| Chain sequence(s) |
A: DIQMTQTPSSLSASLGDRVTINCRASQDIENHLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISNLEQEDIATYFCQQGNTLPATFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: DVQLQESGPGLVKSSQSLSLTCSVTGYSITSGYFWNWIRQFPGNKLEWMGEMTYDGSNNYNPSLKNRISITRDTSKNQFFLKLNSVTAEDTATYYCARDGHLPFDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 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] (00:00:01)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:01)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:01)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:01)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:02)
[INFO] FoldX: Starting FoldX energy minimization (00:00:02)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:28)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/8ea6dbfb340aa7/tmp/folded.pdb (00:04:28)
[INFO] Main: Simulation completed successfully. (00:07:18)
|
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 | -2.1882 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.2878 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.4890 | |
| 6 | Q | A | -1.1926 | |
| 7 | T | A | -0.8387 | |
| 8 | P | A | -0.5619 | |
| 9 | S | A | -0.6807 | |
| 10 | S | A | -0.5680 | |
| 11 | L | A | -0.3670 | |
| 12 | S | A | -0.6370 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.2977 | |
| 15 | L | A | -0.8025 | |
| 16 | G | A | -1.5134 | |
| 17 | D | A | -2.1885 | |
| 18 | R | A | -2.7009 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6475 | |
| 21 | I | A | 0.0000 | |
| 22 | N | A | -1.5436 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -3.1642 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.3338 | |
| 27 | Q | A | -3.0456 | |
| 28 | D | A | -3.4478 | |
| 29 | I | A | 0.0000 | |
| 30 | E | A | -2.8841 | |
| 31 | N | A | -2.0092 | |
| 32 | H | A | -1.2518 | |
| 33 | L | A | 0.0000 | |
| 34 | N | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | 0.0000 | |
| 38 | Q | A | -0.8912 | |
| 39 | K | A | -1.4701 | |
| 40 | P | A | -1.6425 | |
| 41 | D | A | -2.3101 | |
| 42 | G | A | -1.4949 | |
| 43 | T | A | -1.2305 | |
| 44 | V | A | -0.9205 | |
| 45 | K | A | -1.0815 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | -0.3036 | |
| 50 | Y | A | -0.4245 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.0566 | |
| 53 | R | A | -1.5603 | |
| 54 | L | A | -0.5277 | |
| 55 | H | A | -0.7251 | |
| 56 | S | A | -0.5851 | |
| 57 | G | A | -0.4788 | |
| 58 | V | A | -0.2984 | |
| 59 | P | A | -0.3258 | |
| 60 | S | A | -0.5292 | |
| 61 | R | A | -1.1138 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.6271 | |
| 64 | G | A | -0.6310 | |
| 65 | S | A | -0.9660 | |
| 66 | G | A | -1.2440 | |
| 67 | S | A | -1.7646 | |
| 68 | G | A | -2.4062 | |
| 69 | T | A | -2.6420 | |
| 70 | D | A | -2.6323 | |
| 71 | F | A | 0.0000 | |
| 72 | S | A | -1.0876 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.8604 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.9765 | |
| 77 | N | A | -2.4832 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -1.8885 | |
| 80 | Q | A | -2.1284 | |
| 81 | E | A | -2.6401 | |
| 82 | D | A | 0.0000 | |
| 83 | I | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | 0.0000 | |
