| Chain sequence(s) |
A: DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
B: QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC 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 (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:04:19)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/54f565f4b7a92b3/tmp/folded.pdb (00:04:19)
[INFO] Main: Simulation completed successfully. (00:06:23)
|
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 | -2.3177 | |
| 2 | I | A | 0.0000 | |
| 3 | E | A | -2.9419 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | -1.4869 | |
| 6 | Q | A | -1.1461 | |
| 7 | S | A | -0.8313 | |
| 8 | P | A | -0.5333 | |
| 9 | A | A | -0.5424 | |
| 10 | T | A | -0.6358 | |
| 11 | L | A | -0.5325 | |
| 12 | S | A | -0.9624 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.6678 | |
| 15 | P | A | -1.9763 | |
| 16 | G | A | -2.0141 | |
| 17 | D | A | -2.5160 | |
| 18 | S | A | -1.8490 | |
| 19 | V | A | -0.7761 | |
| 20 | S | A | -0.4582 | |
| 21 | L | A | 0.0000 | |
| 22 | S | A | -0.9253 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.9330 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | -2.2521 | |
| 27 | Q | A | -2.2684 | |
| 28 | S | A | -1.5665 | |
| 29 | I | A | 0.0000 | |
| 30 | S | A | -1.1855 | |
| 31 | N | A | -1.2847 | |
| 32 | N | A | -0.8826 | |
| 33 | L | A | 0.0000 | |
| 34 | H | A | 0.0000 | |
| 35 | W | A | 0.0000 | |
| 36 | Y | A | 0.0000 | |
| 37 | Q | A | -1.1039 | |
| 38 | Q | A | 0.0000 | |
| 39 | K | A | -2.9021 | |
| 40 | S | A | -2.2681 | |
| 41 | H | A | -2.5346 | |
| 42 | E | A | -3.2523 | |
| 43 | S | A | -1.9168 | |
| 44 | P | A | 0.0000 | |
| 45 | R | A | -1.3448 | |
| 46 | L | A | 0.0000 | |
| 47 | L | A | 0.0000 | |
| 48 | I | A | 0.0000 | |
| 49 | K | A | -0.8342 | |
| 50 | Y | A | -0.4645 | |
| 51 | V | A | 0.0000 | |
| 52 | S | A | -1.1217 | |
| 53 | Q | A | -1.4878 | |
| 54 | S | A | -1.0339 | |
| 55 | S | A | -0.7563 | |
| 56 | S | A | -0.5926 | |
| 57 | G | A | -0.4925 | |
| 58 | I | A | -0.2755 | |
| 59 | P | A | -0.3385 | |
| 60 | S | A | -0.6757 | |
| 61 | R | A | -1.1180 | |
| 62 | F | A | 0.0000 | |
| 63 | S | A | -0.8840 | |
| 64 | G | A | -0.6815 | |
| 65 | S | A | -0.8818 | |
| 66 | G | A | -1.2650 | |
| 67 | S | A | -1.2800 | |
| 68 | G | A | -1.4375 | |
| 69 | T | A | -1.8821 | |
| 70 | D | A | -2.1257 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -0.8313 | |
| 73 | L | A | 0.0000 | |
| 74 | S | A | -0.6779 | |
| 75 | I | A | 0.0000 | |
| 76 | N | A | -2.1992 | |
| 77 | S | A | -2.0709 | |
