| Chain sequence(s) |
A: QVQLVQSGAEVKKPGSSVKVSCKASGGSFSRLAFSWVRQAPGQGLEWMGGIIPIIGTADYAQKFQGRVTITADESTNTAYMELSSLRSEDTAVYYCARDLSSGYSDALDIWGQGSVITVSSASTKGPEVQLVESGGGVVQPGRSLRLSCTASGFAFGDYAMSWVRQAPGKGLEWVGFIRSKTYGATTEYAASVKGRFAISRDDSKGIAYLQMNSLRAEDTAVYYCARGITGYAGYDYWGQGTLVTVSS
B: SYELTQPLSVSVSPGQTSTITCSGEALGDRYASWYQQRPGQSPILVIYQDTKRPSGIPERFSGSSSRGTATLTISGTQATDEADYYCQTWDRSTGVFGTGTKVTVLRTVAAPSVFIFPPDIQMTQSPSTLSASVGDRVTITCRASYSVSPWLAWYQQKPGKAPKLLIYAASSLQRGVPSRFSGSGSGTEFTLTISSLQAEDVAVYYCQQSYSAPLTFGGGTKVEIK 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 (00:04:23)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/568c625ae8a7958/tmp/folded.pdb (00:04:23)
[INFO] Main: Simulation completed successfully. (00:06:29)
|
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 | Q | A | -1.5154 | |
| 2 | V | A | -1.0898 | |
| 3 | Q | A | -1.0856 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.4315 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.5768 | |
| 8 | G | A | -0.6623 | |
| 9 | A | A | -0.4022 | |
| 10 | E | A | -0.9687 | |
| 11 | V | A | -0.2255 | |
| 12 | K | A | -1.2913 | |
| 13 | K | A | -2.0170 | |
| 14 | P | A | -1.4589 | |
| 15 | G | A | -1.1998 | |
| 16 | S | A | -1.0876 | |
| 17 | S | A | -1.3087 | |
| 18 | V | A | 0.0000 | |
| 19 | K | A | -2.1810 | |
| 20 | V | A | 0.0000 | |
| 21 | S | A | -0.5217 | |
| 22 | C | A | 0.0000 | |
| 23 | K | A | -0.6506 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -0.9342 | |
| 26 | G | A | -1.2973 | |
| 27 | G | A | -1.2553 | |
| 28 | S | A | -0.9536 | |
| 29 | F | A | 0.0000 | |
| 30 | S | A | -0.5546 | |
| 31 | R | A | -1.1159 | |
| 32 | L | A | 0.0000 | |
| 33 | A | A | 0.0000 | |
| 34 | F | A | 0.0000 | |
| 35 | S | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | 0.0000 | |
| 40 | A | A | 0.0000 | |
| 41 | P | A | 0.0000 | |
| 42 | G | A | -0.3427 | |
| 43 | Q | A | -0.6250 | |
| 44 | G | A | -0.5538 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -0.7216 | |
| 47 | W | A | 0.0000 | |
| 48 | M | A | 0.0000 | |
| 49 | G | A | 0.0000 | |
| 50 | G | A | 0.0000 | |
| 51 | I | A | 0.0000 | |
| 52 | I | A | 0.7151 | |
| 53 | P | A | 0.0000 | |
| 54 | I | A | 2.0491 | |
| 55 | I | A | 2.5269 | |
| 56 | G | A | 0.8646 | |
| 57 | T | A | 0.5489 | |
| 58 | A | A | -0.0401 | |
| 59 | D | A | -0.8196 | |
| 60 | Y | A | -1.0631 | |
| 61 | A | A | -1.4610 | |
| 62 | Q | A | -2.4838 | |
| 63 | K | A | -2.6751 | |
| 64 | F | A | 0.0000 | |
| 65 | Q | A | -2.4705 | |
| 66 | G | A | -1.6553 | |
| 67 | R | A | -1.4767 | |
| 68 | V | A | 0.0000 | |
| 69 | T | A | -0.9621 | |
| 70 | I | A | 0.0000 | |
| 71 | T | A | -0.4684 | |
| 72 | A | A | -0.4044 | |
| 73 | D | A | -1.4160 | |
| 74 | E | A | -1.6153 | |
| 75 | S | A | -1.1978 | |
| 76 | T | A | -1.0974 | |
| 77 | N | A | -1.5538 | |
| 78 | T | A | 0.0000 | |
| 79 | A | A | 0.0000 | |
