| Chain sequence(s) |
C: EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSTWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLVQSGAEVKKSGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIFYPGDSSTRYSPSFQGQVTISADKSVNTAYLQWSSLKASDTAMYYCARRRNWGNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC input PDB |
| Selected Chain(s) | 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] (00:00:01)
[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 (00:06:47)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/9d52025a1028873/tmp/folded.pdb (00:06:47)
[INFO] Main: Simulation completed successfully. (00:10:31)
|
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 | B | -2.0670 | |
| 2 | V | B | -1.1423 | |
| 3 | Q | B | -1.2935 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.2327 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.5286 | |
| 8 | G | B | -0.5626 | |
| 9 | A | B | -0.1678 | |
| 10 | E | B | -0.2989 | |
| 11 | V | B | 0.2673 | |
| 12 | K | B | -1.3214 | |
| 13 | K | B | -2.4173 | |
| 14 | S | B | -2.2425 | |
| 15 | G | B | -2.0440 | |
| 16 | E | B | -2.3031 | |
| 17 | S | B | -1.7999 | |
| 18 | L | B | 0.0000 | |
| 19 | K | B | -1.7971 | |
| 20 | I | B | 0.0000 | |
| 21 | S | B | -0.5893 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -0.8592 | |
| 24 | G | B | 0.0000 | |
| 25 | S | B | -0.8477 | |
| 26 | G | B | -1.1803 | |
| 27 | Y | B | -0.5562 | |
| 28 | S | B | -0.2799 | |
| 29 | F | B | 0.0000 | |
| 30 | T | B | -0.8434 | |
| 31 | S | B | -0.2890 | |
| 32 | Y | B | -0.0075 | |
| 33 | W | B | 0.0475 | |
| 34 | I | B | 0.0000 | |
| 35 | G | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | R | B | -0.5200 | |
| 39 | Q | B | -0.7738 | |
| 40 | M | B | -0.7951 | |
| 41 | P | B | -0.9302 | |
| 42 | G | B | -1.4312 | |
| 43 | K | B | -2.3069 | |
| 44 | G | B | -1.4814 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.8095 | |
| 47 | W | B | 0.0000 | |
| 48 | M | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | I | B | 0.0000 | |
| 51 | F | B | 0.0000 | |
| 52 | Y | B | -0.5355 | |
| 53 | P | B | 0.0000 | |
| 54 | G | B | -1.2376 | |
| 55 | D | B | -1.9439 | |
| 56 | S | B | -1.4694 | |
| 57 | S | B | -1.0437 | |
| 58 | T | B | -1.1018 | |
| 59 | R | B | -1.9831 | |
| 60 | Y | B | -1.3209 | |
| 61 | S | B | 0.0000 | |
| 62 | P | B | -1.2911 | |
| 63 | S | B | -0.8012 | |
| 64 | F | B | 0.0000 | |
| 65 | Q | B | -1.9571 | |
| 66 | G | B | -1.3887 | |
| 67 | Q | B | -1.3623 | |
| 68 | V | B | 0.0000 | |
| 69 | T | B | -0.7873 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.5651 | |
| 72 | A | B | -0.7871 | |
