| Chain sequence(s) |
A: DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
B: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 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. (00:00:01)
[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/e15b559e9fa1bf4/tmp/folded.pdb (00:04:23)
[INFO] Main: Simulation completed successfully. (00:06:15)
|
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 | -2.2936 | |
| 2 | I | A | 0.0000 | |
| 3 | Q | A | -2.2112 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -1.3987 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.8421 | |
| 8 | P | A | -0.5838 | |
| 9 | S | A | -0.8249 | |
| 10 | S | A | -0.7526 | |
| 11 | L | A | -0.6112 | |
| 12 | S | A | -1.0790 | |
| 13 | A | A | -1.0217 | |
| 14 | S | A | -0.7898 | |
| 15 | V | A | 0.3408 | |
| 16 | G | A | -0.4385 | |
| 17 | D | A | -1.6728 | |
| 18 | R | A | -2.3556 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6594 | |
| 21 | I | A | 0.0000 | |
| 22 | T | A | -0.7959 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.8635 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.3335 | |
| 27 | Q | A | -2.9363 | |
| 28 | D | A | -2.8669 | |
| 29 | V | A | 0.0000 | |
| 30 | N | A | -1.7379 | |
| 31 | T | A | -0.8607 | |
| 32 | A | A | 0.0176 | |
| 33 | V | 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 | 0.0000 | |
| 39 | K | A | -1.9439 | |
| 40 | P | A | -1.5463 | |
| 41 | G | A | -1.7794 | |
| 42 | K | A | -2.6357 | |
| 43 | A | A | -1.7361 | |
| 44 | P | A | 0.0000 | |
| 45 | K | A | -1.9211 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 1.0921 | |
| 50 | S | A | 0.4346 | |
| 51 | A | A | 0.0000 | |
| 52 | S | A | 0.6221 | |
| 53 | F | A | 2.0289 | |
| 54 | L | A | 1.4216 | |
| 55 | Y | A | 0.6079 | |
| 56 | S | A | 0.0249 | |
| 57 | G | A | -0.3898 | |
| 58 | V | A | -0.2624 | |
| 59 | P | A | -0.3111 | |
| 60 | S | A | -0.3791 | |
| 61 | R | A | -0.7551 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | 0.0931 | |
| 64 | G | A | 0.0338 | |
| 65 | S | A | -0.7344 | |
| 66 | R | A | -1.8197 | |
| 67 | S | A | -1.3135 | |
| 68 | G | A | -1.8387 | |
| 69 | T | A | -2.2518 | |
| 70 | D | A | -1.9479 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8213 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6473 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.4726 | |
| 77 | S | A | -1.0607 | |
| 78 | L | A | 0.0000 | |
| 79 | Q | A | -1.0532 | |
| 80 | P | A | -1.6942 | |
| 81 | E | A | -2.2306 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | 0.0000 | |
| 84 | A | A | 0.0000 | |
| 85 | T | A | -0.8174 | |
| 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 | H | A | 0.4751 | |
| 92 | Y | A | 0.6425 | |
| 93 | T | A | 0.0625 | |
| 94 | T | A | -0.2653 | |
| 95 | P | A | -0.6108 | |
| 96 | P | A | 0.0000 | |
| 97 | T | A | -0.6003 | |
| 98 | F | A | -0.5108 | |
| 99 | G | A | 0.0000 | |
| 100 | Q | A | -1.7479 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.3914 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.5067 | |
| 106 | I | A | 0.0000 | |
