| Chain sequence(s) |
A: QFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDGRPDGVPDRFSGSIDRSSNSALLTIKNVQSEDEADYFCHSHSGGINVFGGGTSLTVLGGGGSGGGGSGGGGSEVPLVESGGGLVQPGRSLKLSCAASGFTFSNYLMAWVRHPPKKGLEWVATISSSGSRIYYPDSVKGRFTISRDNARSSLYLQMSSLRSEDTATYYCARHLRDGGFDYWGQGVMVTVSS
B: GNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRAR input PDB |
| Selected Chain(s) | A,B |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage |
A: QFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDGRPDGVPDRFSGSIDRSSNSALLTIKNVQSEDEADYFCHSHSGGINVFGGGTSLTVLGGGG SGGGGSGGGGSE VPLVESGGGLVQPGRSLKLSCAASGFTFSNYLMAWVRHPPKKGLEWVATISSSGSRIYYPDSVKGRFTISRDNARSSLYLQMSSLRSEDTATYYCARHLRDGGFDYWGQGVMVTVSSB: GNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRAR (Red indicates removed residues) |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:04)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:04)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:04)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:04)
[INFO] PDB: Running AlphaCutter (00:00:04)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:25)
[INFO] FoldX: Starting FoldX energy minimization (00:00:25)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:49)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/f4a9722e96e63a9/tmp/folded.pdb (00:05:49)
[INFO] Main: Simulation completed successfully. (00:12:09)
|
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 | -0.8746 | |
| 2 | F | A | 0.0000 | |
| 3 | V | A | 0.7495 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -0.6824 | |
| 6 | Q | A | 0.0000 | |
| 7 | P | A | -1.0311 | |
| 8 | N | A | -1.5305 | |
| 9 | S | A | -0.8370 | |
| 10 | V | A | -0.4484 | |
| 11 | S | A | -0.2337 | |
| 12 | T | A | 0.0000 | |
| 13 | N | A | -1.0897 | |
| 14 | L | A | -0.6927 | |
| 15 | G | A | -1.2638 | |
| 16 | S | A | -1.1240 | |
| 17 | T | A | -1.4862 | |
| 18 | V | A | 0.0000 | |
| 19 | K | A | -1.7712 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.9914 | |
| 22 | C | A | 0.0000 | |
| 23 | K | A | -2.1222 | |
| 24 | R | A | -1.1856 | |
| 25 | S | A | -0.7477 | |
| 26 | T | A | -0.8920 | |
| 27 | G | A | -1.3918 | |
| 28 | N | A | -2.2253 | |
| 29 | I | A | 0.0000 | |
| 30 | G | A | -1.3176 | |
| 31 | S | A | -1.1786 | |
| 32 | N | A | 0.0000 | |
| 33 | Y | A | 0.0000 | |
| 34 | V | A | 0.0000 | |
| 35 | N | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | Y | A | 0.0000 | |
| 38 | Q | A | -0.6736 | |
| 39 | Q | A | 0.0000 | |
| 40 | H | A | -2.4776 | |
| 41 | E | A | -2.9467 | |
| 42 | G | A | -2.4318 | |
| 43 | R | A | -2.9879 | |
| 44 | S | A | -1.7084 | |
| 45 | P | A | 0.0000 | |
| 46 | T | A | -0.3374 | |
| 47 | T | A | 0.0000 | |
| 48 | M | A | 0.0000 | |
