| Chain sequence(s) |
A: EIVLTQSPATLSLSPGERATLSCRVSQNVSSNLAWYQQKPGQAPRLLIYDTSNRATGIPARFSGSGSGRDFTLTISSLEPEDFAVYYCQQRRNWPLTFGGGTKVEIKGGGGSGGGGSGGGGSEVQLLESGGGLVQPGGSLRLSCAASGFTFSRYAMSWVRQAPGKGLEWVSSISASGATTYYADPVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDQDFDILTGYLNWFDPWGQGTLVTVSS
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] (00:00:03)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:03)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:03)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:03)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:05)
[INFO] FoldX: Starting FoldX energy minimization (00:00:05)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:06:31)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/36da711265db1a2/tmp/folded.pdb (00:06:31)
[INFO] Main: Simulation completed successfully. (00:13:31)
|
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 | A | -1.5859 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7378 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6288 | |
| 6 | Q | A | -0.6610 | |
| 7 | S | A | -0.7403 | |
| 8 | P | A | -0.3414 | |
| 9 | A | A | -0.3660 | |
| 10 | T | A | -0.4359 | |
| 11 | L | A | -0.3115 | |
| 12 | S | A | -0.7778 | |
| 13 | L | A | -1.1164 | |
| 14 | S | A | -1.4827 | |
| 15 | P | A | -1.7523 | |
| 16 | G | A | -1.9083 | |
| 17 | E | A | -2.4687 | |
| 18 | R | A | -2.7740 | |
| 19 | A | A | 0.0000 | |
| 20 | T | A | -0.6490 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.9599 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -3.0161 | |
| 25 | V | A | 0.0000 | |
| 26 | S | A | -1.5456 | |
| 27 | Q | A | -2.7140 | |
| 28 | N | A | -3.0302 | |
| 29 | V | A | 0.0000 | |
| 30 | S | A | -1.5259 | |
| 31 | S | A | -0.9628 | |
| 32 | N | A | -0.7656 | |
| 33 | L | 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 | -0.9584 | |
| 40 | P | A | -0.7571 | |
| 41 | G | A | -0.9976 | |
| 42 | Q | A | -1.2681 | |
| 43 | A | A | -0.9909 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.2351 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | Y | A | 0.0000 | |
| 50 | D | A | -0.7864 | |
| 51 | T | A | 0.0000 | |
| 52 | S | A | -1.0887 | |
| 53 | N | A | -1.5003 | |
| 54 | R | A | -1.7380 | |
| 55 | A | A | 0.0000 | |
| 56 | T | A | -0.6755 | |
| 57 | G | A | -0.7734 | |
| 58 | I | A | 0.0000 | |
| 59 | P | A | -0.5079 | |
| 60 | A | A | -0.4602 | |
| 61 | R | A | -0.8575 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.7712 | |
| 64 | G | A | -0.7439 | |
| 65 | S | A | -0.8187 | |
| 66 | G | A | -1.4399 | |
| 67 | S | A | -1.5990 | |
| 68 | G | A | -2.4507 | |
| 69 | R | A | -3.8124 | |
| 70 | D | A | -3.3451 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8479 | |
| 73 | L | A | 0.0000 | |
| 74 | T | A | -0.6513 | |
| 75 | I | A | 0.0000 | |
| 76 | S | A | -1.5657 | |
| 77 | S | A | -1.9183 | |
| 78 | L | A | 0.0000 | |
| 79 | E | A | -2.4036 | |
| 80 | P | A | -1.7536 | |
| 81 | E | A | -2.1917 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | -0.7704 | |
| 84 | A | A | 0.0000 | |
