| Chain sequence(s) |
A: QPRPAFSAIRRNPPMGGNVVIFDTVITNQEEPYQNHSGRFVCTVPGYYYFTFQVLSQWEICLSIVSSSRGQVRRSLGFCDTTNKGLFQVVSGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSGFLIFPS
C: KFQSVFTVTRQTHQPPAPNSLIRFNAVLTNPQGDYDTSTGKFTCKVPGLYYFVYHASHTANLCVLLYRSGVKVVTFCGHTSKTNQVNSGGVLLRLQVGEEVWLAVNDYYDMVGIQGSDSVFSGFLLFPD B: TQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCKVPGLYYFTYHASSRGNLCVNLMRGRERAQKVVTFCDYAYNTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMEGANSIFSGFLLFPD input PDB |
| Selected Chain(s) | A,B,C |
| 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] (00:00:09)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:09)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:09)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:09)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:10)
[INFO] FoldX: Starting FoldX energy minimization (00:00:10)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:19)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/83d201f84622a10/tmp/folded.pdb (00:04:19)
[INFO] Main: Simulation completed successfully. (00:07:07)
|
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 |
|---|---|---|---|---|
| 90 | Q | A | -1.3549 | |
| 91 | P | A | -1.0286 | |
| 92 | R | A | -1.2003 | |
| 93 | P | A | 0.0000 | |
| 94 | A | A | 0.0000 | |
| 95 | F | A | 0.0000 | |
| 96 | S | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | I | A | 0.0000 | |
| 99 | R | A | -1.7182 | |
| 100 | R | A | -2.9006 | |
| 101 | N | A | -2.3768 | |
| 102 | P | A | 0.0000 | |
| 103 | P | A | -0.5621 | |
| 104 | M | A | 0.4634 | |
| 105 | G | A | -0.2531 | |
| 106 | G | A | -0.7027 | |
| 107 | N | A | -0.8544 | |
| 108 | V | A | -0.2462 | |
| 109 | V | A | 0.0000 | |
| 110 | I | A | -0.7434 | |
| 111 | F | A | 0.0000 | |
| 112 | D | A | -1.4441 | |
| 113 | T | A | -0.7782 | |
| 114 | V | A | 0.0917 | |
| 115 | I | A | 0.6901 | |
| 116 | T | A | 0.0000 | |
| 117 | N | A | -1.3406 | |
| 118 | Q | A | -1.7161 | |
| 119 | E | A | -2.2552 | |
| 120 | E | A | -2.6391 | |
| 121 | P | A | 0.0000 | |
| 122 | Y | A | 0.0000 | |
| 123 | Q | A | -1.9268 | |
| 124 | N | A | -1.7495 | |
| 125 | H | A | -1.7139 | |
| 126 | S | A | -1.0872 | |
| 127 | G | A | 0.0000 | |
| 128 | R | A | -0.9622 | |
| 129 | F | A | 0.0000 | |
| 130 | V | A | -0.6627 | |
| 131 | C | A | 0.0000 | |
| 132 | T | A | -0.8488 | |
| 133 | V | A | -0.3291 | |
| 134 | P | A | -0.8561 | |
| 135 | G | A | 0.0000 | |
| 136 | Y | A | 0.0000 | |
| 137 | Y | A | 0.0000 | |
| 138 | Y | A | 0.0000 | |