| 86 | Y | A | 0.0000 | |
| 87 | F | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | G | A | -0.5596 | |
| 92 | N | A | -1.1236 | |
| 93 | T | A | -0.3719 | |
| 94 | L | A | 0.1775 | |
| 95 | P | A | -0.2181 | |
| 96 | A | A | 0.0000 | |
| 97 | T | A | -0.6431 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.4427 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.9594 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.1597 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.6183 | |
| 108 | R | A | -1.2083 | |
| 109 | T | A | -0.2436 | |
| 110 | V | A | 0.2076 | |
| 111 | A | A | -0.0981 | |
| 112 | A | A | -0.1066 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.2224 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.5422 | |
| 120 | P | A | -0.7679 | |
| 121 | S | A | -1.7364 | |
| 122 | D | A | -2.8454 | |
| 123 | E | A | -2.8035 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.1596 | |
| 126 | K | A | -2.7313 | |
| 127 | S | A | -1.6728 | |
| 128 | G | A | -1.3026 | |
| 129 | T | A | -1.0118 | |
| 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 | -0.9604 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.8626 | |
| 142 | R | A | -3.0133 | |
| 143 | E | A | -3.1702 | |
| 144 | A | A | -2.1227 | |
| 145 | K | A | -2.0070 | |
| 146 | V | A | -0.9136 | |
| 147 | Q | A | -0.5819 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.5417 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -1.9644 | |
| 152 | N | A | -1.5302 | |
| 153 | A | A | -0.2482 | |
| 154 | L | A | 0.7385 | |
| 155 | Q | A | -0.2983 | |
| 156 | S | A | -0.6479 | |
| 157 | G | A | -1.2725 | |
| 158 | N | A | -1.5643 | |
| 159 | S | A | -1.5390 | |
| 160 | Q | A | -1.6133 | |
| 161 | E | A | -2.0046 | |
| 162 | S | A | -1.0389 | |
| 163 | V | A | -0.8096 | |
| 164 | T | A | -0.9291 | |
| 165 | E | A | -1.8283 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -1.9599 | |
| 168 | S | A | -2.1455 | |
| 169 | K | A | -2.5650 | |
| 170 | D | A | -1.7743 | |
| 171 | S | A | 0.0000 | |
| 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 | -0.8242 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.6983 | |
| 181 | L | A | -0.9675 | |
| 182 | S | A | -1.2083 | |
| 183 | K | A | -2.2069 | |
| 184 | A | A | -2.1415 | |
| 185 | D | A | -3.0795 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.8886 | |
| 188 | K | A | -3.8992 | |
| 189 | H | A | -3.2084 | |
| 190 | K | A | -3.3906 | |
| 191 | V | A | -1.5369 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.8077 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.0795 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.7012 | |
| 200 | G | A | -0.4037 | |
| 201 | L | A | -0.2045 | |
| 202 | S | A | -0.4420 | |
| 203 | S | A | -0.4450 | |
| 204 | P | A | -0.5496 | |
| 205 | V | A | -0.0583 | |
| 206 | T | A | -0.4289 | |
| 207 | K | A | -0.7127 | |
| 208 | S | A | -0.6181 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -1.9494 | |
| 211 | R | A | -2.5591 | |
| 212 | G | A | -2.1052 | |
| 213 | E | A | -2.4399 | |
| 214 | C | A | -1.5033 | |
| 1 | D | B | -1.9053 | |
| 2 | V | B | -1.0771 | |
