| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGKTYLEWYLQKPGQSPQLLIYKLSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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 (00:04:11)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/b665271bae4fd96/tmp/folded.pdb (00:04:11)
[INFO] Main: Simulation completed successfully. (00:07:04)
|
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 | -1.3608 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7347 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2787 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | 0.0104 | |
| 8 | P | A | 0.4630 | |
| 9 | L | A | 1.2364 | |
| 10 | S | A | 0.0937 | |
| 11 | L | A | -0.2999 | |
| 12 | S | A | -1.1830 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6196 | |
| 15 | P | A | -1.7934 | |
| 16 | G | A | -1.6525 | |
| 17 | Q | A | -1.8234 | |
| 18 | P | A | -1.9466 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8446 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8929 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2741 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -0.9807 | |
| 27 | Q | A | -1.5595 | |
| 28 | S | A | -0.9177 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.0915 | |
| 31 | H | A | -0.4863 | |
| 32 | S | A | -0.6545 | |
| 33 | N | A | -1.1130 | |
| 34 | G | A | -0.9311 | |
| 35 | K | A | -0.8982 | |
| 36 | T | A | -0.3331 | |
| 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 | 0.0000 | |
| 44 | K | A | -1.5227 | |
| 45 | P | A | -1.0446 | |
| 46 | G | A | -1.4807 | |
| 47 | Q | A | -2.0409 | |
| 48 | S | A | -1.2020 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -0.9834 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.3333 | |
| 55 | K | A | -0.5399 | |
| 56 | L | A | -0.5215 | |
| 57 | S | A | -0.8210 | |
| 58 | N | A | -1.1231 | |
| 59 | R | A | -1.7194 | |
| 60 | A | A | 0.0000 | |
| 61 | S | A | -0.6759 | |
| 62 | G | A | -1.0275 | |
| 63 | V | A | -1.0513 | |
| 64 | P | A | -1.3113 | |
| 65 | D | A | -2.4172 | |
| 66 | R | A | -2.2868 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.5164 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.9206 | |
| 71 | G | A | -1.0128 | |
| 72 | S | A | -0.7393 | |
| 73 | G | A | -0.7147 | |
| 74 | T | A | -1.4743 | |
| 75 | D | A | -2.0780 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1242 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.0641 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3089 | |
| 82 | R | A | -3.1402 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.4118 | |
| 85 | A | A | -1.8527 | |
| 86 | E | A | -2.3955 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -1.1294 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0346 | |
| 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 | H | A | -0.9594 | |
| 99 | V | A | -0.6496 | |
| 100 | P | A | 0.0000 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | -0.0035 | |
| 103 | F | A | 0.3063 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0152 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.5694 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.8595 | |
| 111 | I | A | -1.9767 | |
| 112 | K | A | -2.4343 | |
| 113 | G | A | -1.8108 | |
| 114 | G | A | -1.6983 | |
| 115 | G | A | -1.3238 | |
| 116 | G | A | -1.7153 | |
| 117 | S | A | -1.2492 | |
| 118 | G | A | -1.6278 | |
| 119 | G | A | -1.6247 | |
| 120 | G | A | -1.7696 | |
| 121 | G | A | -1.6708 | |
| 122 | S | A | -1.0811 | |
| 123 | G | A | -1.3330 | |
| 124 | G | A | -1.2251 | |
| 125 | G | A | -1.1869 | |
| 126 | G | A | -1.0036 | |
| 127 | S | A | -0.8827 | |
| 128 | V | A | -0.7708 | |
| 129 | Q | A | -1.2439 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | 0.2458 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.6056 | |
| 134 | G | A | -0.6665 | |
| 135 | A | A | -0.1586 | |
| 136 | E | A | -0.3483 | |
| 137 | V | A | 0.8024 | |
| 138 | K | A | -0.9186 | |
| 139 | K | A | -2.0714 | |
| 140 | P | A | -2.0501 | |
| 141 | G | A | -1.4537 | |
| 142 | A | A | -1.1567 | |
| 143 | S | A | -1.2781 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.9138 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.6176 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -0.9397 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.6603 | |
| 152 | G | A | -0.7438 | |
| 153 | Y | A | -0.2258 | |
| 154 | T | A | -0.0986 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0386 | |
| 157 | D | A | -0.0737 | |
| 158 | Y | A | 0.0895 | |
| 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 | -0.5814 | |
| 166 | A | A | -1.0143 | |
| 167 | P | A | -1.0248 | |
| 168 | G | A | -1.2140 | |
| 169 | Q | A | -1.6850 | |
| 170 | G | A | -0.9590 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.5708 | |
| 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 | 0.3081 | |
| 181 | Y | A | 0.5304 | |
| 182 | G | A | -0.0739 | |
| 183 | S | A | -0.1746 | |
| 184 | T | A | -0.1669 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.3018 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | 0.0669 | |
| 189 | K | A | -1.3829 | |
| 190 | F | A | 0.0000 | |
| 191 | Q | A | -1.4246 | |
| 192 | G | A | -1.2560 | |
| 193 | R | A | -1.2658 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.8159 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.6141 | |
| 198 | R | A | -1.0428 | |
| 199 | D | A | -1.2114 | |