| 78 | V | A | 0.0000 | |
| 79 | E | A | -2.6104 | |
| 80 | T | A | -1.9041 | |
| 81 | E | A | -2.5407 | |
| 82 | D | A | 0.0000 | |
| 83 | F | A | 0.0000 | |
| 84 | G | A | -1.4009 | |
| 85 | M | A | -0.9876 | |
| 86 | Y | A | 0.0000 | |
| 87 | F | A | 0.0000 | |
| 88 | C | A | 0.0000 | |
| 89 | Q | A | 0.0000 | |
| 90 | Q | A | 0.0000 | |
| 91 | S | A | -0.4161 | |
| 92 | N | A | -0.7827 | |
| 93 | S | A | -0.3334 | |
| 94 | W | A | 0.3343 | |
| 95 | P | A | -0.5221 | |
| 96 | R | A | 0.0000 | |
| 97 | T | A | -0.9232 | |
| 98 | F | A | 0.0000 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -1.2257 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -1.4774 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.1905 | |
| 106 | I | A | -1.5288 | |
| 107 | K | A | -2.1813 | |
| 108 | R | A | -1.9064 | |
| 109 | A | A | -1.4082 | |
| 110 | D | A | -2.5164 | |
| 111 | A | A | -1.3560 | |
| 112 | A | A | -0.7350 | |
| 113 | P | A | 0.0000 | |
| 114 | T | A | -0.1340 | |
| 115 | V | A | 0.0000 | |
| 116 | S | A | 0.0383 | |
| 117 | I | A | 0.1725 | |
| 118 | F | A | 0.0000 | |
| 119 | P | A | 0.0000 | |
| 120 | P | A | 0.0000 | |
| 121 | S | A | 0.0000 | |
| 122 | S | A | -0.6059 | |
| 123 | E | A | -0.9579 | |
| 124 | Q | A | 0.0000 | |
| 125 | L | A | -0.8133 | |
| 126 | T | A | -0.5641 | |
| 127 | S | A | -0.6165 | |
| 128 | G | A | -1.1806 | |
| 129 | G | A | -1.0109 | |
| 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 | F | A | 0.0000 | |
| 136 | L | A | 0.0000 | |
| 137 | N | A | 0.0000 | |
| 138 | N | A | -1.0489 | |
| 139 | F | A | 0.0000 | |
| 140 | Y | A | 0.0000 | |
| 141 | P | A | -2.3736 | |
| 142 | K | A | -2.7819 | |
| 143 | D | A | -2.9235 | |
| 144 | I | A | 0.0000 | |
| 145 | N | A | -2.0802 | |
| 146 | V | A | -0.7451 | |
| 147 | K | A | -1.7222 | |
| 148 | W | A | 0.0000 | |
| 149 | K | A | -2.2538 | |
| 150 | I | A | 0.0000 | |
| 151 | D | A | -2.2090 | |
| 152 | G | A | -1.7547 | |
| 153 | S | A | -1.9825 | |
| 154 | E | A | -3.1467 | |
| 155 | R | A | -2.5919 | |
| 156 | Q | A | -2.4891 | |
| 157 | N | A | -2.0036 | |
| 158 | G | A | -0.8034 | |
| 159 | V | A | -0.3841 | |
| 160 | L | A | 0.1787 | |
| 161 | N | A | -0.0651 | |
| 162 | S | A | -0.1478 | |
| 163 | W | A | -0.3548 | |
| 164 | T | A | -1.1534 | |
| 165 | D | A | -2.2286 | |
| 166 | Q | A | -2.1182 | |
| 167 | D | A | -2.4569 | |
| 168 | S | A | -2.2571 | |
| 169 | K | A | -2.6520 | |
| 170 | D | A | -2.4576 | |
| 171 | S | A | -2.1931 | |
| 172 | T | A | 0.0000 | |
| 173 | Y | A | 0.0000 | |