| 73 | D | B | -1.3447 | |
| 74 | K | B | -1.6915 | |
| 75 | S | B | -0.5647 | |
| 76 | V | B | 0.2124 | |
| 77 | N | B | -0.9623 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.6027 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.2785 | |
| 83 | W | B | 0.0000 | |
| 84 | S | B | -1.1562 | |
| 85 | S | B | -1.6757 | |
| 86 | L | B | 0.0000 | |
| 87 | K | B | -2.4066 | |
| 88 | A | B | -1.2707 | |
| 89 | S | B | -0.7030 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.2663 | |
| 92 | A | B | 0.0000 | |
| 93 | M | B | 0.1085 | |
| 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 | R | B | -0.3682 | |
| 100 | R | B | -0.4034 | |
| 101 | N | B | -0.3412 | |
| 102 | W | B | 0.5891 | |
| 103 | G | B | 0.0815 | |
| 104 | N | B | -0.2721 | |
| 105 | A | B | 0.0000 | |
| 106 | F | B | 0.0000 | |
| 107 | D | B | -0.6480 | |
| 108 | I | B | -0.3345 | |
| 109 | W | B | -0.4656 | |
| 110 | G | B | 0.0000 | |
| 111 | Q | B | -1.3049 | |
| 112 | G | B | -0.6497 | |
| 113 | T | B | 0.0000 | |
| 114 | M | B | 0.1188 | |
| 115 | V | B | 0.0000 | |
| 116 | T | B | -0.3036 | |
| 117 | V | B | 0.0000 | |
| 118 | S | B | -0.8804 | |
| 119 | S | B | -0.7750 | |
| 120 | A | B | -0.5518 | |
| 121 | S | B | -0.6274 | |
| 122 | T | B | -0.5730 | |
| 123 | K | B | -1.1413 | |
| 124 | G | B | -1.3247 | |
| 125 | P | B | 0.0000 | |
| 126 | S | B | -0.4093 | |
| 127 | V | B | 0.0000 | |
| 128 | F | B | 0.0000 | |
| 129 | P | B | -1.3978 | |
| 130 | L | B | 0.0000 | |
| 131 | A | B | -1.3103 | |
| 132 | P | B | 0.0000 | |
| 133 | S | B | -0.9838 | |
| 134 | S | B | -0.6709 | |
| 135 | K | B | -1.1895 | |
| 136 | S | B | 0.0000 | |
| 137 | T | B | -0.7476 | |
| 138 | S | B | -0.7252 | |
| 139 | G | B | -0.7981 | |
| 140 | G | B | -0.8662 | |
| 141 | T | B | -0.6067 | |
| 142 | A | B | 0.0000 | |
| 143 | A | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | G | B | 0.0000 | |
| 146 | C | B | 0.0000 | |
| 147 | L | B | 0.0000 | |
| 148 | V | B | 0.0000 | |
| 149 | K | B | 0.0000 | |
| 150 | D | B | -0.3417 | |
| 151 | Y | B | 0.0000 | |
| 152 | F | B | 0.0000 | |
| 153 | P | B | 0.0000 | |
| 154 | E | B | -0.8379 | |
| 155 | P | B | -1.0167 | |
| 156 | V | B | -0.7770 | |
| 157 | T | B | -0.6222 | |
| 158 | V | B | -0.1617 | |
| 159 | S | B | -0.3990 | |
| 160 | W | B | 0.0000 | |
| 161 | N | B | -0.8206 | |
| 162 | S | B | -0.6791 | |
| 163 | G | B | -0.5007 | |
| 164 | A | B | -0.2217 | |
| 165 | L | B | 0.0160 | |
| 166 | T | B | -0.1494 | |
| 167 | S | B | -0.1605 | |
| 168 | G | B | -0.1824 | |
| 169 | V | B | 0.1976 | |
| 170 | H | B | -0.3047 | |
| 171 | T | B | 0.0244 | |