| 200 | T | A | -0.6662 | |
| 201 | S | A | -0.5533 | |
| 202 | T | A | -0.6610 | |
| 203 | S | A | -0.7419 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8010 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.4882 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.0728 | |
| 211 | S | A | -1.1056 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.5989 | |
| 214 | S | A | -2.1623 | |
| 215 | E | A | -2.4109 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8415 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.2190 | |
| 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 | 0.0108 | |
| 228 | Y | A | 0.0470 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.1821 | |
| 232 | Y | A | -0.1949 | |
| 233 | W | A | -0.3112 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.2748 | |
| 236 | G | A | -0.5520 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0348 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3230 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.0265 | |
| 243 | S | A | -1.1256 | |
| 1 | A | B | -0.4007 | |
| 2 | Q | B | -1.4726 | |
| 3 | E | B | -2.3131 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.9247 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.5017 | |
| 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 | -1.0535 | |
| 15 | V | B | -0.7018 | |
| 16 | G | B | -1.2566 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.8435 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.8856 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8767 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7156 | |
| 25 | T | B | -1.8034 | |
| 26 | S | B | -1.6482 | |
| 27 | G | B | -1.2450 | |
| 28 | G | B | -1.4573 | |
| 29 | L | B | -1.7186 | |
| 30 | R | B | -2.4596 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.0988 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | 0.0000 | |
| 36 | Q | B | -0.8088 | |
| 37 | L | B | -0.6732 | |
| 38 | G | B | -1.1975 | |
| 39 | P | B | -1.2584 | |
| 40 | Q | B | -1.6830 | |
| 41 | P | B | -1.2950 | |
| 42 | Q | B | -1.3707 | |
| 43 | D | B | -0.9604 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.3978 | |
| 47 | Y | B | 0.1112 | |
| 48 | E | B | -0.7808 | |
| 49 | D | B | -1.8436 | |
| 50 | G | B | -0.3446 | |
| 51 | V | B | 1.3737 | |
| 52 | V | B | 1.9935 | |
| 53 | P | B | 0.7477 | |
| 54 | T | B | 0.0041 | |
| 55 | T | B | -1.3073 | |
| 56 | D | B | -2.0574 | |
| 57 | R | B | -2.9704 | |
| 58 | R | B | -2.2296 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.1426 | |
| 61 | G | B | -2.2333 | |
| 62 | R | B | -2.1129 | |
| 63 | I | B | -1.5641 | |
| 64 | D | B | -1.9386 | |
| 65 | F | B | -0.6500 | |
| 66 | S | B | -0.9170 | |
| 67 | G | B | -1.0995 | |
| 68 | S | B | -1.4571 | |
| 69 | Q | B | 0.0000 | |
| 70 | D | B | -2.3045 | |
| 71 | N | B | -2.2006 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0225 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9131 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7096 | |
| 78 | R | B | -2.2140 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.0481 | |
| 81 | L | B | 0.0363 | |
| 82 | S | B | -0.1394 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0957 | |
| 85 | G | B | -0.1892 | |
| 86 | T | B | -0.1463 | |
| 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 | -0.4213 | |
| 93 | T | B | -0.9379 | |
| 94 | E | B | -1.3279 | |
| 95 | V | B | 0.7188 | |
| 96 | N | B | 0.0616 | |
| 97 | V | B | -0.1282 | |
| 98 | Y | B | -0.3873 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.6844 | |
| 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 | -3.0535 | |
| 109 | E | B | -3.3397 | |
| 110 | Q | B | -2.9590 | |
| 111 | S | B | -2.0109 | |
| 112 | Q | B | -2.3192 | |
| 113 | G | B | -1.4894 | |
| 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 | 0.0000 | |
| 120 | A | B | -0.3386 | |
| 121 | P | B | -0.7100 | |
| 122 | P | B | -1.1447 | |
| 123 | R | B | -1.9781 | |
| 124 | A | B | -0.9761 | |
| 125 | S | B | -0.7231 | |
| 126 | A | B | -0.3199 | |
| 127 | L | B | -0.1310 | |
| 128 | P | B | -0.2022 | |
| 129 | A | B | 0.0386 | |
| 130 | P | B | -0.4313 | |
| 131 | P | B | -0.5012 | |
| 132 | T | B | -0.4720 | |
| 133 | G | B | -0.4077 | |
| 134 | S | B | -0.0889 | |
| 135 | A | B | 0.2064 | |
| 136 | L | B | 0.8140 | |
| 137 | P | B | -0.6728 | |
| 138 | D | B | -1.9893 | |
| 139 | P | B | -1.5423 | |
| 140 | Q | B | -1.9474 | |
| 141 | T | B | -1.0143 | |
| 142 | A | B | -0.2049 | |
| 143 | S | B | 0.0176 | |
| 144 | A | B | 0.3692 | |
| 145 | L | B | 0.9051 | |
| 146 | P | B | -0.4991 | |
| 147 | D | B | -1.6896 | |
| 148 | P | B | -1.0477 | |
| 149 | P | B | -0.8781 | |
| 150 | A | B | -0.4362 | |
| 151 | A | B | 0.1208 | |
| 152 | S | B | 0.2034 | |
| 153 | A | B | 0.6643 | |
| 154 | L | B | 1.4053 | |
| 155 | P | B | 0.4753 |
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 | -0.3948 | 3.7347 | View | CSV | PDB |
| 4.5 | -0.4336 | 3.573 | View | CSV | PDB |
| 5.0 | -0.4807 | 3.3803 | View | CSV | PDB |
| 5.5 | -0.5288 | 3.175 | View | CSV | PDB |
| 6.0 | -0.5707 | 2.9652 | View | CSV | PDB |
| 6.5 | -0.6012 | 2.8763 | View | CSV | PDB |
| 7.0 | -0.6184 | 2.8763 | View | CSV | PDB |
| 7.5 | -0.6256 | 2.8763 | View | CSV | PDB |
| 8.0 | -0.6264 | 2.8763 | View | CSV | PDB |
| 8.5 | -0.6216 | 2.8763 | View | CSV | PDB |
| 9.0 | -0.6109 | 2.8763 | 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