| 80 | Y | A | -0.6340 | |
| 81 | M | A | 0.0000 | |
| 82 | E | A | -1.6959 | |
| 83 | L | A | 0.0000 | |
| 84 | S | A | -1.0467 | |
| 85 | S | A | -0.8908 | |
| 86 | L | A | 0.0000 | |
| 87 | R | A | -0.9196 | |
| 88 | S | A | 0.0000 | |
| 89 | E | A | 0.0000 | |
| 90 | D | A | 0.0000 | |
| 91 | T | A | 0.0000 | |
| 92 | A | A | 0.0000 | |
| 93 | V | A | 0.0000 | |
| 94 | Y | A | 0.0000 | |
| 95 | Y | A | 0.0000 | |
| 96 | C | A | 0.0000 | |
| 97 | A | A | 0.0000 | |
| 98 | R | A | -0.0962 | |
| 99 | D | A | 0.0000 | |
| 100 | L | A | 0.4145 | |
| 101 | S | A | -0.3033 | |
| 102 | S | A | -0.5590 | |
| 103 | G | A | -0.3930 | |
| 104 | Y | A | -0.4527 | |
| 105 | S | A | -0.4885 | |
| 106 | D | A | -0.0560 | |
| 107 | A | A | 0.0000 | |
| 108 | L | A | 0.0000 | |
| 109 | D | A | 0.1320 | |
| 110 | I | A | 0.1084 | |
| 111 | W | A | 0.0000 | |
| 112 | G | A | 0.0000 | |
| 113 | Q | A | -1.2450 | |
| 114 | G | A | -0.6647 | |
| 115 | S | A | 0.0000 | |
| 116 | V | A | -0.0481 | |
| 117 | I | A | 0.0000 | |
| 118 | T | A | 0.0000 | |
| 119 | V | A | 0.0000 | |
| 120 | S | A | 0.0000 | |
| 121 | S | A | -0.9666 | |
| 122 | A | A | -1.1674 | |
| 123 | S | A | -1.3136 | |
| 124 | T | A | -1.6662 | |
| 125 | K | A | -2.3281 | |
| 126 | G | A | -1.8454 | |
| 127 | P | A | -1.8151 | |
| 128 | E | A | -2.4480 | |
| 129 | V | A | -1.0237 | |
| 130 | Q | A | -0.9148 | |
| 131 | L | A | 0.0000 | |
| 132 | V | A | 0.5552 | |
| 133 | E | A | 0.0000 | |
| 134 | S | A | -0.4138 | |
| 135 | G | A | -0.8390 | |
| 136 | G | A | 0.0688 | |
| 137 | G | A | 0.8875 | |
| 138 | V | A | 1.6389 | |
| 139 | V | A | -0.3042 | |
| 140 | Q | A | -1.7212 | |
| 141 | P | A | -2.0488 | |
| 142 | G | A | -2.2069 | |
| 143 | R | A | -2.7981 | |
| 144 | S | A | -2.1136 | |
| 145 | L | A | -1.3936 | |
| 146 | R | A | -2.0797 | |
| 147 | L | A | 0.0000 | |
| 148 | S | A | -0.4531 | |
| 149 | C | A | 0.0000 | |
| 150 | T | A | -0.0701 | |
| 151 | A | A | -0.1903 | |
| 152 | S | A | -0.6559 | |
| 153 | G | A | -0.9639 | |
| 154 | F | A | -0.3454 | |
| 155 | A | A | -0.0889 | |
| 156 | F | A | 0.0000 | |
| 157 | G | A | -1.1730 | |
| 158 | D | A | -1.0059 | |
| 159 | Y | A | 0.0000 | |
| 160 | A | A | 0.0000 | |
| 161 | M | A | 0.0000 | |
| 162 | S | A | 0.0000 | |
| 163 | W | A | 0.0000 | |
| 164 | V | A | 0.0000 | |
| 165 | R | A | 0.0000 | |
| 166 | Q | A | -0.6700 | |
| 167 | A | A | -1.0589 | |
| 168 | P | A | -0.8529 | |
| 169 | G | A | -1.4546 | |
| 170 | K | A | -2.2777 | |
| 171 | G | A | -1.3874 | |
| 172 | L | A | 0.0000 | |
| 173 | E | A | -0.9768 | |
| 174 | W | A | 0.0000 | |
| 175 | V | A | 0.0000 | |
| 176 | G | A | 0.0000 | |
| 177 | F | A | 0.0000 | |
| 178 | I | A | 0.0000 | |
| 179 | R | A | 0.0000 | |
| 180 | S | A | 0.0000 | |
| 181 | K | A | -2.0574 | |
| 182 | T | A | -1.2720 | |
| 183 | Y | A | -0.8859 | |
