | Y | A | 1.2340 | |
| 179 | N | A | 0.0493 | |
| 180 | Y | A | -0.9622 | |
| 181 | A | A | -1.7057 | |
| 182 | Q | A | -2.7726 | |
| 183 | K | A | -2.9212 | |
| 184 | F | A | 0.0000 | |
| 185 | K | A | -3.1403 | |
| 186 | D | A | -3.1006 | |
| 187 | R | A | -2.1942 | |
| 188 | V | A | 0.0000 | |
| 189 | T | A | -0.8879 | |
| 190 | M | A | 0.0000 | |
| 191 | T | A | -0.3603 | |
| 192 | R | A | -1.1393 | |
| 193 | D | A | -1.2321 | |
| 194 | T | A | -0.8251 | |
| 195 | S | A | -0.5803 | |
| 196 | T | A | -0.6933 | |
| 197 | S | A | -0.8548 | |
| 198 | T | A | 0.0000 | |
| 199 | V | A | 0.0000 | |
| 200 | Y | A | -0.7850 | |
| 201 | M | A | 0.0000 | |
| 202 | E | A | -1.4947 | |
| 203 | L | A | 0.0000 | |
| 204 | S | A | -1.2782 | |
| 205 | S | A | -1.2521 | |
| 206 | L | A | 0.0000 | |
| 207 | R | A | -2.8951 | |
| 208 | S | A | -2.2822 | |
| 209 | E | A | -2.4964 | |
| 210 | D | A | 0.0000 | |
| 211 | T | A | -0.8631 | |
| 212 | A | A | 0.0000 | |
| 213 | V | A | 0.1597 | |
| 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 | -0.5822 | |
| 221 | D | A | -1.2747 | |
| 222 | D | A | -2.1503 | |
| 223 | H | A | -1.3311 | |
| 224 | Y | A | -0.6613 | |
| 225 | C | A | 0.0000 | |
| 226 | L | A | 0.0000 | |
| 227 | D | A | 0.0000 | |
| 228 | Y | A | -0.1165 | |
| 229 | W | A | -0.0384 | |
| 230 | G | A | 0.0000 | |
| 231 | Q | A | -0.7310 | |
| 232 | G | A | -0.1879 | |
| 233 | T | A | 0.0000 | |
| 234 | T | A | 0.0254 | |
| 235 | V | A | 0.0000 | |
| 236 | T | A | -0.2950 | |
| 237 | V | A | 0.0000 | |
| 238 | S | A | -0.8410 | |
| 239 | S | A | -0.9509 | |
| 1 | M | B | 0.8195 | |
| 2 | Q | B | -0.5805 | |
| 3 | S | B | -0.9498 | |
| 4 | I | B | -1.4215 | |
| 5 | K | B | -2.3762 | |
| 6 | G | B | -1.9565 | |
| 7 | N | B | -1.8311 | |
| 8 | H | B | 0.0000 | |
| 9 | L | B | -1.3435 | |
| 10 | V | B | 0.0000 | |
| 11 | K | B | -0.4616 | |
| 12 | V | B | 0.0000 | |
| 13 | Y | B | 0.8544 | |
| 14 | D | B | 0.0000 | |
| 15 | Y | B | 0.6861 | |
| 16 | Q | B | -1.0748 | |
| 17 | E | B | -2.5787 | |
| 18 | D | B | -2.7001 | |
| 19 | G | B | -1.4388 | |
| 20 | S | B | -1.2307 | |
| 21 | V | B | 0.0000 | |
| 22 | L | B | -0.4064 | |
| 23 | L | B | 0.0000 | |
| 24 | T | B | -1.3926 | |
| 25 | C | B | 0.0000 | |
| 26 | D | B | -2.4982 | |
| 27 | A | B | -2.6908 | |
| 28 | E | B | -3.1030 | |
| 29 | A | B | -2.9314 | |
| 30 | K | B | -3.6907 | |
| 31 | N | B | -2.5069 | |
| 32 | I | B | 0.0000 | |
| 33 | T | B | 0.5173 | |
| 34 | W | B | 0.0000 | |
| 35 | F | B | 0.0000 | |
| 36 | K | B | -1.4489 | |
| 37 | D | B | -1.9894 | |
