| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCRASQSIWRWLAWYQQKPGKAPKLLIHDASQLFEGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQFDLLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYYMSWVRQAPGKGLEWVSAISLSGGSTYYAASHKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVREVGASTHNYYGMDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT 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] (00:00:13)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:13)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:13)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:13)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:13)
[INFO] FoldX: Starting FoldX energy minimization (00:00:14)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:45)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/13a2bf268e77647/tmp/folded.pdb (00:04:45)
[INFO] Main: Simulation completed successfully. (00:07:49)
|
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 | -1.8950 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.1725 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.3013 | |
| 6 | Q | A | -0.9589 | |
| 7 | S | A | -0.6617 | |
| 8 | P | A | -0.5394 | |
| 9 | S | A | -0.7202 | |
| 10 | S | A | -0.7553 | |
| 11 | L | A | -0.5449 | |
| 12 | S | A | -0.9573 | |
| 13 | A | A | -1.0189 | |
| 14 | S | A | -0.8971 | |
| 15 | V | A | -0.0124 | |
| 16 | G | A | -0.8073 | |
| 17 | D | A | -1.8449 | |
| 18 | R | A | -2.3031 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6388 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.8313 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.5485 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -1.8320 | |
| 27 | Q | A | -1.6466 | |
| 28 | S | A | -0.9078 | |
| 29 | I | A | 0.0000 | |
| 30 | W | A | -0.0975 | |
| 31 | R | A | -1.4911 | |
| 32 | W | A | -0.2310 | |
| 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 | -1.2504 | |
| 39 | K | A | -1.7573 | |
| 40 | P | A | -1.5208 | |
| 41 | G | A | -1.7962 | |
| 42 | K | A | -2.5135 | |
| 43 | A | A | -1.6360 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -1.4440 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | H | A | -0.4410 | |
| 50 | D | A | -0.8940 | |
| 51 | A | A | 0.0000 | |
| 52 | S | A | -0.9446 | |
| 53 | Q | A | -0.9571 | |
| 54 | L | A | -0.3760 | |
| 55 | F | A | -0.9469 | |
| 56 | E | A | -1.9205 | |
| 57 | G | A | -1.2498 | |
| 58 | V | A | 0.0000 | |
| 59 | P | A | -0.5756 | |
| 60 | S | A | -0.3862 | |
| 61 | R | A | -0.7628 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.4104 | |
| 64 | G | A | -0.4854 | |
| 65 | S | A | -1.0525 | |
| 66 | G | A | -1.2743 | |
| 67 | S | A | -1.1438 | |
| 68 | G | A | -0.8643 | |
| 69 | T | A | -1.5588 | |
| 70 | D | A | -2.1338 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.7688 | |
| 73 | F | A | 0.0000 | |
| 74 | T | A | -0.6178 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.3553 | |
| 77 | S | A | -1.2082 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -0.9340 | |
| 80 | P | A | -1.4265 | |
| 81 | E | A | -1.5647 | |
| 82 | D | A | 0.0000 | |
| 83 | I | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -0.7274 | |
| 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 | F | A | 0.0000 | |
| 92 | D | A | 0.1766 | |