| 174 | S | A | 0.0000 | |
| 175 | M | A | 0.0000 | |
| 176 | S | A | 0.0000 | |
| 177 | S | A | 0.0000 | |
| 178 | T | A | 0.0000 | |
| 179 | L | A | 0.0000 | |
| 180 | T | A | -0.1270 | |
| 181 | L | A | -0.8075 | |
| 182 | T | A | -1.4722 | |
| 183 | K | A | -2.5393 | |
| 184 | D | A | -3.3070 | |
| 185 | E | A | -2.7959 | |
| 186 | Y | A | 0.0000 | |
| 187 | E | A | -3.0736 | |
| 188 | R | A | -3.4238 | |
| 189 | H | A | -2.6074 | |
| 190 | N | A | -2.3638 | |
| 191 | S | A | -1.6647 | |
| 192 | Y | A | 0.0000 | |
| 193 | T | A | -0.7510 | |
| 194 | C | A | 0.0000 | |
| 195 | E | A | -0.5738 | |
| 196 | A | A | 0.0000 | |
| 197 | T | A | -1.0718 | |
| 198 | H | A | 0.0000 | |
| 199 | K | A | -2.6876 | |
| 200 | T | A | -1.3212 | |
| 201 | S | A | -0.7369 | |
| 202 | T | A | -0.5614 | |
| 203 | S | A | -0.3999 | |
| 204 | P | A | -0.3696 | |
| 205 | I | A | 0.6391 | |
| 206 | V | A | 0.7450 | |
| 207 | K | A | -0.0340 | |
| 208 | S | A | -0.1982 | |
| 209 | F | A | -0.6000 | |
| 210 | N | A | -1.6719 | |
| 211 | R | A | -2.2036 | |
| 212 | N | A | -2.4741 | |
| 213 | E | A | -2.2642 | |
| 214 | C | A | -0.5568 | |
| 1 | Q | B | -1.3359 | |
| 2 | V | B | -0.6381 | |
| 3 | Q | B | -1.3753 | |
| 4 | L | B | 0.0000 | |
| 5 | Q | B | -1.9426 | |
| 6 | E | B | 0.0000 | |
| 7 | S | B | -1.0008 | |
| 8 | G | B | -0.8956 | |
| 9 | A | B | -0.2104 | |
| 10 | E | B | -0.2858 | |
| 11 | V | B | 0.2739 | |
| 12 | M | B | -0.4922 | |
| 13 | K | B | -1.7400 | |
| 14 | P | B | -1.3942 | |
| 15 | G | B | -1.1360 | |
| 16 | A | B | -0.8569 | |
| 17 | S | B | -0.9570 | |
| 18 | V | B | 0.0000 | |
| 19 | K | B | -1.2667 | |
| 20 | I | B | 0.0000 | |
| 21 | S | B | -0.7929 | |
| 22 | C | B | 0.0000 | |
| 23 | K | B | -1.5645 | |
| 24 | A | B | 0.0000 | |
| 25 | T | B | -0.9881 | |
| 26 | G | B | -0.7962 | |
| 27 | Y | B | -0.2663 | |
| 28 | T | B | -0.1047 | |
| 29 | F | B | 0.0000 | |
| 30 | S | B | -0.1953 | |
| 31 | T | B | 0.1390 | |
| 32 | Y | B | 0.5996 | |
| 33 | W | B | 0.5834 | |
| 34 | I | B | 0.0000 | |
| 35 | E | B | 0.0000 | |
| 36 | W | B | 0.0000 | |
| 37 | V | B | 0.0000 | |
| 38 | K | B | 0.0000 | |
| 39 | Q | B | -0.7711 | |
| 40 | R | B | -1.3907 | |
| 41 | P | B | -1.0024 | |
| 42 | G | B | -1.2890 | |
| 43 | H | B | -1.6813 | |
| 44 | G | B | -1.1236 | |
| 45 | L | B | 0.0000 | |
| 46 | E | B | -0.7869 | |
| 47 | W | B | 0.0000 | |
| 48 | I | B | 0.0000 | |
| 49 | G | B | 0.0000 | |
| 50 | E | B | 0.0000 | |
| 51 | I | B | 0.0000 | |
| 52 | L | B | 0.2838 | |
| 53 | P | B | 0.0000 | |