| 85 | V | A | -0.2301 | |
| 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 | R | A | -0.6372 | |
| 92 | R | A | -1.2245 | |
| 93 | N | A | -1.3451 | |
| 94 | W | A | -0.9353 | |
| 95 | P | A | -0.9074 | |
| 96 | L | A | 0.0000 | |
| 97 | T | A | 0.0000 | |
| 98 | F | A | 0.1478 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7757 | |
| 101 | G | A | -0.7225 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.9215 | |
| 104 | V | A | 0.0000 | |
| 105 | E | A | -1.0484 | |
| 106 | I | A | -0.9849 | |
| 107 | K | A | -1.9389 | |
| 108 | G | A | -1.5189 | |
| 109 | G | A | -1.4216 | |
| 110 | G | A | -1.2686 | |
| 111 | G | A | -1.3193 | |
| 112 | S | A | -0.9358 | |
| 113 | G | A | -1.4243 | |
| 114 | G | A | -1.3349 | |
| 115 | G | A | -1.4660 | |
| 116 | G | A | -1.3694 | |
| 117 | S | A | -1.2410 | |
| 118 | G | A | -1.3459 | |
| 119 | G | A | -1.3851 | |
| 120 | G | A | -1.4287 | |
| 121 | G | A | -1.6234 | |
| 122 | S | A | -1.6774 | |
| 123 | E | A | -2.4114 | |
| 124 | V | A | -1.5699 | |
| 125 | Q | A | -1.4955 | |
| 126 | L | A | 0.0000 | |
| 127 | L | A | 0.7978 | |
| 128 | E | A | 0.1446 | |
| 129 | S | A | -0.3393 | |
| 130 | G | A | -0.7756 | |
| 131 | G | A | 0.1218 | |
| 132 | G | A | 0.6976 | |
| 133 | L | A | 1.4349 | |
| 134 | V | A | -0.0258 | |
| 135 | Q | A | -1.3359 | |
| 136 | P | A | -1.5556 | |
| 137 | G | A | -1.3680 | |
| 138 | G | A | -0.9527 | |
| 139 | S | A | -1.2931 | |
| 140 | L | A | -0.9724 | |
| 141 | R | A | -2.2470 | |
| 142 | L | A | 0.0000 | |
| 143 | S | A | -0.4914 | |
| 144 | C | A | 0.0000 | |
| 145 | A | A | -0.1868 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -0.8560 | |
| 148 | G | A | -1.2885 | |
| 149 | F | A | -0.9202 | |
| 150 | T | A | -0.6668 | |
| 151 | F | A | 0.0000 | |
| 152 | S | A | -1.5672 | |
| 153 | R | A | -2.2520 | |
| 154 | Y | A | -1.2489 | |
| 155 | A | A | -0.5921 | |
| 156 | M | A | 0.0000 | |
| 157 | S | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | R | A | 0.0000 | |
| 161 | Q | A | -0.6496 | |
| 162 | A | A | -1.0461 | |
| 163 | P | A | -0.8288 | |
| 164 | G | A | -1.4484 | |
| 165 | K | A | -2.2728 | |
| 166 | G | A | -1.3669 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -0.9847 | |
| 169 | W | A | 0.0000 | |
| 170 | V | A | 0.0000 | |
| 171 | S | A | 0.0000 | |
| 172 | S | A | 0.0725 | |
| 173 | I | A | 0.0000 | |
| 174 | S | A | -0.4005 | |
| 175 | A | A | 0.0000 | |
| 176 | S | A | -0.7912 | |
| 177 | G | A | -0.3838 | |
| 178 | A | A | -0.0913 | |
| 179 | T | A | -0.0087 | |
| 180 | T | A | 0.1146 | |
| 181 | Y | A | -0.0838 | |
| 182 | Y | A | -0.7551 | |
| 183 | A | A | 0.0000 | |
| 184 | D | A | -2.4477 | |
| 185 | P | A | -1.7489 | |
| 186 | V | A | 0.0000 | |
| 187 | K | A | -2.5577 | |
| 188 | G | A | -1.7003 | |
| 189 | R | A | -1.4601 | |
| 190 | F | A | 0.0000 | |
| 191 | T | A | -0.8966 | |
| 192 | I | A | 0.0000 | |
| 193 | S | A | -0.4413 | |
| 194 | R | A | -0.9442 | |
| 195 | D | A | -1.5213 | |
| 196 | N | A | -1.8438 | |
| 197 | S | A | -1.5699 | |
| 198 | K | A | -2.3597 | |