| 139 | F | A | 0.0000 | |
| 140 | T | A | 0.0000 | |
| 141 | F | A | 0.0000 | |
| 142 | Q | A | 0.0000 | |
| 143 | V | A | 0.0000 | |
| 144 | L | A | 0.0000 | |
| 145 | S | A | 0.0000 | |
| 146 | Q | A | -0.7552 | |
| 147 | W | A | -1.0901 | |
| 148 | E | A | -1.5813 | |
| 149 | I | A | 0.0000 | |
| 150 | C | A | 0.0000 | |
| 151 | L | A | 0.0000 | |
| 152 | S | A | -0.6399 | |
| 153 | I | A | 0.0000 | |
| 154 | V | A | 0.0000 | |
| 155 | S | A | 0.0000 | |
| 156 | S | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | R | A | -2.6446 | |
| 159 | G | A | -1.9151 | |
| 160 | Q | A | -1.9960 | |
| 161 | V | A | -0.9428 | |
| 162 | R | A | -1.5259 | |
| 163 | R | A | -2.1168 | |
| 164 | S | A | -0.9872 | |
| 165 | L | A | -0.3738 | |
| 166 | G | A | -0.7226 | |
| 167 | F | A | 0.0000 | |
| 168 | C | A | 0.0000 | |
| 169 | D | A | 0.0000 | |
| 170 | T | A | 0.0000 | |
| 171 | T | A | -1.4188 | |
| 172 | N | A | -2.1041 | |
| 173 | K | A | -2.0997 | |
| 174 | G | A | -1.1622 | |
| 175 | L | A | -0.3151 | |
| 176 | F | A | 0.0000 | |
| 177 | Q | A | 0.0000 | |
| 178 | V | A | 0.1757 | |
| 179 | V | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | G | A | 0.0000 | |
| 182 | G | A | 0.0000 | |
| 183 | M | A | 0.0000 | |
| 184 | V | A | 0.0000 | |
| 185 | L | A | -0.1968 | |
| 186 | Q | A | -1.0293 | |
| 187 | L | A | 0.0000 | |
| 188 | Q | A | -1.5143 | |
| 189 | Q | A | -1.7593 | |
| 190 | G | A | -1.5440 | |
| 191 | D | A | 0.0000 | |
| 192 | Q | A | -1.0374 | |
| 193 | V | A | 0.0000 | |
| 194 | W | A | 0.0000 | |
| 195 | V | A | 0.0000 | |
| 196 | E | A | -0.7983 | |
| 197 | K | A | -1.4201 | |
| 198 | D | A | -1.9084 | |
| 199 | P | A | -1.9141 | |
| 200 | K | A | -2.4810 | |
| 201 | K | A | -1.9418 | |
| 202 | G | A | -1.6612 | |
| 203 | H | A | -1.6135 | |
| 204 | I | A | -0.5720 | |
| 205 | Y | A | -1.0240 | |
| 206 | Q | A | -2.0785 | |
| 207 | G | A | -1.9719 | |
| 208 | S | A | -1.8349 | |
| 209 | E | A | -2.1698 | |
| 210 | A | A | 0.0000 | |
| 211 | D | A | -1.1580 | |
| 212 | S | A | 0.0000 | |
| 213 | V | A | 0.0000 | |
| 214 | F | A | 0.0000 | |
| 215 | S | A | 0.0000 | |
| 216 | G | A | 0.0000 | |
| 217 | F | A | 0.0000 | |
| 218 | L | A | 0.0000 | |
| 219 | I | A | 0.0894 | |
| 220 | F | A | 0.0000 | |
| 221 | P | A | -0.4651 | |
| 222 | S | A | -0.4430 | |
| 92 | T | B | -0.5782 | |
| 93 | Q | B | -1.1815 | |
| 94 | K | B | -1.1242 | |
| 95 | I | B | 0.0000 | |
| 96 | A | B | 0.0000 | |
| 97 | F | B | 0.0000 | |
| 98 | S | B | 0.0000 | |