| 49 | I | A | 0.0000 | |
| 50 | Y | A | -1.1157 | |
| 51 | R | A | -1.9862 | |
| 52 | D | A | -1.6890 | |
| 53 | D | A | -2.4465 | |
| 54 | G | A | -1.9386 | |
| 55 | R | A | -2.2619 | |
| 56 | P | A | -1.7967 | |
| 57 | D | A | -2.3946 | |
| 58 | G | A | -1.6402 | |
| 59 | V | A | -1.3529 | |
| 60 | P | A | -1.6365 | |
| 61 | D | A | -2.4911 | |
| 62 | R | A | -1.8933 | |
| 63 | F | A | 0.0000 | |
| 64 | S | A | -1.5422 | |
| 65 | G | A | 0.0000 | |
| 66 | S | A | -1.0705 | |
| 67 | I | A | -0.9842 | |
| 68 | D | A | -1.7128 | |
| 69 | R | A | -2.7415 | |
| 70 | S | A | -1.4133 | |
| 71 | S | A | -1.6101 | |
| 72 | N | A | -2.2366 | |
| 73 | S | A | 0.0000 | |
| 74 | A | A | 0.0000 | |
| 75 | L | A | -0.7983 | |
| 76 | L | A | 0.0000 | |
| 77 | T | A | 0.0000 | |
| 78 | I | A | 0.0000 | |
| 79 | K | A | -2.3355 | |
| 80 | N | A | -2.1505 | |
| 81 | V | A | 0.0000 | |
| 82 | Q | A | -1.8863 | |
| 83 | S | A | -1.7817 | |
| 84 | E | A | -2.5182 | |
| 85 | D | A | 0.0000 | |
| 86 | E | A | -2.2486 | |
| 87 | A | A | -1.6570 | |
| 88 | D | A | -1.2554 | |
| 89 | Y | A | 0.0000 | |
| 90 | F | A | 0.0000 | |
| 91 | C | A | 0.0000 | |
| 92 | H | A | 0.0000 | |
| 93 | S | A | 0.0000 | |
| 94 | H | A | 0.0000 | |
| 95 | S | A | -0.0108 | |
| 96 | G | A | 0.0000 | |
| 97 | G | A | 0.0000 | |
| 98 | I | A | 0.6543 | |
| 99 | N | A | 0.0000 | |
| 100 | V | A | 0.0000 | |
| 101 | F | A | 0.2420 | |
| 102 | G | A | 0.0000 | |
| 103 | G | A | -0.9786 | |
| 104 | G | A | 0.0000 | |
| 105 | T | A | 0.0000 | |
| 106 | S | A | -0.9684 | |
| 107 | L | A | 0.0000 | |
| 108 | T | A | -0.4812 | |
| 109 | V | A | 0.0000 | |
| 110 | L | A | 0.1416 | |
| 111 | G | A | -0.4651 | |
| 112 | G | A | -0.9822 | |
| 113 | G | A | -0.6957 | |
| 114 | G | A | -0.8186 | |
| 127 | V | A | 1.7503 | |
| 128 | P | A | 0.8816 | |
| 129 | L | A | 0.0000 | |
| 130 | V | A | 1.1166 | |
| 131 | E | A | 0.0000 | |
| 132 | S | A | -0.3787 | |
| 133 | G | A | -0.8301 | |
| 134 | G | A | -0.2119 | |
| 135 | G | A | 0.5547 | |
| 136 | L | A | 1.2436 | |
| 137 | V | A | 0.0000 | |
| 138 | Q | A | -1.6952 | |
| 139 | P | A | -2.0631 | |
| 140 | G | A | -2.0996 | |
| 141 | R | A | -2.5203 | |
| 142 | S | A | -1.8713 | |
| 143 | L | A | -1.2207 | |
| 144 | K | A | -1.8710 | |
| 145 | L | A | 0.0000 | |
| 146 | S | A | -0.4154 | |
| 147 | C | A | 0.0000 | |
| 148 | A | A | 0.0020 | |
| 149 | A | A | 0.0000 | |
| 150 | S | A | -0.1520 | |
| 151 | G | A | -0.2338 | |
| 152 | F | A | -0.0354 | |
| 153 | T | A | -0.5916 | |
| 154 | F | A | 0.0000 | |
| 155 | S | A | -1.0194 | |
| 156 | N | A | -1.1039 | |
| 157 | Y | A | -0.1798 | |
| 158 | L | A | 0.0000 | |
| 159 | M | A | 0.0000 | |
