| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGNTYLEWYLQKPGQPPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSQVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
B: AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALPDPPAASALP 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] (00:00:00)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:00)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:00)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:00)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:01)
[INFO] FoldX: Starting FoldX energy minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:03:06)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/2c09d70e3ea5fc4/tmp/folded.pdb (00:03:06)
[INFO] Main: Simulation completed successfully. (00:04:58)
|
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 | -1.4083 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7533 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2097 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | 0.0586 | |
| 8 | P | A | 0.4415 | |
| 9 | L | A | 1.2663 | |
| 10 | S | A | 0.1713 | |
| 11 | L | A | -0.3244 | |
| 12 | S | A | -1.1130 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.5405 | |
| 15 | P | A | -1.6106 | |
| 16 | G | A | -1.5038 | |
| 17 | Q | A | -1.7407 | |
| 18 | P | A | -1.9288 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.9211 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8370 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.0705 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9685 | |
| 27 | Q | A | -1.4582 | |
| 28 | S | A | -0.7675 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.5999 | |
| 31 | H | A | -0.3309 | |
| 32 | S | A | -0.6575 | |
| 33 | N | A | -1.3936 | |
| 34 | G | A | -0.8719 | |
| 35 | N | A | -0.5227 | |
| 36 | T | A | -0.0096 | |
| 37 | Y | A | 0.0000 | |
| 38 | L | A | 0.0000 | |
| 39 | E | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -1.0134 | |
| 44 | K | A | -1.7738 | |
| 45 | P | A | -1.1401 | |
| 46 | G | A | -1.4798 | |
| 47 | Q | A | -2.1038 | |
| 48 | P | A | -1.3003 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -1.0956 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | 0.1926 | |
| 55 | K | A | -0.0100 | |
| 56 | L | A | -0.0627 | |
| 57 | S | A | 0.0211 | |
| 58 | Y | A | 0.6421 | |
| 59 | R | A | -1.0148 | |
| 60 | A | A | 0.0000 | |
| 61 | S | A | -0.5804 | |
| 62 | G | A | -1.1287 | |
| 63 | V | A | 0.0000 | |
| 64 | P | A | -1.4686 | |
| 65 | D | A | -2.5204 | |
| 66 | R | A | -2.2377 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.3416 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.7670 | |
| 71 | G | A | -1.0749 | |
| 72 | S | A | -0.6847 | |
| 73 | G | A | -0.5885 | |
| 74 | T | A | -1.3602 | |
| 75 | D | A | -1.9833 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1531 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.2455 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3232 | |
| 82 | R | A | -3.0553 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.0327 | |
| 85 | A | A | -1.8580 | |
| 86 | E | A | -2.4436 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -0.9965 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0914 | |
| 91 | Y | A | 0.0000 | |
| 92 | Y | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | G | A | 0.0000 | |
| 97 | S | A | 0.0000 | |
| 98 | Q | A | -1.2671 | |
| 99 | V | A | -0.6277 | |
| 100 | P | A | 0.0000 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | -0.0308 | |
| 103 | F | A | 0.3121 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0187 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4205 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.6424 | |
| 111 | I | A | -1.8353 | |
| 112 | K | A | -2.3983 | |
| 113 | G | A | -1.8057 | |
| 114 | G | A | -1.7017 | |
| 115 | G | A | -1.3473 | |
| 116 | G | A | -1.7061 | |
| 117 | S | A | -1.2969 | |
| 118 | G | A | -1.6625 | |
| 119 | G | A | -1.5803 | |
| 120 | G | A | -1.6794 | |