| 99 | A | B | 0.0000 | |
| 100 | T | B | 0.0000 | |
| 101 | R | B | 0.0000 | |
| 102 | T | B | -0.3656 | |
| 103 | I | B | 0.2099 | |
| 104 | N | B | -0.0986 | |
| 105 | V | B | 1.0039 | |
| 106 | P | B | -0.2707 | |
| 107 | L | B | 0.0000 | |
| 108 | R | B | -3.7557 | |
| 109 | R | B | -4.6531 | |
| 110 | D | B | -3.8345 | |
| 111 | Q | B | -2.9760 | |
| 112 | T | B | -1.5360 | |
| 113 | I | B | 0.0000 | |
| 114 | R | B | -1.4131 | |
| 115 | F | B | 0.0000 | |
| 116 | D | B | -1.1807 | |
| 117 | H | B | -0.7640 | |
| 118 | V | B | 0.2164 | |
| 119 | I | B | 0.4199 | |
| 120 | T | B | 0.0000 | |
| 121 | N | B | -0.8700 | |
| 122 | M | B | -1.2855 | |
| 123 | N | B | -2.0188 | |
| 124 | N | B | -2.0725 | |
| 125 | N | B | 0.0000 | |
| 126 | Y | B | 0.0000 | |
| 127 | E | B | -1.6107 | |
| 128 | P | B | -1.7805 | |
| 129 | R | B | -2.4403 | |
| 130 | S | B | -1.5124 | |
| 131 | G | B | 0.0000 | |
| 132 | K | B | -1.0945 | |
| 133 | F | B | 0.0000 | |
| 134 | T | B | -1.5326 | |
| 135 | C | B | 0.0000 | |
| 136 | K | B | -2.5338 | |
| 137 | V | B | -1.8390 | |
| 138 | P | B | -2.2325 | |
| 139 | G | B | 0.0000 | |
| 140 | L | B | 0.0000 | |
| 141 | Y | B | 0.0000 | |
| 142 | Y | B | 0.0000 | |
| 143 | F | B | 0.0000 | |
| 144 | T | B | 0.0000 | |
| 145 | Y | B | 0.0000 | |
| 146 | H | B | 0.0000 | |
| 147 | A | B | 0.0000 | |
| 148 | S | B | 0.0000 | |
| 149 | S | B | 0.0000 | |
| 150 | R | B | -1.6885 | |
| 151 | G | B | -1.0231 | |
| 152 | N | B | -1.0107 | |
| 153 | L | B | 0.0000 | |
| 154 | C | B | 0.0000 | |
| 155 | V | B | 0.0000 | |
| 156 | N | B | -1.0183 | |
| 157 | L | B | 0.0000 | |
| 158 | M | B | 0.0000 | |
| 159 | R | B | -2.0069 | |
| 160 | G | B | -2.8056 | |
| 161 | R | B | -3.7442 | |
| 162 | E | B | -3.6792 | |
| 163 | R | B | -3.5798 | |
| 164 | A | B | -2.7957 | |
| 165 | Q | B | -2.8682 | |
| 166 | K | B | -2.2356 | |
| 167 | V | B | -0.8787 | |
| 168 | V | B | 0.0000 | |
| 169 | T | B | 0.0000 | |
| 170 | F | B | 0.0000 | |
| 171 | C | B | 0.0000 | |
| 172 | D | B | 0.0000 | |
| 173 | Y | B | -0.0398 | |
| 174 | A | B | 0.0000 | |
| 175 | Y | B | 0.2882 | |
| 176 | N | B | -0.9367 | |
| 177 | T | B | -0.5269 | |
| 178 | F | B | -0.2309 | |
| 179 | Q | B | 0.0000 | |
| 180 | V | B | 0.0000 | |
| 181 | T | B | 0.0000 | |
| 182 | T | B | 0.0000 | |
| 183 | G | B | 0.0000 | |
| 184 | G | B | 0.0000 | |
| 185 | M | B | 0.0000 | |
| 186 | V | B | 0.0000 | |
| 187 | L | B | 0.0000 | |
| 188 | K | B | -1.4621 | |
| 189 | L | B | 0.0000 | |
| 190 | E | B | -3.1695 | |
