| Chain sequence(s) |
A: EVQLVESGGGLVQPGGSLRLSCAASGFNFNDYFMNWVRQAPGKGLEWVAQMRNKNYQYGTYYAESLEGRFTISRDDSKNSLYLQMNSLKTEDTAVYYCARESYYGFTSYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVES
B: DIQMTQSPSSLSASVGDRVTITCQASQDIGISLSWYQQKPGKAPKLLIYNANNLADGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQHNSAPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 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. (00:00:03)
[INFO] FoldX: Starting FoldX energy minimization (00:00:03)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:07)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d6a5077e895d180/tmp/folded.pdb (00:06:07)
[INFO] Main: Simulation completed successfully. (00:09:19)
|
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 | A | -2.1827 | |
| 2 | V | A | -1.4999 | |
| 3 | Q | A | -1.3414 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 1.0356 | |
| 6 | E | A | 0.2106 | |
| 7 | S | A | -0.3775 | |
| 8 | G | A | -0.9657 | |
| 9 | G | A | -0.5759 | |
| 10 | G | A | -0.0224 | |
| 11 | L | A | 0.0118 | |
| 12 | V | A | 0.0000 | |
| 13 | Q | A | -1.5899 | |
| 14 | P | A | -1.7290 | |
| 15 | G | A | -1.5289 | |
| 16 | G | A | 0.0000 | |
| 17 | S | A | -1.5610 | |
| 18 | L | A | -1.3854 | |
| 19 | R | A | -2.2504 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.4767 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -0.1535 | |
| 24 | A | A | 0.0000 | |
| 25 | S | A | -1.1091 | |
| 26 | G | A | -1.5241 | |
| 27 | F | A | -1.3744 | |
| 28 | N | A | -1.9490 | |
| 29 | F | A | 0.0000 | |
| 30 | N | A | -2.5219 | |
| 31 | D | A | -2.5502 | |
| 32 | Y | A | -0.9829 | |
| 33 | F | A | -0.0363 | |
| 34 | M | A | 0.0000 | |
| 35 | N | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | V | A | 0.0000 | |
| 38 | R | A | 0.0000 | |
| 39 | Q | A | -0.7971 | |
| 40 | A | A | -1.2095 | |
| 41 | P | A | -0.9896 | |
| 42 | G | A | -1.5227 | |
| 43 | K | A | -2.3657 | |
| 44 | G | A | -1.8374 | |
| 45 | L | A | 0.0000 | |
| 46 | E | A | -1.0645 | |
| 47 | W | A | 0.0000 | |
| 48 | V | A | 0.0000 | |
| 49 | A | A | 0.0000 | |
| 50 | Q | A | 0.0000 | |
| 51 | M | A | 0.0000 | |
| 52 | R | A | -0.8477 | |
| 53 | N | A | -1.8043 | |
| 54 | K | A | -2.7768 | |
| 55 | N | A | -2.3096 | |
| 56 | Y | A | -0.8257 | |
| 57 | Q | A | -1.6546 | |
| 58 | Y | A | -0.8151 | |
| 59 | G | A | -0.4116 | |
| 60 | T | A | 0.2284 | |
| 61 | Y | A | 0.3086 | |
| 62 | Y | A | -0.5488 | |
| 63 | A | A | -1.4572 | |
| 64 | E | A | -2.7968 | |
| 65 | S | A | -1.7918 | |
| 66 | L | A | 0.0000 | |
| 67 | E | A | -2.7160 | |
| 68 | G | A | -1.9344 | |
| 69 | R | A | -1.8266 | |
| 70 | F | A | 0.0000 | |