| 172 | F | B | 0.0000 | |
| 173 | P | B | -0.3344 | |
| 174 | A | B | 0.1203 | |
| 175 | V | B | 0.4718 | |
| 176 | L | B | 1.0436 | |
| 177 | Q | B | 0.2621 | |
| 178 | S | B | -0.0620 | |
| 179 | S | B | -0.2041 | |
| 180 | G | B | 0.0276 | |
| 181 | L | B | 0.0402 | |
| 182 | Y | B | 0.2876 | |
| 183 | S | B | 0.0000 | |
| 184 | L | B | 0.0000 | |
| 185 | S | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | V | B | 0.0000 | |
| 188 | V | B | 0.0000 | |
| 189 | T | B | -0.1218 | |
| 190 | V | B | 0.0000 | |
| 191 | P | B | -0.6001 | |
| 192 | S | B | -0.5627 | |
| 193 | S | B | -0.5666 | |
| 194 | S | B | -0.5389 | |
| 195 | L | B | -0.7448 | |
| 196 | G | B | -0.9230 | |
| 197 | T | B | -0.6557 | |
| 198 | Q | B | -1.1156 | |
| 199 | T | B | -1.1260 | |
| 200 | Y | B | 0.0000 | |
| 201 | I | B | -1.5002 | |
| 202 | C | B | 0.0000 | |
| 203 | N | B | -1.5663 | |
| 204 | V | B | 0.0000 | |
| 205 | N | B | -1.8891 | |
| 206 | H | B | 0.0000 | |
| 207 | K | B | -2.7545 | |
| 208 | P | B | -1.6589 | |
| 209 | S | B | -1.8080 | |
| 210 | N | B | -2.5478 | |
| 211 | T | B | -2.0307 | |
| 212 | K | B | -2.6927 | |
| 213 | V | B | -1.6530 | |
| 214 | D | B | -2.6447 | |
| 215 | K | B | -2.3679 | |
| 216 | R | B | -2.7747 | |
| 217 | V | B | 0.0000 | |
| 218 | E | B | -2.9461 | |
| 219 | P | B | -1.8902 | |
| 220 | K | B | -2.2423 | |
| 221 | S | B | -0.8677 | |
| 222 | C | B | 0.0153 | |
| 1 | E | C | -1.5030 | |
| 2 | I | C | -0.2597 | |
| 3 | V | C | 0.7458 | |
| 4 | L | C | 0.0000 | |
| 5 | T | C | -0.7557 | |
| 6 | Q | C | 0.0000 | |
| 7 | S | C | -0.8550 | |
| 8 | P | C | -0.4734 | |
| 9 | G | C | -0.8236 | |
| 10 | T | C | -0.3575 | |
| 11 | L | C | -0.1745 | |
| 12 | S | C | -0.5120 | |
| 13 | L | C | -0.9950 | |
| 14 | S | C | -1.4832 | |
| 15 | P | C | -1.6858 | |
| 16 | G | C | -1.9812 | |
| 17 | E | C | -2.6403 | |
| 18 | R | C | -3.0560 | |
| 19 | A | C | 0.0000 | |
| 20 | T | C | -0.6514 | |
| 21 | L | C | 0.0000 | |
| 22 | S | C | -0.9246 | |
| 23 | C | C | 0.0000 | |
| 24 | R | C | -2.3412 | |
| 25 | A | C | 0.0000 | |
| 26 | S | C | -0.9696 | |
| 27 | Q | C | -1.6789 | |
| 28 | S | C | -1.3894 | |
| 29 | V | C | 0.0000 | |
| 30 | S | C | -0.5203 | |
| 31 | S | C | -0.5230 | |
| 32 | S | C | -0.1013 | |
| 33 | Y | C | 0.1437 | |
| 34 | L | C | 0.0000 | |
| 35 | A | C | 0.0000 | |
| 36 | W | C | 0.0000 | |
| 37 | Y | C | 0.0000 | |
| 38 | Q | C | 0.0000 | |
| 39 | Q | C | 0.0000 | |
| 40 | K | C | -1.5920 | |
| 41 | P | C | -1.4388 | |
| 42 | G | C | -1.4866 | |
| 43 | Q | C | -2.1540 | |
| 44 | A | C | -1.4398 | |
| 45 | P | C | 0.0000 | |