| 191 | Q | B | -3.0409 | |
| 192 | G | B | -2.4191 | |
| 193 | E | B | 0.0000 | |
| 194 | N | B | -1.9057 | |
| 195 | V | B | 0.0000 | |
| 196 | F | B | 0.0000 | |
| 197 | L | B | 0.0000 | |
| 198 | Q | B | -1.8312 | |
| 199 | A | B | 0.0000 | |
| 200 | T | B | -3.1345 | |
| 201 | D | B | -3.6314 | |
| 202 | K | B | -2.3282 | |
| 203 | N | B | -2.5726 | |
| 204 | S | B | -1.1368 | |
| 205 | L | B | -0.2660 | |
| 206 | L | B | -0.2045 | |
| 207 | G | B | -0.0620 | |
| 208 | M | B | -0.5774 | |
| 209 | E | B | -1.8695 | |
| 210 | G | B | -1.2351 | |
| 211 | A | B | -0.4357 | |
| 212 | N | B | -0.4130 | |
| 213 | S | B | 0.0000 | |
| 214 | I | B | 0.0000 | |
| 215 | F | B | 0.0000 | |
| 216 | S | B | 0.0000 | |
| 217 | G | B | 0.0000 | |
| 218 | F | B | 0.0000 | |
| 219 | L | B | 0.0000 | |
| 220 | L | B | -0.1308 | |
| 221 | F | B | 0.0000 | |
| 222 | P | B | -1.3320 | |
| 223 | D | B | -2.3019 | |
| 89 | K | C | -1.1366 | |
| 90 | F | C | 0.7251 | |
| 91 | Q | C | -0.0488 | |
| 92 | S | C | 0.0000 | |
| 93 | V | C | 0.0000 | |
| 94 | F | C | 0.0000 | |
| 95 | T | C | 0.0000 | |
| 96 | V | C | 0.0000 | |
| 97 | T | C | 0.0000 | |
| 98 | R | C | -1.2838 | |
| 99 | Q | C | -1.6897 | |
| 100 | T | C | -1.5431 | |
| 101 | H | C | -1.8461 | |
| 102 | Q | C | -1.8183 | |
| 103 | P | C | -0.9885 | |
| 104 | P | C | 0.0000 | |
| 105 | A | C | -0.6826 | |
| 106 | P | C | -1.1191 | |
| 107 | N | C | -1.7184 | |
| 108 | S | C | -0.8981 | |
| 109 | L | C | -0.3138 | |
| 110 | I | C | 0.0000 | |
| 111 | R | C | -1.5966 | |
| 112 | F | C | 0.0000 | |
| 113 | N | C | -1.1066 | |
| 114 | A | C | 0.0156 | |
| 115 | V | C | 1.0955 | |
| 116 | L | C | 1.2519 | |
| 117 | T | C | 0.3974 | |
| 118 | N | C | -0.1133 | |
| 119 | P | C | -0.5092 | |
| 120 | Q | C | -0.9123 | |
| 121 | G | C | -1.0508 | |
| 122 | D | C | 0.0000 | |
| 123 | Y | C | 0.0000 | |
| 124 | D | C | -1.4715 | |
| 125 | T | C | -1.0502 | |
| 126 | S | C | -0.9402 | |
| 127 | T | C | -0.8717 | |
| 128 | G | C | 0.0000 | |
| 129 | K | C | -1.2309 | |
| 130 | F | C | 0.0000 | |
| 131 | T | C | -1.1991 | |
| 132 | C | C | 0.0000 | |
| 133 | K | C | -1.5939 | |
| 134 | V | C | 0.0000 | |
| 135 | P | C | -1.0265 | |
| 136 | G | C | 0.0000 | |
| 137 | L | C | 0.0000 | |
| 138 | Y | C | 0.0000 | |
| 139 | Y | C | 0.0000 | |
| 140 | F | C | 0.0000 | |
| 141 | V | C | 0.0000 | |
| 142 | Y | C | 0.0000 | |
| 143 | H | C | 0.0000 | |
| 144 | A | C | 0.0000 | |
| 145 | S | C | 0.0000 | |
| 146 | H | C | 0.0000 | |