| 121 | G | A | -1.5300 | |
| 122 | S | A | -1.0980 | |
| 123 | G | A | -1.2798 | |
| 124 | G | A | -1.2384 | |
| 125 | G | A | -1.2362 | |
| 126 | G | A | -1.1009 | |
| 127 | S | A | -0.9271 | |
| 128 | V | A | -0.8522 | |
| 129 | Q | A | -1.3968 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | -0.0373 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.6082 | |
| 134 | G | A | -0.6662 | |
| 135 | A | A | -0.1225 | |
| 136 | E | A | -0.2211 | |
| 137 | V | A | 0.8003 | |
| 138 | K | A | -0.9539 | |
| 139 | K | A | -2.1060 | |
| 140 | P | A | -2.0987 | |
| 141 | G | A | -1.4688 | |
| 142 | A | A | -1.1720 | |
| 143 | S | A | -1.1975 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.5312 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.5945 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -1.1935 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.7890 | |
| 152 | G | A | -0.7893 | |
| 153 | Y | A | -0.2143 | |
| 154 | T | A | -0.0598 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.1487 | |
| 157 | D | A | 0.0000 | |
| 158 | Y | A | 0.1753 | |
| 159 | I | A | 0.0000 | |
| 160 | M | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | W | A | 0.0000 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | 0.0000 | |
| 165 | Q | A | -0.5798 | |
| 166 | A | A | -1.0093 | |
| 167 | P | A | -1.0202 | |
| 168 | G | A | -1.2149 | |
| 169 | Q | A | -1.6841 | |
| 170 | G | A | -0.9595 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5595 | |
| 173 | W | A | 0.0000 | |
| 174 | M | A | 0.0000 | |
| 175 | G | A | 0.0000 | |
| 176 | N | A | 0.0000 | |
| 177 | I | A | 0.0000 | |
| 178 | D | A | 0.0000 | |
| 179 | P | A | 0.0000 | |
| 180 | Y | A | 0.4119 | |
| 181 | Y | A | 0.6155 | |
| 182 | G | A | 0.0155 | |
| 183 | S | A | -0.1380 | |
| 184 | T | A | -0.2514 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.3295 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | 0.0844 | |
| 189 | K | A | -1.3856 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.4354 | |
| 192 | G | A | -1.2488 | |
| 193 | R | A | -1.2336 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.7496 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.5712 | |
| 198 | R | A | -1.0171 | |
| 199 | D | A | -1.2273 | |
| 200 | T | A | -0.6740 | |
| 201 | S | A | -0.5659 | |
| 202 | T | A | -0.7069 | |
| 203 | S | A | -0.8117 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.7155 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.2924 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -0.9986 | |
| 211 | S | A | -1.0767 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.7119 | |
| 214 | S | A | -2.2173 | |
| 215 | E | A | -2.4549 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.7731 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.2137 | |
| 220 | Y | A | 0.0000 | |
| 221 | Y | A | 0.0000 | |
| 222 | C | A | 0.0000 | |
| 223 | A | A | 0.0000 | |
| 224 | R | A | 0.0000 | |
| 225 | D | A | 0.0000 | |
| 226 | G | A | 0.0000 | |
| 227 | N | A | -0.3970 | |
| 228 | Y | A | 0.1227 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.2539 | |
| 232 | Y | A | -0.2866 | |
| 233 | W | A | -0.3736 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.3309 | |
| 236 | G | A | -0.6306 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0120 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3201 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.0415 | |
| 243 | S | A | -0.9852 | |
| 1 | A | B | -0.4689 | |
| 2 | Q | B | -1.4007 | |
| 3 | E | B | -2.3593 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -2.0454 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.4521 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | 0.0000 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.8977 | |
| 15 | V | B | -0.4829 | |
| 16 | G | B | -1.2223 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.7789 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.9257 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8622 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7896 | |