| 93 | L | A | 0.8569 | |
| 94 | L | A | 0.9427 | |
| 95 | P | A | 0.2836 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | -0.5041 | |
| 98 | F | A | -0.3477 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.1573 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.2243 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.3206 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.4699 | |
| 108 | R | A | -0.8991 | |
| 109 | T | A | -0.1445 | |
| 110 | V | A | 0.2586 | |
| 111 | A | A | -0.0658 | |
| 112 | A | A | -0.1219 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.2197 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.5375 | |
| 120 | P | A | -0.8483 | |
| 121 | S | A | -1.9115 | |
| 122 | D | A | -3.2339 | |
| 123 | E | A | -3.2144 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.3605 | |
| 126 | K | A | -2.9405 | |
| 127 | S | A | -1.8178 | |
| 128 | G | A | -1.2763 | |
| 129 | T | A | -0.9998 | |
| 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 | -0.8580 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.7593 | |
| 142 | R | A | -3.0038 | |
| 143 | E | A | -3.2247 | |
| 144 | A | A | -2.3521 | |
| 145 | K | A | -2.5190 | |
| 146 | V | A | -1.1903 | |
| 147 | Q | A | -0.8079 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -0.5831 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -1.8237 | |
| 152 | N | A | -1.5031 | |
| 153 | A | A | -0.3129 | |
| 154 | L | A | 0.5066 | |
| 155 | Q | A | -0.4004 | |
| 156 | S | A | -0.7190 | |
| 157 | G | A | -1.2869 | |
| 158 | N | A | -1.6228 | |
| 159 | S | A | -1.4213 | |
| 160 | Q | A | -1.3035 | |
| 161 | E | A | -1.4543 | |
| 162 | S | A | -0.7918 | |
| 163 | V | A | -0.7551 | |
| 164 | T | A | -1.1272 | |
| 165 | E | A | -2.2005 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -1.9382 | |
| 168 | S | A | -2.0706 | |
| 169 | K | A | -2.4354 | |
| 170 | D | A | -1.7226 | |
| 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 | -0.6514 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.6138 | |
| 181 | L | A | -0.7099 | |
| 182 | S | A | -0.8917 | |
| 183 | K | A | -1.8674 | |
| 184 | A | A | -1.6378 | |
| 185 | D | A | -2.1523 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.1355 | |
| 188 | K | A | -3.3495 | |
| 189 | H | A | -2.6868 | |
| 190 | K | A | -2.8638 | |
| 191 | V | A | -1.1694 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.7181 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.2554 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.7601 | |
| 200 | G | A | -0.4321 | |
| 201 | L | A | -0.2325 | |
| 202 | S | A | -0.4485 | |
| 203 | S | A | -0.4072 | |
| 204 | P | A | -0.5231 | |
| 205 | V | A | 0.1120 | |
| 206 | T | A | -0.3371 | |
| 207 | K | A | -0.6656 | |
| 208 | S | A | -0.5727 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -1.5761 | |
| 211 | R | A | -2.1842 | |
| 212 | G | A | -1.8105 | |
| 213 | E | A | -2.0584 | |
| 214 | C | A | -1.2920 | |
| 1 | E | B | -1.6614 | |
| 2 | V | B | -0.3307 | |
| 3 | Q | B | -0.5417 | |
| 4 | L | B | 0.0000 | |
| 5 | L | B | 0.5840 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.3996 | |
| 8 | G | B | -0.7217 | |
| 9 | G | B | -0.5326 | |
| 10 | G | B | -0.4452 | |
| 11 | L | B | -0.1149 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.6867 | |