| 147 | T | C | -0.7426 | |
| 148 | A | C | -0.6793 | |
| 149 | N | C | -0.7295 | |
| 150 | L | C | 0.0000 | |
| 151 | C | C | 0.0000 | |
| 152 | V | C | 0.0000 | |
| 153 | L | C | 0.0000 | |
| 154 | L | C | 0.0000 | |
| 155 | Y | C | -0.2282 | |
| 156 | R | C | -0.4896 | |
| 157 | S | C | -0.5389 | |
| 158 | G | C | -0.2087 | |
| 159 | V | C | 0.6504 | |
| 160 | K | C | -0.9587 | |
| 161 | V | C | -0.2646 | |
| 162 | V | C | 0.0000 | |
| 163 | T | C | 0.0000 | |
| 164 | F | C | 0.0000 | |
| 165 | C | C | 0.1467 | |
| 166 | G | C | 0.0000 | |
| 167 | H | C | -0.6816 | |
| 168 | T | C | -0.7682 | |
| 169 | S | C | -1.2221 | |
| 170 | K | C | -1.8768 | |
| 171 | T | C | -1.1585 | |
| 172 | N | C | 0.0000 | |
| 173 | Q | C | -0.4269 | |
| 174 | V | C | 0.0000 | |
| 175 | N | C | 0.0000 | |
| 176 | S | C | 0.0000 | |
| 177 | G | C | 0.0000 | |
| 178 | G | C | 0.0000 | |
| 179 | V | C | 0.0000 | |
| 180 | L | C | 0.0000 | |
| 181 | L | C | 0.0000 | |
| 182 | R | C | -1.8960 | |
| 183 | L | C | 0.0000 | |
| 184 | Q | C | -1.4425 | |
| 185 | V | C | 0.2546 | |
| 186 | G | C | -0.6165 | |
| 187 | E | C | -1.1363 | |
| 188 | E | C | -1.2000 | |
| 189 | V | C | 0.0000 | |
| 190 | W | C | -0.5969 | |
| 191 | L | C | 0.0000 | |
| 192 | A | C | 0.0000 | |
| 193 | V | C | 0.0000 | |
| 194 | N | C | -1.3496 | |
| 195 | D | C | -1.9176 | |
| 196 | Y | C | -0.4030 | |
| 197 | Y | C | -0.1418 | |
| 198 | D | C | -0.2799 | |
| 199 | M | C | 0.0000 | |
| 200 | V | C | -0.3467 | |
| 201 | G | C | -0.6854 | |
| 202 | I | C | -0.5596 | |
| 203 | Q | C | -1.2726 | |
| 204 | G | C | -0.9495 | |
| 205 | S | C | 0.0000 | |
| 206 | D | C | -0.7305 | |
| 207 | S | C | 0.0000 | |
| 208 | V | C | 0.0000 | |
| 209 | F | C | 0.0000 | |
| 210 | S | C | 0.0000 | |
| 211 | G | C | 0.0000 | |
| 212 | F | C | 0.0000 | |
| 213 | L | C | 0.0000 | |
| 214 | L | C | 0.1379 | |
| 215 | F | C | -0.5891 | |
| 216 | P | C | -0.7562 | |
| 217 | D | C | -2.1602 |
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 | -0.6562 | 2.1 | View | CSV | PDB |
| 4.5 | -0.6872 | 2.1 | View | CSV | PDB |
| 5.0 | -0.7231 | 2.1 | View | CSV | PDB |
| 5.5 | -0.7566 | 2.1 | View | CSV | PDB |
| 6.0 | -0.7792 | 2.1576 | View | CSV | PDB |
| 6.5 | -0.7867 | 2.3571 | View | CSV | PDB |
| 7.0 | -0.7819 | 2.622 | View | CSV | PDB |
| 7.5 | -0.7703 | 2.9196 | View | CSV | PDB |
| 8.0 | -0.7544 | 3.2296 | View | CSV | PDB |
| 8.5 | -0.7344 | 3.5428 | View | CSV | PDB |
| 9.0 | -0.7095 | 3.8544 | 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