| 46 | R | C | -1.5506 | |
| 47 | L | C | 0.0000 | |
| 48 | L | C | 0.0000 | |
| 49 | I | C | 0.0000 | |
| 50 | Y | C | -0.1621 | |
| 51 | G | C | -0.1709 | |
| 52 | A | C | 0.0000 | |
| 53 | S | C | -0.6935 | |
| 54 | S | C | -0.7443 | |
| 55 | R | C | -1.4975 | |
| 56 | A | C | 0.0000 | |
| 57 | T | C | -0.6044 | |
| 58 | G | C | -0.8908 | |
| 59 | I | C | 0.0000 | |
| 60 | P | C | -1.3158 | |
| 61 | D | C | -2.2068 | |
| 62 | R | C | -1.8626 | |
| 63 | F | C | 0.0000 | |
| 64 | S | C | -0.9285 | |
| 65 | G | C | 0.0000 | |
| 66 | S | C | -0.6860 | |
| 67 | G | C | -1.1285 | |
| 68 | S | C | -1.1281 | |
| 69 | G | C | -1.2594 | |
| 70 | T | C | -1.8058 | |
| 71 | D | C | -2.2441 | |
| 72 | F | C | 0.0000 | |
| 73 | T | C | -0.7899 | |
| 74 | L | C | 0.0000 | |
| 75 | T | C | -0.7599 | |
| 76 | I | C | 0.0000 | |
| 77 | S | C | -2.1764 | |
| 78 | R | C | -2.8930 | |
| 79 | L | C | 0.0000 | |
| 80 | E | C | -2.1290 | |
| 81 | P | C | -1.5636 | |
| 82 | E | C | -2.1682 | |
| 83 | D | C | 0.0000 | |
| 84 | F | C | -0.5127 | |
| 85 | A | C | 0.0000 | |
| 86 | V | C | -0.0904 | |
| 87 | Y | C | 0.0000 | |
| 88 | Y | C | 0.0000 | |
| 89 | C | C | 0.0000 | |
| 90 | Q | C | 0.0000 | |
| 91 | Q | C | 0.0000 | |
| 92 | Y | C | 0.0000 | |
| 93 | G | C | -0.3442 | |
| 94 | S | C | -0.5456 | |
| 95 | S | C | -0.8321 | |
| 96 | T | C | -0.8425 | |
| 97 | W | C | -0.0280 | |
| 98 | T | C | -0.0280 | |
| 99 | F | C | 0.1256 | |
| 100 | G | C | 0.0000 | |
| 101 | Q | C | -1.4144 | |
| 102 | G | C | 0.0000 | |
| 103 | T | C | 0.0000 | |
| 104 | K | C | -0.5276 | |
| 105 | V | C | 0.0000 | |
| 106 | E | C | 0.0000 | |
| 107 | I | C | -0.7164 | |
| 108 | K | C | -1.5215 | |
| 109 | R | C | -1.0738 | |
| 110 | T | C | -0.1663 | |
| 111 | V | C | 0.3472 | |
| 112 | A | C | 0.0098 | |
| 113 | A | C | -0.0569 | |
| 114 | P | C | 0.0000 | |
| 115 | S | C | -0.2234 | |
| 116 | V | C | 0.0000 | |
| 117 | F | C | 0.0000 | |
| 118 | I | C | 0.0000 | |
| 119 | F | C | 0.0000 | |
| 120 | P | C | -0.5649 | |
| 121 | P | C | 0.0000 | |
| 122 | S | C | -1.8707 | |
| 123 | D | C | -3.1579 | |
| 124 | E | C | -3.0759 | |
| 125 | Q | C | 0.0000 | |
| 126 | L | C | -2.2926 | |
| 127 | K | C | -2.8806 | |
| 128 | S | C | -1.7863 | |
| 129 | G | C | -1.2715 | |
| 130 | T | C | -0.9933 | |
| 131 | A | C | 0.0000 | |
| 132 | S | C | 0.0000 | |
| 133 | V | C | 0.0000 | |
| 134 | V | C | 0.0000 | |
| 135 | C | C | 0.0000 | |
| 136 | L | C | 0.0000 | |
| 137 | L | C | 0.0000 | |
| 138 | N | C | 0.0000 | |
| 139 | N | C | -0.8545 | |
| 140 | F | C | 0.0000 | |
| 141 | Y | C | 0.0000 | |
| 142 | P | C | -1.5334 | |
