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DisResClusteredDB |
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- Find homologues in whole Protein Data Bank.
- Make statistical analysis of unstructured amino acid residues in protein structures.
- Search for disordered patterns and homo-repeats.
- Search for disordered regions in different chains of the same protein.
- Download the clusters from our database.
- Observe 3D structure interactively using MView.
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Search the residue sequence by FASTA-template. Use '%' for any symbol: |
Nu - The number of classes in which there are more disordered residues than ordered
Ns - The number of classes in which there are less disordered residues than ordered
In each cluster with ID> = 75%, we calculated the average number of unstructured (u) and structured (s) residues. Then u & s were summarized over all clusters and received the total number of unstructured (U) and structured (S) residues covered by the pattern throughout the database.
There are 20 homo-repeats
Pattern |
U |
S |
U-S |
Nu |
Ns |
Length |
|---|---|---|---|---|---|---|
| HHHH | 70972.05 | 4129.52 | 66842.53 | 10729 | 498 | 4 |
| CCCCCC | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| MMMMMM | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| FFFFFF | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| IIIIII | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| LLLLLL | 83.69 | 30.75 | 52.94 | 5 | 2 | 6 |
| VVVVVV | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| WWWWWW | 0.00 | 0.00 | 0.00 | 0 | 0 | 6 |
| YYYYYY | 0.50 | 17.07 | -16.57 | 0 | 4 | 6 |
| AAAAAA | 259.69 | 445.88 | -186.19 | 20 | 38 | 6 |
| GGGGGG | 329.25 | 112.78 | 216.47 | 34 | 13 | 6 |
| TTTTTT | 51.64 | 7.73 | 43.91 | 5 | 1 | 6 |
| SSSSSS | 123.43 | 65.33 | 58.10 | 12 | 9 | 6 |
| QQQQQQ | 145.18 | 33.66 | 111.53 | 8 | 2 | 6 |
| NNNNNN | 68.57 | 1.20 | 67.37 | 10 | 0 | 6 |
| EEEEEE | 262.33 | 150.30 | 112.03 | 23 | 5 | 6 |
| DDDDDD | 59.83 | 2.50 | 57.33 | 6 | 0 | 6 |
| RRRRRR | 27.50 | 3.50 | 24.00 | 3 | 0 | 6 |
| KKKKKK | 86.36 | 14.10 | 72.26 | 9 | 3 | 6 |
| PPPPPP | 202.91 | 73.63 | 129.28 | 10 | 4 | 6 |
There are 1214 patterns
There are 518 patterns
Undefined amino acid residues are highlighted by yellow and are labeled by U (unstructured).
Revision date: 16 January 2019
Number of PDB files: 148 389
Number of protein chains in PDB-files: 277 583
Number of unique amino-acid sequences: 74 378
Quantity of clusters:
The statistical analysis of disordered residues was done considering 74 378 unique protein chains taken from the PDB database. In this database, 4.75% of residues are disordered (i.e. invisible in X-ray structures). For statistics we used the clusters of protein chains where identity between chains inside of the cluster exceeds 75%. The statistics was obtained separately for the N- and C-termini as well as for the central part of the protein chain. It has been shown that frequencies of occurrence of disordered residues of 20 types at the termini of protein chains differ from the ones in the middle part of the protein chain. For statistical analysis we considered all chains but with different weights. For example:
First we selected all 100% homologues in the entire PDB. Let some chain X enter the cluster A from 8 100% homologues. Then we grouped 100% homologues into clusters with an identity greater than 75%. Let the cluster A enter the cluster B, moreover between all chains identity > 75%. Let in the cluster B there are 3 clusters with identity = 100%.
Then the weight of chain A is: w = 1 / (8 * 3) = 1/24.
Percent unfolded:
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Downloads
| Description | Link |
|---|---|
| Whole database in text format | download |
| Whole database in SQL format | download |
| Fixed patterns | download |
Filtered database contains one protein chain for each cluster
| Clusters | Link |
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| All clusters generated using 100% identity | download |
| All clusters generated using 75% identity | download |
| All clusters generated using 50% identity | download |
| All clusters generated using 25% identity | download |
| All clusters generated using 5% identity | download |
HELP
This database contains only X-Ray structures
In our database, molecules are grouped in CLUSTERSby different levels of identity: 5%, 25%, 50%, 75% and 100%.
- Find your PDB-structure on the HOME tab using the PDB-code or name. Press Search or Enter.
- For example: see cadherin
- Press show results. You will be redirected to the Searching results tab.
- You can see number of entities in 5%, 25%, 50%, 75% and 100% clusters.
- For example: cadherin 1edh, chain A has 79 sequences with 5% identity, 48 sequences with 25% identity, 27 sequences with 50% identity, 22 sequences with 75% identity, and only 2 identical sequences with 100% identity.
- You can see the 5%, 25%, 50%, 75% and 100% identity groups by pressing the mouse in the corresponding column
. You will be redirected to the Selected Group tab. - For example: choose the 75% column. You will see 22 chains.
- You can see all PDBs with sequences by choosing the Sequence column. You will be redirected to the Disordered residues tab.
- For example: press the first sequence. You will see two chains of 4qd2 and chain A of the 2qvf protein.
- Undefined amino acid residues are highlighted by yellow and are labeled by U (unstructured).
- You can see any PDB structure by pressing
. You will be redirected to the 3D-View tab. - You can work interactively with protein structures using the 3D-View tab. Move the mouse and press the left mouse button to rotate the protein structure. Move the mouse and press the left mouse button to translate the structure.
Galzitskaya O.V.
Team Leader
ogalzit@vega.protresr.ru Lobanov M.Yu.
Programming
m.u.lobanov@mail.ru Likhachev I.V.
Web-programming
ilya_lihachev@mail.ru Driver-Inter, Ltd
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