| 3 | Q | B | -1.4413 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -1.1880 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.6587 | |
| 8 | G | B | -0.6706 | |
| 9 | P | B | -0.6225 | |
| 10 | G | B | -0.6021 | |
| 11 | L | B | -0.4491 | |
| 12 | V | B | 0.0000 | |
| 13 | K | B | -2.2075 | |
| 14 | S | B | -1.7061 | |
| 15 | S | B | -1.3947 | |
| 16 | Q | B | -1.8501 | |
| 17 | S | B | -1.4524 | |
| 18 | L | B | 0.0000 | |
| 19 | S | B | -0.8077 | |
| 20 | L | B | 0.0000 | |
| 21 | T | B | -0.4540 | |
| 22 | C | B | 0.0000 | |
| 23 | S | B | -0.8874 | |
| 24 | V | B | 0.0000 | |
| 25 | T | B | -0.9963 | |
| 26 | G | B | -0.8909 | |
| 27 | Y | B | -0.0702 | |
| 28 | S | B | -0.1365 | |
| 29 | I | B | 0.0000 | |
| 30 | T | B | -0.4160 | |
| 31 | S | B | -0.2240 | |
| 32 | G | B | -0.3470 | |
| 33 | Y | B | -0.0068 | |
| 34 | F | B | -0.1296 | |
| 35 | W | B | 0.0000 | |
| 36 | N | B | 0.0000 | |
| 37 | W | B | 0.0000 | |
| 38 | I | B | 0.0000 | |
| 39 | R | B | 0.0000 | |
| 40 | Q | B | 0.0000 | |
| 41 | F | B | -1.0133 | |
| 42 | P | B | -1.0986 | |
| 43 | G | B | -1.4046 | |
| 44 | N | B | -1.8853 | |
| 45 | K | B | -2.2682 | |
| 46 | L | B | -1.0839 | |
| 47 | E | B | -0.6264 | |
| 48 | W | B | 0.0000 | |
| 49 | M | B | 0.0000 | |
| 50 | G | B | 0.0000 | |
| 51 | E | B | 0.0000 | |
| 52 | M | B | 0.0000 | |
| 53 | T | B | -0.5150 | |
| 54 | Y | B | -0.4196 | |
| 55 | D | B | -1.6665 | |
| 56 | G | B | -1.1135 | |
| 57 | S | B | -0.9677 | |
| 58 | N | B | -0.9514 | |
| 59 | N | B | -0.9420 | |
| 60 | Y | B | -0.8216 | |
| 61 | N | B | 0.0000 | |
| 62 | P | B | -1.2906 | |
| 63 | S | B | -1.1864 | |
| 64 | L | B | 0.0000 | |
| 65 | K | B | -2.5749 | |
| 66 | N | B | -2.3929 | |
| 67 | R | B | -1.9028 | |
| 68 | I | B | 0.0000 | |
| 69 | S | B | -1.0992 | |
| 70 | I | B | 0.0000 | |
| 71 | T | B | -0.6011 | |
| 72 | R | B | -0.9921 | |
| 73 | D | B | -1.3370 | |
| 74 | T | B | -1.1629 | |
| 75 | S | B | -1.3622 | |
| 76 | K | B | -2.2195 | |
| 77 | N | B | -1.4614 | |
| 78 | Q | B | -1.2468 | |
| 79 | F | B | 0.0000 | |
| 80 | F | B | -0.2319 | |
| 81 | L | B | 0.0000 | |
| 82 | K | B | -1.1632 | |
| 83 | L | B | 0.0000 | |
| 84 | N | B | -1.4468 | |
| 85 | S | B | -1.2940 | |
| 86 | V | B | 0.0000 | |
| 87 | T | B | -1.2877 | |
| 88 | A | B | -1.1541 | |
| 89 | E | B | -1.8011 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.5267 | |
| 92 | A | B | 0.0000 | |
| 93 | T | B | -0.2036 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | D | B | 0.0000 | |
| 100 | G | B | -0.5925 | |
| 101 | H | B | -1.0103 | |
| 102 | L | B | 0.0000 | |
| 103 | P | B | -0.2740 | |
| 104 | F | B | 0.0000 | |
| 105 | D | B | -0.3624 | |
| 106 | Y | B | -0.4234 | |
| 107 | W | B | 0.0000 | |
| 108 | G | B | 0.0000 | |
| 109 | Q | B | -1.6707 | |
| 110 | G | B | 0.0000 | |
| 111 | T | B | -0.5227 | |
| 112 | T | B | -0.1825 | |
| 113 | L | B | 0.0000 | |
| 114 | T | B | -0.5766 | |
| 115 | V | B | 0.0000 | |
| 116 | S | B | -0.9623 | |
| 117 | S | B | -0.8850 | |
| 118 | A | B | -0.5838 | |
| 119 | S | B | -0.6755 | |
| 120 | T | B | -0.7093 | |
| 121 | K | B | -1.1149 | |
| 122 | G | B | -1.3441 | |
| 123 | P | B | 0.0000 | |
| 124 | S | B | -0.3666 | |
| 125 | V | B | 0.0000 | |