| 54 | G | B | -0.9673 | |
| 55 | S | B | -0.6875 | |
| 56 | G | B | -0.7167 | |
| 57 | S | B | -0.1491 | |
| 58 | T | B | 0.4619 | |
| 59 | Y | B | 0.7308 | |
| 60 | Y | B | -0.8098 | |
| 61 | N | B | -1.8792 | |
| 62 | E | B | -3.1948 | |
| 63 | K | B | -3.2298 | |
| 64 | F | B | 0.0000 | |
| 65 | K | B | -2.9785 | |
| 66 | G | B | -2.0474 | |
| 67 | K | B | -1.7672 | |
| 68 | A | B | 0.0000 | |
| 69 | T | B | -0.6879 | |
| 70 | F | B | 0.0000 | |
| 71 | T | B | -0.3442 | |
| 72 | A | B | -0.7168 | |
| 73 | D | B | -1.2366 | |
| 74 | T | B | -0.9299 | |
| 75 | S | B | -0.7390 | |
| 76 | S | B | -0.8457 | |
| 77 | N | B | -1.0626 | |
| 78 | T | B | 0.0000 | |
| 79 | A | B | 0.0000 | |
| 80 | Y | B | -0.4088 | |
| 81 | M | B | 0.0000 | |
| 82 | Q | B | -1.0616 | |
| 83 | L | B | 0.0000 | |
| 84 | S | B | -0.8658 | |
| 85 | S | B | -0.8337 | |
| 86 | L | B | 0.0000 | |
| 87 | T | B | -1.2457 | |
| 88 | S | B | -1.4275 | |
| 89 | E | B | -2.0357 | |
| 90 | D | B | 0.0000 | |
| 91 | S | B | -0.6832 | |
| 92 | A | B | 0.0000 | |
| 93 | V | B | -0.1563 | |
| 94 | Y | B | 0.0000 | |
| 95 | Y | B | 0.0000 | |
| 96 | C | B | 0.0000 | |
| 97 | A | B | 0.0000 | |
| 98 | R | B | 0.0000 | |
| 99 | G | B | 0.0670 | |
| 100 | D | B | -0.3108 | |
| 101 | G | B | -0.4533 | |
| 102 | N | B | 0.0000 | |
| 103 | Y | B | 0.0000 | |
| 104 | G | B | -0.2947 | |
| 105 | Y | B | 0.0826 | |
| 106 | W | B | -0.5475 | |
| 107 | G | B | 0.0000 | |
| 108 | Q | B | -2.0672 | |
| 109 | G | B | -1.2562 | |
| 110 | T | B | 0.0000 | |
| 111 | T | B | -0.2036 | |
| 112 | L | B | 0.0000 | |
| 113 | T | B | -0.3293 | |
| 114 | V | B | 0.0000 | |
| 115 | S | B | -0.9796 | |
| 116 | S | B | -1.0999 | |
| 117 | A | B | -0.8594 | |
| 118 | S | B | -0.6084 | |
| 119 | T | B | -0.3363 | |
| 120 | T | B | -0.2448 | |
| 121 | P | B | -0.6212 | |
| 122 | P | B | 0.0000 | |
| 123 | S | B | -0.3488 | |
| 124 | V | B | 0.0000 | |
| 125 | F | B | 0.0000 | |
| 126 | P | B | -0.4882 | |
| 127 | L | B | 0.0000 | |
| 128 | A | B | 0.0000 | |
| 129 | P | B | 0.0000 | |
| 130 | G | B | -0.1812 | |
| 131 | S | B | -0.2938 | |
| 132 | A | B | -0.3672 | |
| 133 | A | B | -0.4142 | |
| 134 | Q | B | -0.7158 | |
| 135 | T | B | -0.8086 | |
| 136 | N | B | -1.3150 | |
| 137 | S | B | -0.6284 | |
| 138 | M | B | 0.1153 | |
| 139 | V | B | 0.0000 | |
| 140 | T | B | 0.0000 | |
| 141 | L | B | 0.0000 | |
| 142 | G | B | 0.0000 | |
| 143 | C | B | 0.0000 | |
| 144 | L | B | 0.0000 | |
| 145 | V | B | 0.0000 | |
| 146 | K | B | -0.2786 | |
| 147 | G | B | -0.3547 | |