| 71 | T | A | -0.7437 | |
| 72 | I | A | 0.0000 | |
| 73 | S | A | -0.3638 | |
| 74 | R | A | -0.8725 | |
| 75 | D | A | -1.4644 | |
| 76 | D | A | -2.2203 | |
| 77 | S | A | -1.5958 | |
| 78 | K | A | -2.3864 | |
| 79 | N | A | -2.0023 | |
| 80 | S | A | 0.0000 | |
| 81 | L | A | 0.0000 | |
| 82 | Y | A | -0.6810 | |
| 83 | L | A | 0.0000 | |
| 84 | Q | A | -1.6992 | |
| 85 | M | A | 0.0000 | |
| 86 | N | A | -2.1537 | |
| 87 | S | A | -1.5013 | |
| 88 | L | A | 0.0000 | |
| 89 | K | A | -2.2903 | |
| 90 | T | A | -1.7815 | |
| 91 | E | A | -2.2299 | |
| 92 | D | A | 0.0000 | |
| 93 | T | A | -0.7193 | |
| 94 | A | A | 0.0000 | |
| 95 | V | A | 0.1498 | |
| 96 | Y | A | 0.0000 | |
| 97 | Y | A | 0.0000 | |
| 98 | C | A | 0.0000 | |
| 99 | A | A | 0.0000 | |
| 100 | R | A | 0.1609 | |
| 101 | E | A | 0.0000 | |
| 102 | S | A | 1.2216 | |
| 103 | Y | A | 1.8285 | |
| 104 | Y | A | 1.8436 | |
| 105 | G | A | 0.0000 | |
| 106 | F | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | S | A | 0.3326 | |
| 109 | Y | A | 0.1944 | |
| 110 | W | A | -0.0860 | |
| 111 | G | A | 0.0000 | |
| 112 | Q | A | -1.3571 | |
| 113 | G | A | -0.5190 | |
| 114 | T | A | -0.0644 | |
| 115 | L | A | 0.2170 | |
| 116 | V | A | 0.0000 | |
| 117 | T | A | 0.0000 | |
| 118 | V | A | 0.0000 | |
| 119 | S | A | -0.9692 | |
| 120 | S | A | -0.7304 | |
| 121 | A | A | -0.5667 | |
| 122 | S | A | -0.6836 | |
| 123 | T | A | -0.7815 | |
| 124 | K | A | -1.6008 | |
| 125 | G | A | -1.6498 | |
| 126 | P | A | 0.0000 | |
| 127 | S | A | -0.5322 | |
| 128 | V | A | 0.0000 | |
| 129 | F | A | 0.0000 | |
| 130 | P | A | -1.2536 | |
| 131 | L | A | 0.0000 | |
| 132 | A | A | -0.6206 | |
| 133 | P | A | -0.6203 | |
| 134 | C | A | -0.7559 | |
| 135 | S | A | -1.2637 | |
| 136 | R | A | -2.2491 | |
| 137 | S | A | -1.7012 | |
| 138 | T | A | -1.2021 | |
| 139 | S | A | -1.2648 | |
| 140 | E | A | -1.9735 | |
| 141 | S | A | -1.1133 | |
| 142 | T | A | -0.7594 | |
| 143 | A | A | -0.7574 | |
| 144 | A | A | 0.0000 | |
| 145 | L | A | 0.0000 | |
| 146 | G | A | 0.0000 | |
| 147 | C | A | 0.0000 | |
| 148 | L | A | 0.0000 | |
| 149 | V | A | 0.0000 | |
| 150 | K | A | 0.0000 | |
| 151 | D | A | -0.5550 | |
| 152 | Y | A | 0.0000 | |
| 153 | F | A | 0.0000 | |
| 154 | P | A | 0.0000 | |
| 155 | E | A | -0.4395 | |
| 156 | P | A | -0.7816 | |
| 157 | V | A | -0.8338 | |
| 158 | T | A | -0.7536 | |
| 159 | V | A | -0.3202 | |
| 160 | S | A | -0.6034 | |
| 161 | W | A | 0.0000 | |
| 162 | N | A | -1.1704 | |
| 163 | S | A | -0.8537 | |
| 164 | G | A | -0.6431 | |
| 165 | A | A | -0.3106 | |
| 166 | L | A | -0.1221 | |