| 184 | G | A | -1.0371 | |
| 185 | A | A | -0.9579 | |
| 186 | T | A | -0.5881 | |
| 187 | T | A | -0.3629 | |
| 188 | E | A | -0.7588 | |
| 189 | Y | A | -0.7235 | |
| 190 | A | A | 0.0000 | |
| 191 | A | A | -0.6354 | |
| 192 | S | A | -0.9113 | |
| 193 | V | A | 0.0000 | |
| 194 | K | A | -2.0249 | |
| 195 | G | A | -1.4592 | |
| 196 | R | A | -1.2558 | |
| 197 | F | A | 0.0000 | |
| 198 | A | A | -0.8386 | |
| 199 | I | A | 0.0000 | |
| 200 | S | A | -0.3563 | |
| 201 | R | A | -0.9913 | |
| 202 | D | A | -1.2832 | |
| 203 | D | A | -1.6279 | |
| 204 | S | A | -1.3771 | |
| 205 | K | A | -2.0565 | |
| 206 | G | A | -1.1328 | |
| 207 | I | A | -0.5476 | |
| 208 | A | A | 0.0000 | |
| 209 | Y | A | -0.5340 | |
| 210 | L | A | 0.0000 | |
| 211 | Q | A | -1.1959 | |
| 212 | M | A | 0.0000 | |
| 213 | N | A | -1.8921 | |
| 214 | S | A | -1.8011 | |
| 215 | L | A | 0.0000 | |
| 216 | R | A | -2.5559 | |
| 217 | A | A | -1.7045 | |
| 218 | E | A | -2.2454 | |
| 219 | D | A | 0.0000 | |
| 220 | T | A | -0.3759 | |
| 221 | A | A | 0.0000 | |
| 222 | V | A | 0.6502 | |
| 223 | Y | A | 0.0000 | |
| 224 | Y | A | 0.0000 | |
| 225 | C | A | 0.0000 | |
| 226 | A | A | 0.0000 | |
| 227 | R | A | 0.0000 | |
| 228 | G | A | 0.0000 | |
| 229 | I | A | 0.0000 | |
| 230 | T | A | 0.0000 | |
| 231 | G | A | 0.0000 | |
| 232 | Y | A | 0.0000 | |
| 233 | A | A | 0.0000 | |
| 234 | G | A | 0.0000 | |
| 235 | Y | A | 0.0000 | |
| 236 | D | A | -0.2429 | |
| 237 | Y | A | 0.2081 | |
| 238 | W | A | -0.2010 | |
| 239 | G | A | 0.0000 | |
| 240 | Q | A | -1.2136 | |
| 241 | G | A | 0.0000 | |
| 242 | T | A | 0.3984 | |
| 243 | L | A | 1.3561 | |
| 244 | V | A | 0.0000 | |
| 245 | T | A | 0.4095 | |
| 246 | V | A | 0.0000 | |
| 247 | S | A | -0.5995 | |
| 248 | S | A | -0.6369 | |
| 1 | S | B | -0.5188 | |
| 2 | Y | B | -0.2038 | |
| 3 | E | B | -1.7188 | |
| 4 | L | B | 0.0000 | |
| 5 | T | B | -0.5546 | |
| 6 | Q | B | 0.0000 | |
| 7 | P | B | 0.6167 | |
| 8 | L | B | 1.6234 | |
| 9 | S | B | 1.2098 | |
| 10 | V | B | 0.9723 | |
| 11 | S | B | 1.0341 | |
| 12 | V | B | 0.0000 | |
| 13 | S | B | -0.9128 | |
| 14 | P | B | -1.2280 | |
| 15 | G | B | -1.3027 | |
| 16 | Q | B | -1.5140 | |
| 17 | T | B | -0.9211 | |
| 18 | S | B | 0.0000 | |
| 19 | T | B | -0.0956 | |
| 20 | I | B | 0.0000 | |
| 21 | T | B | -0.1667 | |
| 22 | C | B | 0.0000 | |
| 23 | S | B | -1.1257 | |
| 24 | G | B | -1.4152 | |
| 25 | E | B | -2.2981 | |
| 26 | A | B | 0.0000 | |
| 27 | L | B | 0.0000 | |
| 28 | G | B | -2.1964 | |
| 29 | D | B | -2.6257 | |
| 30 | R | B | -1.4101 | |
| 31 | Y | B | 0.2144 | |
| 32 | A | B | 0.0000 | |
| 33 | S | B | 0.0000 | |
| 34 | W | B | 0.0000 | |
| 35 | Y | B | 0.0000 | |
| 36 | Q | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | R | B | -1.2843 | |
| 39 | P | B | -1.0692 | |