| 14 | P | B | -1.7799 | |
| 15 | G | B | -1.4797 | |
| 16 | G | B | -1.1731 | |
| 17 | S | B | -1.3421 | |
| 18 | L | B | -1.1616 | |
| 19 | R | B | -2.0792 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.4547 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.2153 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -0.7195 | |
| 26 | G | B | -0.8175 | |
| 27 | F | B | -0.2393 | |
| 28 | T | B | -0.1332 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.3056 | |
| 31 | S | B | 0.0227 | |
| 32 | Y | B | 0.3126 | |
| 33 | Y | B | 0.4053 | |
| 34 | M | B | 0.0000 | |
| 35 | S | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.8571 | |
| 40 | A | B | -1.2412 | |
| 41 | P | B | -0.9989 | |
| 42 | G | B | -1.4485 | |
| 43 | K | B | -2.2669 | |
| 44 | G | B | -1.4115 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.0096 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | S | B | 0.0000 | |
| 50 | A | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | S | B | 0.0719 | |
| 53 | L | B | 0.1938 | |
| 54 | S | B | -0.3898 | |
| 55 | G | B | -0.5464 | |
| 56 | G | B | -0.6157 | |
| 57 | S | B | -0.2209 | |
| 58 | T | B | 0.0840 | |
| 59 | Y | B | 0.4715 | |
| 60 | Y | B | -0.0750 | |
| 61 | A | B | -0.4374 | |
| 62 | A | B | -0.7643 | |
| 63 | S | B | -0.7288 | |
| 64 | H | B | 0.0000 | |
| 65 | K | B | -1.9022 | |
| 66 | G | B | -1.4962 | |
| 67 | R | B | -1.3069 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -0.7977 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.4680 | |
| 72 | R | B | -0.9448 | |
| 73 | D | B | -1.4818 | |
| 74 | N | B | -1.5861 | |
| 75 | S | B | -1.5598 | |
| 76 | K | B | -2.3566 | |
| 77 | N | B | -1.7399 | |
| 78 | T | B | -1.0406 | |
| 79 | L | B | 0.0000 | |
| 80 | Y | B | -0.5429 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.2608 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.5088 | |
| 85 | S | B | -1.2941 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.3111 | |
| 88 | A | B | -1.7108 | |
| 89 | E | B | -2.2125 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.7704 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.0634 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | V | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | E | B | 0.0000 | |
| 100 | V | B | 0.0000 | |
| 101 | G | B | 0.0000 | |
| 102 | A | B | -0.6309 | |
| 103 | S | B | -0.4925 | |
| 104 | T | B | -0.5233 | |
| 105 | H | B | -0.9523 | |
| 106 | N | B | -1.3732 | |
| 107 | Y | B | -0.5584 | |
| 108 | Y | B | -0.1540 | |
| 109 | G | B | 0.0000 | |
| 110 | M | B | 0.0000 | |
| 111 | D | B | -0.4758 | |
| 112 | V | B | -0.1496 | |
| 113 | W | B | 0.0000 | |
| 114 | G | B | 0.0000 | |
| 115 | Q | B | -1.3880 | |
| 116 | G | B | 0.0000 | |
| 117 | T | B | 0.0000 | |
| 118 | M | B | 0.1078 | |
| 119 | V | B | 0.0000 | |
| 120 | T | B | 0.0000 | |
| 121 | V | B | 0.0000 | |
| 122 | S | B | -1.0010 | |
| 123 | S | B | -0.7444 | |
| 124 | A | B | -0.4621 | |
| 125 | S | B | -0.5586 | |
| 126 | T | B | -0.7092 | |
| 127 | K | B | -1.1472 | |
| 128 | G | B | -1.3139 | |
| 129 | P | B | 0.0000 | |
| 130 | S | B | -0.4083 | |
| 131 | V | B | 0.0000 | |
| 132 | F | B | 0.0000 | |
| 133 | P | B | -1.3067 | |
| 134 | L | B | 0.0000 | |