| 148 | Y | B | 0.0000 | |
| 149 | F | B | 0.0000 | |
| 150 | P | B | -0.6481 | |
| 151 | E | B | -1.0126 | |
| 152 | P | B | -0.8615 | |
| 153 | V | B | 0.0000 | |
| 154 | T | B | -0.4238 | |
| 155 | V | B | -0.2539 | |
| 156 | T | B | -0.3843 | |
| 157 | W | B | 0.0000 | |
| 158 | N | B | -0.9440 | |
| 159 | S | B | -0.7819 | |
| 160 | G | B | -0.6346 | |
| 161 | S | B | -0.4840 | |
| 162 | L | B | -0.1902 | |
| 163 | S | B | -0.3496 | |
| 164 | S | B | -0.2766 | |
| 165 | G | B | -0.1149 | |
| 166 | V | B | 0.2649 | |
| 167 | H | B | -0.1153 | |
| 168 | T | B | 0.0740 | |
| 169 | F | B | 0.0000 | |
| 170 | P | B | -0.1004 | |
| 171 | A | B | 0.2537 | |
| 172 | V | B | 0.8886 | |
| 173 | L | B | 1.1794 | |
| 174 | Q | B | 0.0177 | |
| 175 | S | B | -0.7521 | |
| 176 | D | B | -1.4523 | |
| 177 | L | B | -0.4425 | |
| 178 | Y | B | 0.1357 | |
| 179 | T | B | 0.2451 | |
| 180 | L | B | 0.0000 | |
| 181 | S | B | 0.0000 | |
| 182 | S | B | 0.0000 | |
| 183 | S | B | 0.0000 | |
| 184 | V | B | 0.0000 | |
| 185 | T | B | 0.1310 | |
| 186 | V | B | 0.0000 | |
| 187 | P | B | -0.2621 | |
| 188 | S | B | -0.7226 | |
| 189 | S | B | -0.8015 | |
| 190 | P | B | -0.9278 | |
| 191 | R | B | 0.0000 | |
| 192 | P | B | -0.7280 | |
| 193 | S | B | -1.3066 | |
| 194 | E | B | -2.0804 | |
| 195 | T | B | -1.1840 | |
| 196 | V | B | 0.0000 | |
| 197 | T | B | -1.4201 | |
| 198 | C | B | 0.0000 | |
| 199 | N | B | -1.5357 | |
| 200 | V | B | 0.0000 | |
| 201 | A | B | -1.0051 | |
| 202 | H | B | 0.0000 | |
| 203 | P | B | -0.8347 | |
| 204 | A | B | -0.4689 | |
| 205 | S | B | -0.5385 | |
| 206 | S | B | -0.7606 | |
| 207 | T | B | -0.9382 | |
| 208 | K | B | -1.9706 | |
| 209 | V | B | -1.2942 | |
| 210 | D | B | -2.5875 | |
| 211 | K | B | -1.7329 | |
| 212 | K | B | -1.9121 | |
| 213 | I | B | 0.0000 | |
| 214 | V | B | 0.8412 | |
| 215 | P | B | 0.0939 | |
| 216 | R | B | -0.6961 | |
| 217 | D | B | -1.3497 | |
| 218 | C | B | -0.2955 |
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 | -0.6504 | 2.2745 | View | CSV | PDB |
| 4.5 | -0.7022 | 2.2153 | View | CSV | PDB |
| 5.0 | -0.7639 | 2.1392 | View | CSV | PDB |
| 5.5 | -0.8244 | 2.0554 | View | CSV | PDB |
| 6.0 | -0.8716 | 1.9687 | View | CSV | PDB |
| 6.5 | -0.8971 | 1.8811 | View | CSV | PDB |
| 7.0 | -0.902 | 1.7934 | View | CSV | PDB |
| 7.5 | -0.8937 | 1.7062 | View | CSV | PDB |
| 8.0 | -0.878 | 1.6206 | View | CSV | PDB |
| 8.5 | -0.8559 | 1.6418 | View | CSV | PDB |
| 9.0 | -0.826 | 1.7216 | 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