| 167 | T | A | -0.2123 | |
| 168 | S | A | -0.2074 | |
| 169 | G | A | -0.2612 | |
| 170 | V | A | 0.1389 | |
| 171 | H | A | -0.3171 | |
| 172 | T | A | 0.0241 | |
| 173 | F | A | 0.0000 | |
| 174 | P | A | -0.4917 | |
| 175 | A | A | 0.1180 | |
| 176 | V | A | 0.3211 | |
| 177 | L | A | 0.9809 | |
| 178 | Q | A | 0.2202 | |
| 179 | S | A | -0.0752 | |
| 180 | S | A | -0.2060 | |
| 181 | G | A | 0.0043 | |
| 182 | L | A | -0.0274 | |
| 183 | Y | A | 0.2801 | |
| 184 | S | A | 0.0000 | |
| 185 | L | A | 0.0000 | |
| 186 | S | A | 0.0000 | |
| 187 | S | A | 0.0000 | |
| 188 | V | A | 0.0000 | |
| 189 | V | A | 0.0000 | |
| 190 | T | A | -0.1252 | |
| 191 | V | A | 0.0000 | |
| 192 | P | A | -0.5699 | |
| 193 | S | A | -1.0149 | |
| 194 | S | A | -0.5627 | |
| 195 | S | A | -0.7019 | |
| 196 | L | A | -1.1602 | |
| 197 | G | A | -1.3033 | |
| 198 | T | A | -1.1274 | |
| 199 | K | A | -2.0582 | |
| 200 | T | A | -1.7738 | |
| 201 | Y | A | 0.0000 | |
| 202 | T | A | 0.0000 | |
| 203 | C | A | 0.0000 | |
| 204 | N | A | -1.8262 | |
| 205 | V | A | 0.0000 | |
| 206 | D | A | -2.4208 | |
| 207 | H | A | 0.0000 | |
| 208 | K | A | -2.8960 | |
| 209 | P | A | -1.7230 | |
| 210 | S | A | -1.9966 | |
| 211 | N | A | -2.7692 | |
| 212 | T | A | -2.2855 | |
| 213 | K | A | -2.8703 | |
| 214 | V | A | -1.8663 | |
| 215 | D | A | -2.8316 | |
| 216 | K | A | -2.2972 | |
| 217 | R | A | -2.9504 | |
| 218 | V | A | 0.0000 | |
| 219 | E | A | -2.5917 | |
| 220 | S | A | -1.6483 | |
| 1 | D | B | -2.5977 | |
| 2 | I | B | 0.0000 | |
| 3 | Q | B | -2.1042 | |
| 4 | M | B | 0.0000 | |
| 5 | T | B | -1.2588 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.6406 | |
| 8 | P | B | -0.6996 | |
| 9 | S | B | -1.0266 | |
| 10 | S | B | -0.9681 | |
| 11 | L | B | -0.6063 | |
| 12 | S | B | -0.8328 | |
| 13 | A | B | 0.0000 | |
| 14 | S | B | -1.0718 | |
| 15 | V | B | -0.4582 | |
| 16 | G | B | -1.2586 | |
| 17 | D | B | -2.2997 | |
| 18 | R | B | -2.6057 | |
| 19 | V | B | 0.0000 | |
| 20 | T | B | -0.4849 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.7610 | |
| 23 | C | B | 0.0000 | |
| 24 | Q | B | -2.4039 | |
| 25 | A | B | 0.0000 | |
| 26 | S | B | -2.2704 | |
| 27 | Q | B | -2.9335 | |
| 28 | D | B | -2.8352 | |
| 29 | I | B | 0.0000 | |
| 30 | G | B | -0.7862 | |
| 31 | I | B | 0.1437 | |
| 32 | S | B | 0.0510 | |
| 33 | L | B | 0.0000 | |
| 34 | S | B | 0.0000 | |
| 35 | W | B | 0.0000 | |
| 36 | Y | B | 0.0000 | |
| 37 | Q | B | 0.0000 | |
| 38 | Q | B | 0.0000 | |
| 39 | K | B | -1.7371 | |
| 40 | P | B | -1.6559 | |
| 41 | G | B | -1.7106 | |
| 42 | K | B | -2.6305 | |
| 43 | A | B | -1.6218 | |