| 38 | G | B | 0.0000 | |
| 39 | K | B | -1.7304 | |
| 40 | M | B | 0.2487 | |
| 41 | I | B | 0.6767 | |
| 42 | G | B | 1.2543 | |
| 43 | F | B | 1.7242 | |
| 44 | L | B | -1.0852 | |
| 45 | T | B | -2.5919 | |
| 46 | E | B | -4.7917 | |
| 47 | D | B | -4.3641 | |
| 48 | K | B | -4.2837 | |
| 49 | K | B | -4.2780 | |
| 50 | K | B | -2.8578 | |
| 51 | W | B | -1.1151 | |
| 52 | N | B | -1.6637 | |
| 53 | L | B | 0.0000 | |
| 54 | G | B | -1.1292 | |
| 55 | S | B | -1.3440 | |
| 56 | N | B | -1.2588 | |
| 57 | A | B | -1.0615 | |
| 58 | K | B | -2.0621 | |
| 59 | D | B | -1.4383 | |
| 60 | P | B | 0.0000 | |
| 61 | R | B | -1.3205 | |
| 62 | G | B | -0.9340 | |
| 63 | M | B | 0.0000 | |
| 64 | Y | B | 0.0000 | |
| 65 | Q | B | -0.7408 | |
| 66 | C | B | 0.0000 | |
| 67 | K | B | -1.6137 | |
| 68 | G | B | -2.2094 | |
| 69 | S | B | -1.8747 | |
| 70 | Q | B | -2.1549 | |
| 71 | N | B | -2.1897 | |
| 72 | K | B | -1.6673 | |
| 73 | S | B | 0.0000 | |
| 74 | K | B | -1.1547 | |
| 75 | P | B | 0.0000 | |
| 76 | L | B | 0.0000 | |
| 77 | Q | B | 0.0000 | |
| 78 | V | B | 0.0000 | |
| 79 | Y | B | -0.5005 | |
| 80 | Y | B | 0.0000 | |
| 81 | R | B | -0.9278 | |
| 82 | M | B | -1.0021 | |
| 83 | G | B | -1.4026 | |
| 84 | S | B | -1.2802 | |
| 85 | A | B | -1.7061 | |
| 86 | D | B | -3.3273 | |
| 87 | D | B | -3.9881 | |
| 88 | A | B | -3.1540 | |
| 89 | K | B | -3.8695 | |
| 90 | K | B | -4.2668 | |
| 91 | D | B | -4.1227 | |
| 92 | A | B | -3.1004 | |
| 93 | A | B | -3.2222 | |
| 94 | K | B | -4.2591 | |
| 95 | K | B | -4.5086 | |
| 96 | D | B | -4.5967 | |
| 97 | D | B | -4.6090 | |
| 98 | A | B | -3.9346 | |
| 99 | K | B | -4.5422 | |
| 100 | K | B | -4.4406 | |
| 101 | D | B | -4.3670 | |
| 102 | D | B | -4.1580 | |
| 103 | A | B | -3.3550 | |
| 104 | K | B | -3.8502 | |
| 105 | K | B | -3.8908 | |
| 106 | D | B | -3.5235 | |
| 107 | G | B | -2.5547 | |
| 108 | S | B | -2.2932 | |
| 109 | D | B | -3.0200 | |
| 110 | G | B | -2.8925 | |
| 111 | N | B | -3.3996 | |
| 112 | E | B | -3.6480 | |
| 113 | E | B | -3.1364 | |
| 114 | M | B | -1.7632 | |
| 115 | G | B | -1.4454 | |
| 116 | G | B | -1.1827 | |
| 117 | I | B | -0.7533 | |
| 118 | T | B | -0.5344 | |
| 119 | Q | B | -0.8372 | |
| 120 | T | B | -0.7865 | |
| 121 | P | B | -0.8394 | |
| 122 | Y | B | 0.0000 | |
| 123 | K | B | -1.6593 | |
| 124 | V | B | -0.5030 | |
| 125 | S | B | -0.1115 | |
| 126 | I | B | 0.3725 | |
| 127 | S | B | -0.0616 | |
| 128 | G | B | -0.5463 | |
| 129 | T | B | -1.0306 | |
| 130 | T | B | -0.8869 | |
| 131 | V | B | 0.0000 | |
| 132 | I | B | -0.1513 | |