| 160 | A | A | 0.0000 | |
| 161 | W | A | 0.0000 | |
| 162 | V | A | 0.0000 | |
| 163 | R | A | 0.0000 | |
| 164 | H | A | -0.9511 | |
| 165 | P | A | 0.0000 | |
| 166 | P | A | -1.7949 | |
| 167 | K | A | -2.6422 | |
| 168 | K | A | -2.7913 | |
| 169 | G | A | -1.7447 | |
| 170 | L | A | 0.0000 | |
| 171 | E | A | -0.7509 | |
| 172 | W | A | 0.0000 | |
| 173 | V | A | 0.0000 | |
| 174 | A | A | 0.0000 | |
| 175 | T | A | 0.0000 | |
| 176 | I | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | S | A | -0.5561 | |
| 179 | S | A | -0.9146 | |
| 180 | G | A | -0.5210 | |
| 181 | S | A | -0.6519 | |
| 182 | R | A | -0.4367 | |
| 183 | I | A | 0.7295 | |
| 184 | Y | A | 0.0000 | |
| 185 | Y | A | -0.5831 | |
| 186 | P | A | -1.2546 | |
| 187 | D | A | -2.5804 | |
| 188 | S | A | -1.8696 | |
| 189 | V | A | 0.0000 | |
| 190 | K | A | -2.6888 | |
| 191 | G | A | -1.7396 | |
| 192 | R | A | -1.4871 | |
| 193 | F | A | 0.0000 | |
| 194 | T | A | -0.7513 | |
| 195 | I | A | 0.0000 | |
| 196 | S | A | -0.2840 | |
| 197 | R | A | -0.8241 | |
| 198 | D | A | -1.2915 | |
| 199 | N | A | -1.4267 | |
| 200 | A | A | -1.2250 | |
| 201 | R | A | -2.1693 | |
| 202 | S | A | -1.3173 | |
| 203 | S | A | -0.8171 | |
| 204 | L | A | 0.0000 | |
| 205 | Y | A | -0.4555 | |
| 206 | L | A | 0.0000 | |
| 207 | Q | A | -1.3592 | |
| 208 | M | A | 0.0000 | |
| 209 | S | A | -1.4622 | |
| 210 | S | A | -1.5660 | |
| 211 | L | A | 0.0000 | |
| 212 | R | A | -2.8043 | |
| 213 | S | A | -2.0721 | |
| 214 | E | A | -2.4702 | |
| 215 | D | A | 0.0000 | |
| 216 | T | A | -0.7681 | |
| 217 | A | A | 0.0000 | |
| 218 | T | A | -0.0354 | |
| 219 | Y | A | 0.0000 | |
| 220 | Y | A | 0.0000 | |
| 221 | C | A | 0.0000 | |
| 222 | A | A | 0.0000 | |
| 223 | R | A | 0.0000 | |
| 224 | H | A | 0.0000 | |
| 225 | L | A | -0.0096 | |
| 226 | R | A | -0.6105 | |
| 227 | D | A | -0.4941 | |
| 228 | G | A | 0.0000 | |
| 229 | G | A | 0.0000 | |
| 230 | F | A | 0.0000 | |
| 231 | D | A | -0.0163 | |
| 232 | Y | A | 0.6248 | |
| 233 | W | A | 0.0000 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -0.8432 | |
| 236 | G | A | 0.0000 | |
| 237 | V | A | 0.1510 | |
| 238 | M | A | 0.6497 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.0328 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -0.8130 | |
| 243 | S | A | -0.6708 | |
| 1 | G | B | -1.8412 | |
| 2 | N | B | -2.7627 | |
| 3 | E | B | -3.2306 | |
| 4 | E | B | -2.8440 | |
| 5 | M | B | -0.5579 | |
| 6 | G | B | -0.4791 | |
| 7 | G | B | 0.0485 | |
| 8 | I | B | 1.4204 | |
| 9 | T | B | 0.1630 | |
| 10 | Q | B | -0.8322 | |
| 11 | T | B | -0.4144 | |
| 12 | P | B | -0.6682 | |
| 13 | Y | B | 0.0000 | |
| 14 | K | B | -1.6102 | |
| 15 | V | B | 0.1716 | |