| 135 | A | B | -1.3216 | |
| 136 | P | B | 0.0000 | |
| 137 | S | B | -0.9664 | |
| 138 | S | B | -0.6137 | |
| 139 | K | B | -1.0968 | |
| 140 | S | B | 0.0000 | |
| 141 | T | B | -0.7099 | |
| 142 | S | B | -0.7030 | |
| 143 | G | B | -0.7930 | |
| 144 | G | B | -0.8644 | |
| 145 | T | B | -0.6028 | |
| 146 | A | B | 0.0000 | |
| 147 | A | B | 0.0000 | |
| 148 | L | B | 0.0000 | |
| 149 | G | B | 0.0000 | |
| 150 | C | B | 0.0000 | |
| 151 | L | B | 0.0000 | |
| 152 | V | B | 0.0000 | |
| 153 | K | B | 0.0000 | |
| 154 | D | B | -0.3460 | |
| 155 | Y | B | 0.0000 | |
| 156 | F | B | 0.0000 | |
| 157 | P | B | 0.0000 | |
| 158 | E | B | -0.4304 | |
| 159 | P | B | -0.6488 | |
| 160 | V | B | -0.7106 | |
| 161 | T | B | -0.6600 | |
| 162 | V | B | -0.2252 | |
| 163 | S | B | -0.4073 | |
| 164 | W | B | 0.0000 | |
| 165 | N | B | -0.6922 | |
| 166 | S | B | -0.6269 | |
| 167 | G | B | -0.4698 | |
| 168 | A | B | -0.2182 | |
| 169 | L | B | 0.0316 | |
| 170 | T | B | -0.1622 | |
| 171 | S | B | -0.1769 | |
| 172 | G | B | -0.2090 | |
| 173 | V | B | 0.1653 | |
| 174 | H | B | -0.3023 | |
| 175 | T | B | -0.1430 | |
| 176 | F | B | 0.0000 | |
| 177 | P | B | -0.3145 | |
| 178 | A | B | 0.2696 | |
| 179 | V | B | 0.5619 | |
| 180 | L | B | 1.1872 | |
| 181 | Q | B | 0.3030 | |
| 182 | S | B | -0.0621 | |
| 183 | S | B | -0.2064 | |
| 184 | G | B | 0.0424 | |
| 185 | L | B | 0.1488 | |
| 186 | Y | B | 0.4799 | |
| 187 | S | B | 0.0000 | |
| 188 | L | B | 0.0000 | |
| 189 | S | B | 0.0000 | |
| 190 | S | B | 0.0000 | |
| 191 | V | B | 0.0000 | |
| 192 | V | B | 0.0000 | |
| 193 | T | B | -0.1346 | |
| 194 | V | B | 0.0000 | |
| 195 | P | B | -0.6061 | |
| 196 | S | B | -0.5687 | |
| 197 | S | B | -0.5742 | |
| 198 | S | B | -0.5456 | |
| 199 | L | B | -0.7539 | |
| 200 | G | B | -0.9264 | |
| 201 | T | B | -0.6553 | |
| 202 | Q | B | -1.0898 | |
| 203 | T | B | -1.0117 | |
| 204 | Y | B | 0.0000 | |
| 205 | I | B | -1.1135 | |
| 206 | C | B | 0.0000 | |
| 207 | N | B | -1.4670 | |
| 208 | V | B | 0.0000 | |
| 209 | N | B | -2.2121 | |
| 210 | H | B | 0.0000 | |
| 211 | K | B | -2.6693 | |
| 212 | P | B | -1.4765 | |
| 213 | S | B | -1.7727 | |
| 214 | N | B | -2.5709 | |
| 215 | T | B | -2.0984 | |
| 216 | K | B | -2.7760 | |
| 217 | V | B | -1.5752 | |
| 218 | D | B | -2.4084 | |
| 219 | K | B | -1.9748 | |
| 220 | K | B | -2.2987 | |
| 221 | V | B | 0.0000 | |
| 222 | E | B | -2.8195 | |
| 223 | P | B | -1.8599 | |
| 224 | K | B | -2.5796 | |
| 225 | S | B | -1.9256 | |
| 226 | C | B | -1.8431 | |
| 227 | D | B | -2.8835 | |
| 228 | K | B | -2.8388 | |
| 229 | T | B | -1.9589 | |
| 230 | H | B | -1.8989 | |
| 231 | T | B | -0.8520 |
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 | -0.7558 | 2.0474 | View | CSV | PDB |
| 4.5 | -0.7946 | 1.9719 | View | CSV | PDB |
| 5.0 | -0.8399 | 1.868 | View | CSV | PDB |
| 5.5 | -0.8823 | 1.7622 | View | CSV | PDB |
| 6.0 | -0.9109 | 1.6504 | View | CSV | PDB |
| 6.5 | -0.9165 | 1.5364 | View | CSV | PDB |
| 7.0 | -0.8995 | 1.4219 | View | CSV | PDB |
| 7.5 | -0.8677 | 1.308 | View | CSV | PDB |
| 8.0 | -0.828 | 1.306 | View | CSV | PDB |
| 8.5 | -0.7827 | 1.4626 | View | CSV | PDB |
| 9.0 | -0.7317 | 1.6198 | 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