| 44 | P | B | 0.0000 | |
| 45 | K | B | -1.4788 | |
| 46 | L | B | -0.4513 | |
| 47 | L | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | Y | B | 0.2553 | |
| 50 | N | B | 0.0200 | |
| 51 | A | B | 0.0000 | |
| 52 | N | B | -1.3393 | |
| 53 | N | B | -1.0349 | |
| 54 | L | B | -0.4815 | |
| 55 | A | B | -1.0025 | |
| 56 | D | B | -1.8700 | |
| 57 | G | B | -1.2083 | |
| 58 | V | B | -0.7601 | |
| 59 | P | B | -0.4970 | |
| 60 | S | B | -0.3719 | |
| 61 | R | B | -0.8102 | |
| 62 | F | B | 0.0000 | |
| 63 | S | B | -0.6376 | |
| 64 | G | B | -0.8078 | |
| 65 | S | B | -0.9711 | |
| 66 | G | B | -0.9471 | |
| 67 | S | B | -0.9254 | |
| 68 | G | B | -1.5562 | |
| 69 | T | B | -2.1804 | |
| 70 | D | B | -2.5446 | |
| 71 | F | B | 0.0000 | |
| 72 | T | B | -0.8841 | |
| 73 | L | B | 0.0000 | |
| 74 | T | B | -0.5879 | |
| 75 | I | B | 0.0000 | |
| 76 | S | B | -1.4760 | |
| 77 | S | B | -1.5507 | |
| 78 | L | B | 0.0000 | |
| 79 | Q | B | -1.1501 | |
| 80 | P | B | -1.2975 | |
| 81 | E | B | -1.8619 | |
| 82 | D | B | 0.0000 | |
| 83 | F | B | -0.7847 | |
| 84 | A | B | 0.0000 | |
| 85 | T | B | -0.9563 | |
| 86 | Y | B | 0.0000 | |
| 87 | Y | B | 0.0000 | |
| 88 | C | B | 0.0000 | |
| 89 | L | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | H | B | 0.0000 | |
| 92 | N | B | -0.7167 | |
| 93 | S | B | -0.7034 | |
| 94 | A | B | -0.3496 | |
| 95 | P | B | -0.6465 | |
| 96 | Y | B | 0.0000 | |
| 97 | T | B | -0.9281 | |
| 98 | F | B | 0.0000 | |
| 99 | G | B | 0.0000 | |
| 100 | Q | B | -1.8289 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | K | B | -1.9560 | |
| 104 | L | B | 0.0000 | |
| 105 | E | B | -1.1109 | |
| 106 | I | B | -0.6969 | |
| 107 | K | B | -1.2369 | |
| 108 | R | B | -0.9295 | |
| 109 | T | B | -0.0818 | |
| 110 | V | B | 0.4793 | |
| 111 | A | B | 0.0788 | |
| 112 | A | B | -0.0507 | |
| 113 | P | B | 0.0000 | |
| 114 | S | B | -0.0569 | |
| 115 | V | B | 0.0318 | |
| 116 | F | B | 0.0396 | |
| 117 | I | B | 0.0000 | |
| 118 | F | B | 0.0000 | |
| 119 | P | B | 0.0000 | |
| 120 | P | B | -0.6944 | |
| 121 | S | B | -1.5396 | |
| 122 | D | B | -2.8816 | |
| 123 | E | B | -3.0411 | |
| 124 | Q | B | 0.0000 | |
| 125 | L | B | -2.2385 | |
| 126 | K | B | -2.8359 | |
| 127 | S | B | -1.7426 | |
| 128 | G | B | -1.2171 | |
| 129 | T | B | -0.8304 | |
| 130 | A | B | 0.0000 | |
| 131 | S | B | 0.0000 | |
| 132 | V | B | 0.0000 | |
| 133 | V | B | 0.0000 | |
| 134 | C | B | 0.0000 | |
| 135 | L | B | 0.0000 | |
| 136 | L | B | 0.0000 | |
| 137 | N | B | 0.0000 | |
| 138 | N | B | -0.7999 | |
| 139 | F | B | 0.0000 | |
| 140 | Y | B | 0.0000 | |