| 16 | S | B | 0.7461 | |
| 17 | I | B | 1.8776 | |
| 18 | S | B | 0.4462 | |
| 19 | G | B | -0.4320 | |
| 20 | T | B | -0.6974 | |
| 21 | T | B | -0.4423 | |
| 22 | V | B | 0.0000 | |
| 23 | I | B | 0.5375 | |
| 24 | L | B | 0.0000 | |
| 25 | T | B | -1.0702 | |
| 26 | C | B | 0.0000 | |
| 27 | P | B | -0.7440 | |
| 28 | Q | B | -0.2988 | |
| 29 | Y | B | -0.2410 | |
| 30 | P | B | -0.6885 | |
| 31 | G | B | -0.7411 | |
| 32 | S | B | -0.3682 | |
| 33 | E | B | 0.0000 | |
| 34 | I | B | 0.0000 | |
| 35 | L | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | Q | B | -1.6556 | |
| 38 | H | B | -1.4522 | |
| 39 | N | B | -1.9661 | |
| 40 | D | B | -3.3575 | |
| 41 | K | B | -3.2113 | |
| 42 | N | B | -2.6069 | |
| 43 | I | B | -1.5992 | |
| 44 | G | B | 0.0000 | |
| 45 | G | B | -1.6957 | |
| 46 | D | B | -1.8794 | |
| 47 | E | B | -3.5035 | |
| 48 | D | B | -3.7790 | |
| 49 | D | B | -3.3455 | |
| 50 | K | B | -3.1498 | |
| 51 | N | B | -2.2709 | |
| 52 | I | B | -1.6879 | |
| 53 | G | B | -1.6816 | |
| 54 | S | B | -1.4812 | |
| 55 | D | B | -2.2264 | |
| 56 | E | B | -2.3132 | |
| 57 | D | B | -1.6690 | |
| 58 | H | B | -1.5241 | |
| 59 | L | B | 0.0000 | |
| 60 | S | B | -0.4220 | |
| 61 | L | B | 0.0000 | |
| 62 | K | B | -1.8176 | |
| 63 | E | B | -2.4147 | |
| 64 | F | B | -1.2585 | |
| 65 | S | B | -1.7050 | |
| 66 | E | B | -2.5255 | |
| 67 | L | B | -0.4508 | |
| 68 | E | B | -1.6621 | |
| 69 | Q | B | -1.7145 | |
| 70 | S | B | -1.2055 | |
| 71 | G | B | -0.3576 | |
| 72 | Y | B | 0.5057 | |
| 73 | Y | B | 0.0000 | |
| 74 | V | B | 0.0000 | |
| 75 | C | B | 0.0000 | |
| 76 | Y | B | 0.0000 | |
| 77 | P | B | -0.1849 | |
| 78 | R | B | 0.0000 | |
| 79 | G | B | 0.0000 | |
| 80 | S | B | -0.9260 | |
| 81 | K | B | -1.5984 | |
| 82 | P | B | -2.1735 | |
| 83 | E | B | -3.2051 | |
| 84 | D | B | -3.0077 | |
| 85 | A | B | -1.8511 | |
| 86 | N | B | -1.6094 | |
| 87 | F | B | -0.1998 | |
| 88 | Y | B | 0.9550 | |
| 89 | L | B | 0.0000 | |
| 90 | Y | B | 1.2421 | |
| 91 | L | B | 0.0000 | |
| 92 | R | B | -2.1835 | |
| 93 | A | B | -2.1888 | |
| 94 | R | B | -2.5574 |
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 | -0.7444 | 2.901 | View | CSV | PDB |
| 4.5 | -0.8062 | 2.901 | View | CSV | PDB |
| 5.0 | -0.8826 | 2.901 | View | CSV | PDB |
| 5.5 | -0.9618 | 2.901 | View | CSV | PDB |
| 6.0 | -1.0305 | 2.901 | View | CSV | PDB |
| 6.5 | -1.0777 | 2.901 | View | CSV | PDB |
| 7.0 | -1.1009 | 2.901 | View | CSV | PDB |
| 7.5 | -1.1068 | 2.901 | View | CSV | PDB |
| 8.0 | -1.102 | 2.901 | View | CSV | PDB |
| 8.5 | -1.0887 | 2.901 | View | CSV | PDB |
| 9.0 | -1.0666 | 2.901 | 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