| 25 | T | B | -1.8544 | |
| 26 | S | B | -1.5899 | |
| 27 | G | B | -1.2202 | |
| 28 | G | B | -1.4037 | |
| 29 | L | B | -1.5250 | |
| 30 | R | B | -2.3540 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0808 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.7773 | |
| 36 | Q | B | -0.7641 | |
| 37 | L | B | -0.4863 | |
| 38 | G | B | -1.0955 | |
| 39 | P | B | -1.1996 | |
| 40 | Q | B | -1.5467 | |
| 41 | P | B | -1.2514 | |
| 42 | Q | B | -1.3638 | |
| 43 | D | B | -1.1435 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3949 | |
| 47 | Y | B | 0.1913 | |
| 48 | E | B | -0.6415 | |
| 49 | D | B | -1.2676 | |
| 50 | G | B | -0.0415 | |
| 51 | V | B | 1.5744 | |
| 52 | V | B | 2.0857 | |
| 53 | P | B | 0.8092 | |
| 54 | T | B | -0.0131 | |
| 55 | T | B | -1.3536 | |
| 56 | D | B | -2.1111 | |
| 57 | R | B | -3.0572 | |
| 58 | R | B | -2.3606 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.2073 | |
| 61 | G | B | -2.2749 | |
| 62 | R | B | -2.1314 | |
| 63 | I | B | -1.5896 | |
| 64 | D | B | -1.9526 | |
| 65 | F | B | -0.6626 | |
| 66 | S | B | -0.8993 | |
| 67 | G | B | -1.2209 | |
| 68 | S | B | -1.5011 | |
| 69 | Q | B | -1.8797 | |
| 70 | D | B | -2.4712 | |
| 71 | N | B | -2.2506 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0039 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9060 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7315 | |
| 78 | R | B | -2.2379 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.9497 | |
| 81 | L | B | 0.1704 | |
| 82 | S | B | -0.0486 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0804 | |
| 85 | G | B | -0.1811 | |
| 86 | T | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.5804 | |
| 93 | T | B | -1.2748 | |
| 94 | E | B | -1.9180 | |
| 95 | V | B | -0.4785 | |
| 96 | N | B | -0.2002 | |
| 97 | V | B | -0.4107 | |
| 98 | Y | B | -0.5479 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -1.0592 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.0000 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | 0.0000 | |
| 108 | E | B | -2.7064 | |
| 109 | E | B | -2.9802 | |
| 110 | Q | B | -2.5963 | |
| 111 | S | B | 0.0000 | |
| 112 | Q | B | -2.5571 | |
| 113 | G | B | -1.7692 | |
| 114 | W | B | 0.0000 | |
| 115 | H | B | 0.0000 | |
| 116 | R | B | 0.0000 | |
| 117 | C | B | 0.0000 | |
| 118 | S | B | 0.0000 | |
| 119 | D | B | -0.4260 | |
| 120 | A | B | 0.0000 | |
| 121 | P | B | -0.6789 | |
| 122 | P | B | -1.2140 | |
| 123 | R | B | -2.2981 | |
| 124 | A | B | -0.8674 | |
| 125 | S | B | -0.5370 | |
| 126 | A | B | -0.1816 | |
| 127 | L | B | 0.4365 | |
| 128 | P | B | -0.0677 | |
| 129 | A | B | -0.4150 | |
| 130 | P | B | -0.6116 | |
| 131 | P | B | -0.6249 | |
| 132 | T | B | -0.5374 | |
| 133 | G | B | -0.4408 | |
| 134 | S | B | -0.0792 | |
| 135 | A | B | 0.1827 | |
| 136 | L | B | 0.7904 | |
| 137 | P | B | -0.6734 | |
| 138 | D | B | -1.9730 | |
| 139 | P | B | -1.5239 | |
| 140 | Q | B | -1.9358 | |
| 141 | T | B | -1.0300 | |
| 142 | A | B | -0.2076 | |
| 143 | S | B | 0.0213 | |
| 144 | A | B | 0.3553 | |
| 145 | L | B | 0.9005 | |
| 146 | P | B | -0.4989 | |
| 147 | D | B | -1.6863 | |
| 148 | P | B | -1.0502 | |
| 149 | P | B | -0.8805 | |
| 150 | A | B | -0.4453 | |
| 151 | A | B | 0.1250 | |
| 152 | S | B | 0.2213 | |
| 153 | A | B | 0.6658 | |
| 154 | L | B | 1.4035 | |
| 155 | P | B | 0.4741 |
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 | -0.361 | 3.7533 | View | CSV | PDB |
| 4.5 | -0.3963 | 3.5922 | View | CSV | PDB |
| 5.0 | -0.4399 | 3.3996 | View | CSV | PDB |
| 5.5 | -0.4847 | 3.2602 | View | CSV | PDB |
| 6.0 | -0.524 | 3.2167 | View | CSV | PDB |
| 6.5 | -0.5528 | 3.183 | View | CSV | PDB |
| 7.0 | -0.569 | 3.1634 | View | CSV | PDB |
| 7.5 | -0.5752 | 3.155 | View | CSV | PDB |
| 8.0 | -0.5748 | 3.1519 | View | CSV | PDB |
| 8.5 | -0.569 | 3.1509 | View | CSV | PDB |
| 9.0 | -0.5573 | 3.1506 | 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