| 107 | K | A | -1.4015 | |
| 108 | R | A | -0.8230 | |
| 109 | T | A | 0.1529 | |
| 110 | V | A | 1.0019 | |
| 111 | A | A | 0.3130 | |
| 112 | A | A | 0.1389 | |
| 113 | P | A | 0.0000 | |
| 114 | S | A | -0.0923 | |
| 115 | V | A | 0.0000 | |
| 116 | F | A | 0.0000 | |
| 117 | I | A | 0.0000 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | -0.6522 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | -1.6190 | |
| 122 | D | A | -3.0101 | |
| 123 | E | A | -3.0224 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -2.2997 | |
| 126 | K | A | -2.8064 | |
| 127 | S | A | -1.7760 | |
| 128 | G | A | -1.3759 | |
| 129 | T | A | -1.0096 | |
| 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 | -0.8613 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -1.6280 | |
| 142 | R | A | -2.8499 | |
| 143 | E | A | -3.2215 | |
| 144 | A | A | -2.3583 | |
| 145 | K | A | -2.4562 | |
| 146 | V | A | -1.2049 | |
| 147 | Q | A | -0.7639 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -1.0481 | |
| 150 | V | A | 0.0000 | |
| 151 | D | A | -2.3207 | |
| 152 | N | A | -1.7767 | |
| 153 | A | A | -0.3811 | |
| 154 | L | A | 0.6405 | |
| 155 | Q | A | -0.1441 | |
| 156 | S | A | -0.4490 | |
| 157 | G | A | -0.8475 | |
| 158 | N | A | -0.7020 | |
| 159 | S | A | -1.0936 | |
| 160 | Q | A | -1.4205 | |
| 161 | E | A | -2.1426 | |
| 162 | S | A | -1.0589 | |
| 163 | V | A | -1.0541 | |
| 164 | T | A | -1.1839 | |
| 165 | E | A | -2.3639 | |
| 166 | Q | A | 0.0000 | |
| 167 | D | A | -2.1948 | |
| 168 | S | A | -2.4205 | |
| 169 | K | A | -2.7175 | |
| 170 | D | A | -1.9978 | |
| 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 | -0.6278 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.3954 | |
| 181 | L | A | -0.6517 | |
| 182 | S | A | -1.0692 | |
| 183 | K | A | -2.1174 | |
| 184 | A | A | -1.9441 | |
| 185 | D | A | -2.5111 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.7049 | |
| 188 | K | A | -3.7158 | |
| 189 | H | A | -3.2389 | |
| 190 | K | A | -3.5304 | |
| 191 | V | A | -1.8358 | |
| 192 | Y | A | 0.0000 | |
| 193 | A | A | 0.0000 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.7502 | |
| 196 | V | A | 0.0000 | |
| 197 | T | A | -1.1230 | |
| 198 | H | A | 0.0000 | |
| 199 | Q | A | -1.6200 | |
| 200 | G | A | -0.1467 | |
| 201 | L | A | -0.0491 | |
| 202 | S | A | -0.3910 | |
| 203 | S | A | -0.3620 | |
| 204 | P | A | -0.5001 | |
| 205 | V | A | 0.1302 | |
| 206 | T | A | -0.3503 | |
| 207 | K | A | -0.6107 | |
| 208 | S | A | -0.7813 | |
| 209 | F | A | 0.0000 | |
| 210 | N | A | -2.2260 | |
| 211 | R | A | -2.9450 | |
| 212 | G | A | -2.3313 | |
| 213 | E | A | -2.3565 | |
| 214 | C | A | -0.6325 | |
| 1 | E | B | -2.0192 | |
| 2 | V | B | -1.3129 | |
| 3 | Q | B | -1.2782 | |
| 4 | L | B | 0.0000 | |
| 5 | V | B | 0.2489 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -0.6314 | |
| 8 | G | B | -0.9299 | |
| 9 | G | B | -0.7510 | |
| 10 | G | B | -0.4202 | |
| 11 | L | B | -0.2015 | |
| 12 | V | B | 0.0000 | |
| 13 | Q | B | -1.7060 | |
| 14 | P | B | -1.5670 | |