| 40 | G | B | -1.2648 | |
| 41 | Q | B | -1.7029 | |
| 42 | S | B | -0.8550 | |
| 43 | P | B | 0.0000 | |
| 44 | I | B | 1.1048 | |
| 45 | L | B | 0.0000 | |
| 46 | V | B | 0.0000 | |
| 47 | I | B | 0.0000 | |
| 48 | Y | B | -0.5596 | |
| 49 | Q | B | -0.5813 | |
| 50 | D | B | -0.6270 | |
| 51 | T | B | -1.0972 | |
| 52 | K | B | -2.1230 | |
| 53 | R | B | -2.2151 | |
| 54 | P | B | -0.9429 | |
| 55 | S | B | -0.8133 | |
| 56 | G | B | -0.8777 | |
| 57 | I | B | -0.7159 | |
| 58 | P | B | -1.3337 | |
| 59 | E | B | -2.2698 | |
| 60 | R | B | -1.4234 | |
| 61 | F | B | 0.0000 | |
| 62 | S | B | -1.1420 | |
| 63 | G | B | -0.7825 | |
| 64 | S | B | -0.5236 | |
| 65 | S | B | -0.9933 | |
| 66 | S | B | -1.5142 | |
| 67 | R | B | -2.4047 | |
| 68 | G | B | -2.0708 | |
| 69 | T | B | -1.3282 | |
| 70 | A | B | 0.0000 | |
| 71 | T | B | -0.2680 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -0.2450 | |
| 74 | I | B | 0.0000 | |
| 75 | S | B | -1.1065 | |
| 76 | G | B | -1.2572 | |
| 77 | T | B | 0.0000 | |
| 78 | Q | B | -1.2221 | |
| 79 | A | B | -0.7774 | |
| 80 | T | B | -0.5240 | |
| 81 | D | B | 0.0000 | |
| 82 | E | B | -0.5840 | |
| 83 | A | B | 0.0000 | |
| 84 | D | B | -0.4741 | |
| 85 | Y | B | 0.0000 | |
| 86 | Y | B | 0.0000 | |
| 87 | C | B | 0.0000 | |
| 88 | Q | B | 0.0000 | |
| 89 | T | B | 0.0000 | |
| 90 | W | B | 0.0000 | |
| 91 | D | B | 0.0000 | |
| 92 | R | B | -1.9766 | |
| 93 | S | B | -1.0837 | |
| 94 | T | B | -0.8305 | |
| 95 | G | B | 0.0000 | |
| 96 | V | B | 0.0000 | |
| 97 | F | B | 0.0000 | |
| 98 | G | B | 0.0000 | |
| 99 | T | B | -0.4586 | |
| 100 | G | B | 0.0164 | |
| 101 | T | B | 0.0000 | |
| 102 | K | B | 0.0395 | |
| 103 | V | B | 0.0000 | |
| 104 | T | B | -0.2273 | |
| 105 | V | B | 0.0000 | |
| 106 | L | B | 0.0573 | |
| 107 | R | B | -1.0804 | |
| 108 | T | B | 0.0003 | |
| 109 | V | B | 1.2292 | |
| 110 | A | B | 0.5757 | |
| 111 | A | B | 0.4053 | |
| 112 | P | B | 0.5602 | |
| 113 | S | B | 1.4596 | |
| 114 | V | B | 3.0530 | |
| 115 | F | B | 3.3566 | |
| 116 | I | B | 3.7426 | |
| 117 | F | B | 3.0439 | |
| 118 | P | B | 1.3615 | |
| 119 | P | B | 0.3730 | |
| 120 | D | B | -0.6689 | |
| 121 | I | B | 0.0000 | |
| 122 | Q | B | -1.5590 | |
| 123 | M | B | 0.0000 | |
| 124 | T | B | -1.0373 | |
| 125 | Q | B | -0.6883 | |
| 126 | S | B | -0.5066 | |
| 127 | P | B | -0.3908 | |
| 128 | S | B | -0.5149 | |
| 129 | T | B | -0.5342 | |
| 130 | L | B | -0.4892 | |
| 131 | S | B | -0.8366 | |
| 132 | A | B | 0.0000 | |
| 133 | S | B | -0.5967 | |
| 134 | V | B | 0.1571 | |
| 135 | G | B | -0.7169 | |
| 136 | D | B | -1.5788 | |
| 137 | R | B | -2.2803 | |
| 138 | V | B | 0.0000 | |
| 139 | T | B | -0.5912 | |
| 140 | I | B | 0.0000 | |
| 141 | T | B | -0.7462 | |
| 142 | C | B | 0.0000 | |
| 143 | R | B | -1.7316 | |
| 144 | A | B | 0.0000 | |