| 199 | N | A | -1.7286 | |
| 200 | T | A | -1.0081 | |
| 201 | L | A | 0.0000 | |
| 202 | Y | A | -0.6561 | |
| 203 | L | A | 0.0000 | |
| 204 | Q | A | -1.5675 | |
| 205 | M | A | 0.0000 | |
| 206 | N | A | -1.3807 | |
| 207 | S | A | -1.1853 | |
| 208 | L | A | 0.0000 | |
| 209 | R | A | -2.1108 | |
| 210 | A | A | -1.6322 | |
| 211 | E | A | -2.1821 | |
| 212 | D | A | 0.0000 | |
| 213 | T | A | -0.3349 | |
| 214 | A | A | 0.0000 | |
| 215 | V | A | 0.7374 | |
| 216 | Y | A | 0.0000 | |
| 217 | Y | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | K | A | 0.0000 | |
| 221 | D | A | 0.0000 | |
| 222 | Q | A | -1.2645 | |
| 223 | D | A | -2.2655 | |
| 224 | F | A | 0.0000 | |
| 225 | D | A | -1.5717 | |
| 226 | I | A | 0.3432 | |
| 227 | L | A | 1.3352 | |
| 228 | T | A | 0.6215 | |
| 229 | G | A | 0.0000 | |
| 230 | Y | A | -0.0508 | |
| 231 | L | A | -0.2930 | |
| 232 | N | A | -0.5709 | |
| 233 | W | A | 0.0000 | |
| 234 | F | A | 0.0000 | |
| 235 | D | A | -0.8761 | |
| 236 | P | A | -0.9486 | |
| 237 | W | A | 0.0000 | |
| 238 | G | A | 0.0000 | |
| 239 | Q | A | -1.1855 | |
| 240 | G | A | -0.1610 | |
| 241 | T | A | 0.5003 | |
| 242 | L | A | 1.6564 | |
| 243 | V | A | 0.0000 | |
| 244 | T | A | 0.3617 | |
| 245 | V | A | 0.0000 | |
| 246 | S | A | -0.6151 | |
| 247 | S | A | -0.4636 | |
| 1 | A | B | -0.4237 | |
| 2 | Q | B | -1.3991 | |
| 3 | E | B | -2.1472 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.9466 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.9308 | |
| 8 | P | B | -1.0701 | |
| 9 | H | B | -1.3421 | |
| 10 | C | B | -0.6387 | |
| 11 | T | B | -0.5936 | |
| 12 | T | B | -0.0154 | |
| 13 | V | B | -0.1772 | |
| 14 | P | B | -1.0310 | |
| 15 | V | B | -0.8168 | |
| 16 | G | B | -0.9875 | |
| 17 | A | B | -0.6334 | |
| 18 | S | B | -1.0201 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -1.3792 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -1.0707 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.7740 | |
| 25 | T | B | -1.6765 | |
| 26 | S | B | -1.6208 | |
| 27 | G | B | -1.4151 | |
| 28 | G | B | -1.4547 | |
| 29 | L | B | -1.8924 | |
| 30 | R | B | -2.5449 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1295 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.5709 | |
| 36 | Q | B | -0.6891 | |
| 37 | L | B | -0.1105 | |
| 38 | G | B | -0.8896 | |
| 39 | P | B | -1.0322 | |
| 40 | Q | B | -1.5298 | |
| 41 | P | B | -1.1949 | |
| 42 | Q | B | -1.4020 | |
| 43 | D | B | -1.3059 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.0360 | |
| 47 | Y | B | -0.4399 | |
| 48 | E | B | -1.4730 | |
| 49 | D | B | -2.4080 | |
| 50 | G | B | -1.4059 | |
| 51 | V | B | -0.8279 | |
| 52 | V | B | 0.0000 | |
| 53 | P | B | -0.3402 | |
| 54 | T | B | -0.2347 | |
| 55 | T | B | -0.6516 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -1.5073 | |
| 58 | R | B | -1.5475 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -1.8007 | |
| 61 | G | B | -1.7607 | |
| 62 | R | B | -1.6690 | |
| 63 | I | B | 0.0000 | |
| 64 | D | B | 0.0000 | |