| 141 | P | B | -1.4098 | |
| 142 | R | B | -2.3516 | |
| 143 | E | B | -2.8944 | |
| 144 | A | B | -2.1617 | |
| 145 | K | B | -2.3336 | |
| 146 | V | B | -1.0443 | |
| 147 | Q | B | -0.4753 | |
| 148 | W | B | 0.0000 | |
| 149 | K | B | -0.4491 | |
| 150 | V | B | 0.0000 | |
| 151 | D | B | -1.7373 | |
| 152 | N | B | -1.4278 | |
| 153 | A | B | -0.1939 | |
| 154 | L | B | 0.8162 | |
| 155 | Q | B | -0.0459 | |
| 156 | S | B | -0.3762 | |
| 157 | G | B | -0.8805 | |
| 158 | N | B | -0.7772 | |
| 159 | S | B | -1.1130 | |
| 160 | Q | B | -1.4626 | |
| 161 | E | B | -1.9942 | |
| 162 | S | B | -0.8810 | |
| 163 | V | B | -0.7737 | |
| 164 | T | B | 0.0000 | |
| 165 | E | B | -2.2304 | |
| 166 | Q | B | -1.8626 | |
| 167 | D | B | -1.9531 | |
| 168 | S | B | -1.9989 | |
| 169 | K | B | -2.3273 | |
| 170 | D | B | -1.8250 | |
| 171 | S | B | 0.0000 | |
| 172 | T | B | 0.0000 | |
| 173 | Y | B | 0.0000 | |
| 174 | S | B | 0.0000 | |
| 175 | L | B | 0.0000 | |
| 176 | S | B | 0.0000 | |
| 177 | S | B | 0.0000 | |
| 178 | T | B | -0.6724 | |
| 179 | L | B | 0.0000 | |
| 180 | T | B | -0.4224 | |
| 181 | L | B | -0.6072 | |
| 182 | S | B | -0.9726 | |
| 183 | K | B | -1.8971 | |
| 184 | A | B | -1.7254 | |
| 185 | D | B | -2.3828 | |
| 186 | Y | B | 0.0000 | |
| 187 | E | B | -3.0308 | |
| 188 | K | B | -3.3492 | |
| 189 | H | B | -2.7613 | |
| 190 | K | B | -2.8302 | |
| 191 | V | B | -1.2102 | |
| 192 | Y | B | 0.0000 | |
| 193 | A | B | -0.7509 | |
| 194 | C | B | 0.0000 | |
| 195 | E | B | -0.7604 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -1.2089 | |
| 198 | H | B | 0.0000 | |
| 199 | Q | B | -1.6480 | |
| 200 | G | B | -0.3767 | |
| 201 | L | B | -0.2085 | |
| 202 | S | B | -0.4562 | |
| 203 | S | B | -0.4397 | |
| 204 | P | B | -0.5684 | |
| 205 | V | B | -0.0405 | |
| 206 | T | B | -0.4555 | |
| 207 | K | B | -0.7118 | |
| 208 | S | B | -0.6176 | |
| 209 | F | B | 0.0000 | |
| 210 | N | B | -1.6254 | |
| 211 | R | B | -2.1211 | |
| 212 | G | B | -1.8987 | |
| 213 | E | B | -2.1383 | |
| 214 | C | B | -0.7371 |
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 | -0.7472 | 2.1012 | View | CSV | PDB |
| 4.5 | -0.7998 | 2.0631 | View | CSV | PDB |
| 5.0 | -0.8619 | 2.0195 | View | CSV | PDB |
| 5.5 | -0.9224 | 1.9738 | View | CSV | PDB |
| 6.0 | -0.9689 | 1.9275 | View | CSV | PDB |
| 6.5 | -0.9915 | 1.9275 | View | CSV | PDB |
| 7.0 | -0.9896 | 1.9273 | View | CSV | PDB |
| 7.5 | -0.9708 | 1.927 | View | CSV | PDB |
| 8.0 | -0.9425 | 1.9258 | View | CSV | PDB |
| 8.5 | -0.9068 | 1.9223 | View | CSV | PDB |
| 9.0 | -0.8635 | 1.9111 | 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