| 15 | G | B | -1.4855 | |
| 16 | G | B | -1.1927 | |
| 17 | S | B | -1.3375 | |
| 18 | L | B | -1.2474 | |
| 19 | R | B | -2.2387 | |
| 20 | L | B | 0.0000 | |
| 21 | S | B | -0.6145 | |
| 22 | C | B | 0.0000 | |
| 23 | A | B | -0.3617 | |
| 24 | A | B | 0.0000 | |
| 25 | S | B | -1.0850 | |
| 26 | G | B | -1.2500 | |
| 27 | F | B | -1.4149 | |
| 28 | N | B | -2.3422 | |
| 29 | I | B | 0.0000 | |
| 30 | K | B | -2.8279 | |
| 31 | D | B | -3.0402 | |
| 32 | T | B | 0.0000 | |
| 33 | Y | B | -0.4359 | |
| 34 | I | B | 0.0000 | |
| 35 | H | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | R | B | 0.0000 | |
| 39 | Q | B | -0.8069 | |
| 40 | A | B | -1.1633 | |
| 41 | P | B | -0.9654 | |
| 42 | G | B | -1.4761 | |
| 43 | K | B | -2.4029 | |
| 44 | G | B | -1.6693 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -1.0755 | |
| 47 | W | B | 0.0000 | |
| 48 | V | B | 0.0000 | |
| 49 | A | B | 0.0000 | |
| 50 | R | B | -0.3215 | |
| 51 | I | B | 0.0000 | |
| 52 | Y | B | -0.3785 | |
| 53 | P | B | 0.0000 | |
| 54 | T | B | -1.2494 | |
| 55 | N | B | -0.8991 | |
| 56 | G | B | -0.5528 | |
| 57 | Y | B | 0.6332 | |
| 58 | T | B | -0.0960 | |
| 59 | R | B | -1.2163 | |
| 60 | Y | B | -1.4569 | |
| 61 | A | B | -1.6790 | |
| 62 | D | B | -2.5423 | |
| 63 | S | B | -1.7903 | |
| 64 | V | B | 0.0000 | |
| 65 | K | B | -2.6998 | |
| 66 | G | B | -1.7042 | |
| 67 | R | B | -1.2793 | |
| 68 | F | B | 0.0000 | |
| 69 | T | B | -1.1288 | |
| 70 | I | B | 0.0000 | |
| 71 | S | B | -0.2673 | |
| 72 | A | B | -0.8678 | |
| 73 | D | B | -1.5033 | |
| 74 | T | B | -1.6625 | |
| 75 | S | B | -1.5825 | |
| 76 | K | B | -2.2301 | |
| 77 | N | B | -1.8270 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | 0.0000 | |
| 81 | L | B | 0.0000 | |
| 82 | Q | B | -1.5532 | |
| 83 | M | B | 0.0000 | |
| 84 | N | B | -1.3600 | |
| 85 | S | B | -1.2670 | |
| 86 | L | B | 0.0000 | |
| 87 | R | B | -2.5199 | |
| 88 | A | B | -1.8101 | |
| 89 | E | B | -2.2834 | |
| 90 | D | B | 0.0000 | |
| 91 | T | B | -0.7481 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | 0.1493 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | S | B | 0.0000 | |
| 98 | R | B | -0.1773 | |
| 99 | W | B | 0.0000 | |
| 100 | G | B | 0.0000 | |
| 101 | G | B | -1.3928 | |
| 102 | D | B | -2.2189 | |
| 103 | G | B | -1.0698 | |
| 104 | F | B | -0.2036 | |
| 105 | Y | B | 0.3933 | |
| 106 | A | B | 0.0000 | |
| 107 | M | B | 0.0000 | |
| 108 | D | B | -0.2586 | |
| 109 | Y | B | -0.5920 | |
| 110 | W | B | -0.6508 | |
| 111 | G | B | 0.0000 | |
| 112 | Q | B | -1.5478 | |
| 113 | G | B | -0.7366 | |
| 114 | T | B | -0.1766 | |
| 115 | L | B | 0.0987 | |
| 116 | V | B | 0.0000 | |
| 117 | T | B | -0.5187 | |
| 118 | V | B | 0.0000 | |
| 119 | S | B | -0.8669 | |
| 120 | S | B | -0.7389 | |
| 121 | A | B | -0.4792 | |
| 122 | S | B | -0.5883 | |
| 123 | T | B | -0.6236 | |
| 124 | K | B | -1.0591 | |
| 125 | G | B | -1.3001 | |
| 126 | P | B | 0.0000 | |
| 127 | S | B | -0.4391 | |
| 128 | V | B | 0.0000 | |
| 129 | F | B | 0.0000 | |
| 130 | P | B | -1.0879 | |