| 145 | S | B | -0.9760 | |
| 146 | Y | B | -0.6382 | |
| 147 | S | B | -0.8247 | |
| 148 | V | B | 0.0000 | |
| 149 | S | B | -0.7125 | |
| 150 | P | B | -0.3295 | |
| 151 | W | B | 0.0000 | |
| 152 | L | B | 0.0000 | |
| 153 | A | B | 0.0000 | |
| 154 | W | B | 0.0000 | |
| 155 | Y | B | 0.0000 | |
| 156 | Q | B | 0.0000 | |
| 157 | Q | B | 0.0000 | |
| 158 | K | B | -1.4857 | |
| 159 | P | B | -1.0789 | |
| 160 | G | B | -1.6608 | |
| 161 | K | B | -2.5432 | |
| 162 | A | B | -1.5377 | |
| 163 | P | B | 0.0000 | |
| 164 | K | B | -1.2903 | |
| 165 | L | B | 0.0000 | |
| 166 | L | B | 0.0000 | |
| 167 | I | B | 0.0000 | |
| 168 | Y | B | 0.0000 | |
| 169 | A | B | -0.0187 | |
| 170 | A | B | 0.0000 | |
| 171 | S | B | -0.3782 | |
| 172 | S | B | -0.1079 | |
| 173 | L | B | -0.2917 | |
| 174 | Q | B | -1.0052 | |
| 175 | R | B | -1.6667 | |
| 176 | G | B | -1.1811 | |
| 177 | V | B | 0.0000 | |
| 178 | P | B | -0.6591 | |
| 179 | S | B | -0.6603 | |
| 180 | R | B | -0.8535 | |
| 181 | F | B | 0.0000 | |
| 182 | S | B | -0.4077 | |
| 183 | G | B | -0.3577 | |
| 184 | S | B | -0.8340 | |
| 185 | G | B | -1.2855 | |
| 186 | S | B | -1.2139 | |
| 187 | G | B | -1.1698 | |
| 188 | T | B | -1.3462 | |
| 189 | E | B | -2.3441 | |
| 190 | F | B | 0.0000 | |
| 191 | T | B | -0.8120 | |
| 192 | L | B | 0.0000 | |
| 193 | T | B | -0.6085 | |
| 194 | I | B | 0.0000 | |
| 195 | S | B | -1.3372 | |
| 196 | S | B | -1.1485 | |
| 197 | L | B | 0.0000 | |
| 198 | Q | B | -0.6627 | |
| 199 | A | B | -0.5941 | |
| 200 | E | B | -1.6121 | |
| 201 | D | B | 0.0000 | |
| 202 | V | B | -0.4257 | |
| 203 | A | B | 0.0000 | |
| 204 | V | B | -0.1237 | |
| 205 | Y | B | 0.0000 | |
| 206 | Y | B | 0.0000 | |
| 207 | C | B | 0.0000 | |
| 208 | Q | B | 0.0000 | |
| 209 | Q | B | 0.0000 | |
| 210 | S | B | 0.0000 | |
| 211 | Y | B | -0.0494 | |
| 212 | S | B | -0.2648 | |
| 213 | A | B | -0.3190 | |
| 214 | P | B | -0.2618 | |
| 215 | L | B | 0.0000 | |
| 216 | T | B | -0.4887 | |
| 217 | F | B | -0.3511 | |
| 218 | G | B | 0.0000 | |
| 219 | G | B | -1.0714 | |
| 220 | G | B | -0.6637 | |
| 221 | T | B | 0.0000 | |
| 222 | K | B | -0.7230 | |
| 223 | V | B | 0.0000 | |
| 224 | E | B | -0.8510 | |
| 225 | I | B | -0.6257 | |
| 226 | K | B | -1.4605 |
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 | -0.4902 | 5.9546 | View | CSV | PDB |
| 4.5 | -0.5177 | 5.9546 | View | CSV | PDB |
| 5.0 | -0.5507 | 5.9546 | View | CSV | PDB |
| 5.5 | -0.5824 | 5.9546 | View | CSV | PDB |
| 6.0 | -0.605 | 5.9546 | View | CSV | PDB |
| 6.5 | -0.6119 | 5.9546 | View | CSV | PDB |
| 7.0 | -0.6027 | 5.9546 | View | CSV | PDB |
| 7.5 | -0.5829 | 5.9546 | View | CSV | PDB |
| 8.0 | -0.5578 | 5.9546 | View | CSV | PDB |
| 8.5 | -0.5295 | 5.9546 | View | CSV | PDB |
| 9.0 | -0.4985 | 5.9546 | 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