| 65 | F | B | -0.1816 | |
| 66 | S | B | -0.7196 | |
| 67 | G | B | -1.1721 | |
| 68 | S | B | -1.5117 | |
| 69 | Q | B | -1.8522 | |
| 70 | D | B | -2.2440 | |
| 71 | N | B | -2.1816 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -0.9728 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.6282 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.5465 | |
| 78 | R | B | -2.1469 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -1.0139 | |
| 81 | L | B | 0.0929 | |
| 82 | S | B | -0.1252 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | 0.1873 | |
| 85 | G | B | 0.1907 | |
| 86 | T | B | 0.1298 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0843 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.5241 | |
| 93 | T | B | -1.1737 | |
| 94 | E | B | -1.4916 | |
| 95 | V | B | 0.4760 | |
| 96 | N | B | -0.3892 | |
| 97 | V | B | -0.0022 | |
| 98 | Y | B | 0.4912 | |
| 99 | G | B | -0.4113 | |
| 100 | S | B | -0.4033 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.4088 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.6627 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | -1.2638 | |
| 108 | E | B | -2.7898 | |
| 109 | E | B | -3.4192 | |
| 110 | Q | B | -2.8109 | |
| 111 | S | B | -2.3753 | |
| 112 | Q | B | -2.0850 | |
| 113 | G | B | -1.9148 | |
| 114 | W | B | -1.7516 | |
| 115 | H | B | -1.9840 | |
| 116 | R | B | -2.5626 | |
| 117 | C | B | -1.5645 | |
| 118 | S | B | -1.8825 | |
| 119 | D | B | -2.4080 | |
| 120 | A | B | -1.5310 | |
| 121 | P | B | -1.5548 | |
| 122 | P | B | -1.5788 | |
| 123 | R | B | -2.0631 | |
| 124 | A | B | -0.7815 | |
| 125 | S | B | -0.3749 | |
| 126 | A | B | 0.3571 | |
| 127 | L | B | 1.3692 | |
| 128 | P | B | 0.3933 | |
| 129 | A | B | 0.1644 | |
| 130 | P | B | -0.2478 | |
| 131 | P | B | -0.6185 | |
| 132 | T | B | -0.5338 | |
| 133 | G | B | -0.4455 | |
| 134 | S | B | -0.0730 | |
| 135 | A | B | 0.2076 | |
| 136 | L | B | 0.8004 | |
| 137 | P | B | -0.6565 | |
| 138 | D | B | -1.9715 | |
| 139 | P | B | -1.5312 | |
| 140 | Q | B | -1.9176 | |
| 141 | T | B | -1.0067 | |
| 142 | A | B | -0.2043 | |
| 143 | S | B | 0.0307 | |
| 144 | A | B | 0.3794 | |
| 145 | L | B | 0.9226 | |
| 146 | P | B | -0.4987 | |
| 147 | D | B | -1.7022 | |
| 148 | P | B | -1.0537 | |
| 149 | P | B | -0.8662 | |
| 150 | A | B | -0.4170 | |
| 151 | A | B | 0.1109 | |
| 152 | S | B | 0.2081 | |
| 153 | A | B | 0.6636 | |
| 154 | L | B | 1.4049 | |
| 155 | P | B | 0.4744 |
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 | -0.421 | 3.8767 | View | CSV | PDB |
| 4.5 | -0.4664 | 3.8767 | View | CSV | PDB |
| 5.0 | -0.521 | 3.8767 | View | CSV | PDB |
| 5.5 | -0.5778 | 3.8767 | View | CSV | PDB |
| 6.0 | -0.6293 | 3.8767 | View | CSV | PDB |
| 6.5 | -0.6705 | 3.8767 | View | CSV | PDB |
| 7.0 | -0.7 | 3.8767 | View | CSV | PDB |
| 7.5 | -0.7203 | 3.8767 | View | CSV | PDB |
| 8.0 | -0.7341 | 3.8767 | View | CSV | PDB |
| 8.5 | -0.7413 | 3.8767 | View | CSV | PDB |
| 9.0 | -0.7405 | 3.8767 | 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