| 131 | L | B | 0.0000 | |
| 132 | A | B | -0.7706 | |
| 133 | P | B | 0.0000 | |
| 134 | S | B | -0.6107 | |
| 135 | S | B | -0.7311 | |
| 136 | K | B | -1.0776 | |
| 137 | S | B | 0.0000 | |
| 138 | T | B | -0.6908 | |
| 139 | S | B | -0.6604 | |
| 140 | G | B | -0.8012 | |
| 141 | G | B | -0.8721 | |
| 142 | T | B | -0.5973 | |
| 143 | A | B | 0.0000 | |
| 144 | A | B | 0.0000 | |
| 145 | L | B | 0.0000 | |
| 146 | G | B | 0.0000 | |
| 147 | C | B | 0.0000 | |
| 148 | L | B | 0.0000 | |
| 149 | V | B | 0.0000 | |
| 150 | K | B | 0.0000 | |
| 151 | D | B | -0.3411 | |
| 152 | Y | B | 0.0000 | |
| 153 | F | B | 0.0000 | |
| 154 | P | B | 0.0000 | |
| 155 | E | B | -0.4150 | |
| 156 | P | B | -0.6114 | |
| 157 | V | B | -0.4013 | |
| 158 | T | B | -0.5075 | |
| 159 | V | B | -0.2635 | |
| 160 | S | B | -0.3424 | |
| 161 | W | B | 0.0000 | |
| 162 | N | B | -0.7906 | |
| 163 | S | B | -0.6593 | |
| 164 | G | B | -0.5136 | |
| 165 | A | B | -0.2399 | |
| 166 | L | B | -0.0212 | |
| 167 | T | B | -0.1689 | |
| 168 | S | B | -0.1634 | |
| 169 | G | B | -0.1748 | |
| 170 | V | B | 0.1804 | |
| 171 | H | B | -0.3348 | |
| 172 | T | B | -0.1454 | |
| 173 | F | B | 0.0000 | |
| 174 | P | B | -0.3592 | |
| 175 | A | B | 0.1987 | |
| 176 | V | B | 0.4381 | |
| 177 | L | B | 1.0588 | |
| 178 | Q | B | 0.2730 | |
| 179 | S | B | -0.0795 | |
| 180 | S | B | -0.1951 | |
| 181 | G | B | 0.0231 | |
| 182 | L | B | 0.1440 | |
| 183 | Y | B | 0.4707 | |
| 184 | S | B | 0.2774 | |
| 185 | L | B | 0.0000 | |
| 186 | S | B | 0.0000 | |
| 187 | S | B | 0.0000 | |
| 188 | V | B | 0.0000 | |
| 189 | V | B | 0.0000 | |
| 190 | T | B | -0.1187 | |
| 191 | V | B | 0.0000 | |
| 192 | P | B | -0.5960 | |
| 193 | S | B | -0.6137 | |
| 194 | S | B | -0.5307 | |
| 195 | S | B | -0.5042 | |
| 196 | L | B | -0.6449 | |
| 197 | G | B | -0.9774 | |
| 198 | T | B | -0.6629 | |
| 199 | Q | B | -1.1254 | |
| 200 | T | B | -1.0822 | |
| 201 | Y | B | 0.0000 | |
| 202 | I | B | -1.3723 | |
| 203 | C | B | 0.0000 | |
| 204 | N | B | 0.0000 | |
| 205 | V | B | 0.0000 | |
| 206 | N | B | -1.7278 | |
| 207 | H | B | 0.0000 | |
| 208 | K | B | -2.6843 | |
| 209 | P | B | -1.5547 | |
| 210 | S | B | -1.8047 | |
| 211 | N | B | -2.4073 | |
| 212 | T | B | -2.0150 | |
| 213 | K | B | -2.6579 | |
| 214 | V | B | -1.7587 | |
| 215 | D | B | -2.5442 | |
| 216 | K | B | -2.2131 | |
| 217 | K | B | -2.4656 | |
| 218 | V | B | 0.0000 | |
| 219 | E | B | -1.9994 | |
| 220 | P | B | -0.8886 |
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 | -0.7458 | 3.4527 | View | CSV | PDB |
| 4.5 | -0.792 | 3.4527 | View | CSV | PDB |
| 5.0 | -0.845 | 3.4527 | View | CSV | PDB |
| 5.5 | -0.8952 | 3.4527 | View | CSV | PDB |
| 6.0 | -0.9316 | 3.4527 | View | CSV | PDB |
| 6.5 | -0.9453 | 3.4527 | View | CSV | PDB |
| 7.0 | -0.9357 | 3.4527 | View | CSV | PDB |
| 7.5 | -0.9106 | 3.4527 | View | CSV | PDB |
| 8.0 | -0.8765 | 3.4526 | View | CSV | PDB |
| 8.5 | -0.8352 | 3.4525 | View | CSV | PDB |
| 9.0 | -0.7864 | 3.4522 | 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