| 133 | L | B | 0.0000 | |
| 134 | T | B | -1.3972 | |
| 135 | C | B | 0.0000 | |
| 136 | P | B | 0.0000 | |
| 137 | Q | B | -1.5772 | |
| 138 | Y | B | -0.9505 | |
| 139 | P | B | -0.9854 | |
| 140 | G | B | -0.8922 | |
| 141 | S | B | -0.7169 | |
| 142 | E | B | 0.0000 | |
| 143 | I | B | 0.0000 | |
| 144 | L | B | -0.6430 | |
| 145 | W | B | 0.0000 | |
| 146 | Q | B | -1.8729 | |
| 147 | H | B | -1.7229 | |
| 148 | N | B | -1.9031 | |
| 149 | D | B | -3.1410 | |
| 150 | K | B | -3.2593 | |
| 151 | N | B | -3.0222 | |
| 152 | I | B | -1.7896 | |
| 153 | G | B | 0.0000 | |
| 154 | G | B | -2.4740 | |
| 155 | D | B | -3.2915 | |
| 156 | E | B | -3.6920 | |
| 157 | D | B | -3.7179 | |
| 158 | D | B | -3.5802 | |
| 159 | K | B | -3.1883 | |
| 160 | N | B | -2.6256 | |
| 161 | I | B | -1.9870 | |
| 162 | G | B | -1.8981 | |
| 163 | S | B | -1.7175 | |
| 164 | D | B | -3.0106 | |
| 165 | E | B | -3.0658 | |
| 166 | D | B | -2.0418 | |
| 167 | H | B | -1.8462 | |
| 168 | L | B | 0.0000 | |
| 169 | S | B | -0.8413 | |
| 170 | L | B | 0.0000 | |
| 171 | K | B | -2.6225 | |
| 172 | E | B | -2.4325 | |
| 173 | F | B | 0.0000 | |
| 174 | S | B | -1.1070 | |
| 175 | E | B | -0.7059 | |
| 176 | L | B | 0.2028 | |
| 177 | E | B | -1.2418 | |
| 178 | Q | B | -1.0002 | |
| 179 | S | B | -0.6964 | |
| 180 | G | B | 0.0000 | |
| 181 | Y | B | 0.0000 | |
| 182 | Y | B | 0.0000 | |
| 183 | V | B | 0.0000 | |
| 184 | C | B | 0.0000 | |
| 185 | Y | B | 0.0000 | |
| 186 | P | B | -0.5318 | |
| 187 | R | B | 0.0000 | |
| 188 | G | B | 0.0000 | |
| 189 | S | B | 0.0000 | |
| 190 | K | B | -1.2652 | |
| 191 | P | B | -1.6648 | |
| 192 | E | B | -2.4324 | |
| 193 | D | B | -2.6880 | |
| 194 | A | B | 0.0000 | |
| 195 | N | B | -1.5517 | |
| 196 | F | B | 0.0000 | |
| 197 | Y | B | 0.0000 | |
| 198 | L | B | 0.0000 | |
| 199 | Y | B | 0.0000 | |
| 200 | L | B | 0.0000 | |
| 201 | R | B | -0.6250 | |
| 202 | A | B | 0.0000 | |
| 203 | R | B | -1.1758 | |
| 204 | V | B | 0.0248 |
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 | -0.9425 | 3.7708 | View | CSV | PDB |
| 4.5 | -1.0237 | 3.773 | View | CSV | PDB |
| 5.0 | -1.1177 | 3.7798 | View | CSV | PDB |
| 5.5 | -1.2091 | 3.7988 | View | CSV | PDB |
| 6.0 | -1.2814 | 3.8432 | View | CSV | PDB |
| 6.5 | -1.3221 | 3.9216 | View | CSV | PDB |
| 7.0 | -1.3307 | 4.0264 | View | CSV | PDB |
| 7.5 | -1.3167 | 4.1441 | View | CSV | PDB |
| 8.0 | -1.2884 | 4.2665 | View | CSV | PDB |
| 8.5 | -1.2471 | 4.3902 | View | CSV | PDB |
| 9.0 | -1.1899 | 4.5133 | 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