| 143 | R | C | -2.5345 | |
| 144 | E | C | -2.9602 | |
| 145 | A | C | -2.1603 | |
| 146 | K | C | -2.2679 | |
| 147 | V | C | -1.0062 | |
| 148 | Q | C | -0.5425 | |
| 149 | W | C | 0.0000 | |
| 150 | K | C | -0.5101 | |
| 151 | V | C | 0.0000 | |
| 152 | D | C | -1.8797 | |
| 153 | N | C | -1.5066 | |
| 154 | A | C | -0.2523 | |
| 155 | L | C | 0.7192 | |
| 156 | Q | C | -0.2939 | |
| 157 | S | C | -0.6435 | |
| 158 | G | C | -1.2608 | |
| 159 | N | C | -1.5639 | |
| 160 | S | C | -1.3833 | |
| 161 | Q | C | -1.3128 | |
| 162 | E | C | -1.4764 | |
| 163 | S | C | -0.8222 | |
| 164 | V | C | -0.7347 | |
| 165 | T | C | -1.1778 | |
| 166 | E | C | -2.2400 | |
| 167 | Q | C | -1.8071 | |
| 168 | D | C | -1.9154 | |
| 169 | S | C | -1.6958 | |
| 170 | K | C | -2.1951 | |
| 171 | D | C | -1.6016 | |
| 172 | S | C | -1.6772 | |
| 173 | T | C | 0.0000 | |
| 174 | Y | C | 0.0000 | |
| 175 | S | C | 0.0000 | |
| 176 | L | C | 0.0000 | |
| 177 | S | C | 0.0000 | |
| 178 | S | C | 0.0000 | |
| 179 | T | C | -0.6485 | |
| 180 | L | C | 0.0000 | |
| 181 | T | C | -0.6143 | |
| 182 | L | C | -0.7030 | |
| 183 | S | C | -0.9015 | |
| 184 | K | C | -1.8966 | |
| 185 | A | C | -1.6336 | |
| 186 | D | C | -2.1262 | |
| 187 | Y | C | 0.0000 | |
| 188 | E | C | -3.1212 | |
| 189 | K | C | -3.3556 | |
| 190 | H | C | -2.7722 | |
| 191 | K | C | -3.1272 | |
| 192 | V | C | -1.5673 | |
| 193 | Y | C | 0.0000 | |
| 194 | A | C | 0.0000 | |
| 195 | C | C | 0.0000 | |
| 196 | E | C | -0.5289 | |
| 197 | V | C | 0.0000 | |
| 198 | T | C | -1.1765 | |
| 199 | H | C | 0.0000 | |
| 200 | Q | C | -1.6957 | |
| 201 | G | C | -0.4152 | |
| 202 | L | C | -0.2432 | |
| 203 | S | C | -0.4651 | |
| 204 | S | C | -0.4305 | |
| 205 | P | C | -0.6028 | |
| 206 | V | C | 0.0939 | |
| 207 | T | C | -0.3252 | |
| 208 | K | C | -0.7450 | |
| 209 | S | C | -0.5875 | |
| 210 | F | C | 0.0000 | |
| 211 | N | C | -1.7625 | |
| 212 | R | C | -2.3043 | |
| 213 | G | C | -1.8039 | |
| 214 | E | C | -1.9832 | |
| 215 | C | C | -0.6767 |
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 | -0.768 | 2.8333 | View | CSV | PDB |
| 4.5 | -0.8088 | 2.8333 | View | CSV | PDB |
| 5.0 | -0.8573 | 2.8333 | View | CSV | PDB |
| 5.5 | -0.904 | 2.8333 | View | CSV | PDB |
| 6.0 | -0.9373 | 2.8333 | View | CSV | PDB |
| 6.5 | -0.9474 | 2.8333 | View | CSV | PDB |
| 7.0 | -0.9326 | 2.8333 | View | CSV | PDB |
| 7.5 | -0.9002 | 2.8333 | View | CSV | PDB |
| 8.0 | -0.8578 | 2.8333 | View | CSV | PDB |
| 8.5 | -0.8088 | 2.8333 | View | CSV | PDB |
| 9.0 | -0.7544 | 2.8332 | 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