| 126 | F | B | 0.0000 | |
| 127 | P | B | -1.0699 | |
| 128 | L | B | 0.0000 | |
| 129 | A | B | -1.3503 | |
| 130 | P | B | 0.0000 | |
| 131 | S | B | -1.1870 | |
| 132 | S | B | -0.8886 | |
| 133 | K | B | -1.0135 | |
| 134 | S | B | 0.0000 | |
| 135 | T | B | -0.6679 | |
| 136 | S | B | -0.7060 | |
| 137 | G | B | -0.8091 | |
| 138 | G | B | -0.8792 | |
| 139 | T | B | -0.6112 | |
| 140 | A | B | 0.0000 | |
| 141 | A | B | 0.0000 | |
| 142 | L | B | 0.0000 | |
| 143 | G | B | 0.0000 | |
| 144 | C | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | V | B | 0.0000 | |
| 147 | K | B | 0.0000 | |
| 148 | D | B | -0.3381 | |
| 149 | Y | B | 0.0000 | |
| 150 | F | B | 0.0000 | |
| 151 | P | B | 0.0000 | |
| 152 | E | B | -0.3956 | |
| 153 | P | B | -0.7065 | |
| 154 | V | B | -0.8032 | |
| 155 | T | B | -0.7357 | |
| 156 | V | B | -0.4518 | |
| 157 | S | B | -0.4415 | |
| 158 | W | B | 0.0000 | |
| 159 | N | B | -0.7091 | |
| 160 | S | B | -0.6397 | |
| 161 | G | B | -0.6043 | |
| 162 | A | B | -0.2759 | |
| 163 | L | B | -0.0343 | |
| 164 | T | B | -0.1995 | |
| 165 | S | B | -0.2007 | |
| 166 | G | B | -0.2427 | |
| 167 | V | B | 0.1560 | |
| 168 | H | B | -0.2736 | |
| 169 | T | B | 0.0047 | |
| 170 | F | B | 0.0000 | |
| 171 | P | B | -0.2877 | |
| 172 | A | B | 0.2058 | |
| 173 | V | B | 0.4658 | |
| 174 | L | B | 1.2226 | |
| 175 | Q | B | 0.3036 | |
| 176 | S | B | -0.0666 | |
| 177 | S | B | -0.2167 | |
| 178 | G | B | 0.0277 | |
| 179 | L | B | 0.2100 | |
| 180 | Y | B | 0.5057 | |
| 181 | S | B | 0.0000 | |
| 182 | L | B | 0.0000 | |
| 183 | S | B | 0.0000 | |
| 184 | S | B | 0.0000 | |
| 185 | V | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | T | B | -0.1305 | |
| 188 | V | B | 0.0000 | |
| 189 | P | B | -0.5339 | |
| 190 | S | B | -0.5786 | |
| 191 | S | B | -0.6017 | |
| 192 | S | B | -0.6086 | |
| 193 | L | B | -0.8179 | |
| 194 | G | B | -0.9863 | |
| 195 | T | B | -0.7652 | |
| 196 | Q | B | -1.2732 | |
| 197 | T | B | -1.0885 | |
| 198 | Y | B | 0.0000 | |
| 199 | I | B | -0.9745 | |
| 200 | C | B | 0.0000 | |
| 201 | N | B | -1.4057 | |
| 202 | V | B | 0.0000 | |
| 203 | N | B | -2.3556 | |
| 204 | H | B | 0.0000 | |
| 205 | K | B | -2.9026 | |
| 206 | P | B | -1.6559 | |
| 207 | S | B | -1.8551 | |
| 208 | N | B | -2.6523 | |
| 209 | T | B | -2.2001 | |
| 210 | K | B | -2.7841 | |
| 211 | V | B | -1.4856 | |
| 212 | D | B | -2.0872 | |
| 213 | K | B | -1.8365 | |
| 214 | K | B | -2.1444 | |
| 215 | V | B | 0.0000 | |
| 216 | E | B | -2.7880 | |
| 217 | P | B | -2.0057 | |
| 218 | K | B | -2.3092 | |
| 219 | S | B | -1.4293 |
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 | -0.8188 | 1.5104 | View | CSV | PDB |
| 4.5 | -0.8661 | 1.4941 | View | CSV | PDB |
| 5.0 | -0.9203 | 1.4736 | View | CSV | PDB |
| 5.5 | -0.9712 | 1.4511 | View | CSV | PDB |
| 6.0 | -1.0073 | 1.4284 | View | CSV | PDB |
| 6.5 | -1.0199 | 1.4075 | View | CSV | PDB |
| 7.0 | -1.0095 | 1.3899 | View | CSV | PDB |
| 7.5 | -0.9835 | 1.3758 | View | CSV | PDB |
| 8.0 | -0.948 | 1.3644 | View | CSV | PDB |
| 8.5 | -0.9049 | 1.4347 | View | CSV | PDB |
| 9.0 | -0.8545 | 1.5423 | 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