ConfC
2016/09/20HTTPS Site: https://dbarchive.biosciencedbc.jp/data/confc/
This database extracts this dynamic information from the protein structure being obtained now.
README Content
1. Database Component
- README
- Data of conformation changes by some binding
- Supplement data for conformation changes by some binding
- Data of evolutionary structure change
- Data of structural flexibility
- Conformation analysis
- Protein structure image
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "ConfC" data. |
| File | README_e.html(English) |
2.2 Data of conformation changes by some binding
| Data name | Data of conformation changes by some binding |
| Description of data contents | A protein structure pair which ID% (sequence identity) is more than 99%, and Dmax (maximum distance between Cα atoms of superimposed protein structures) is more than 20 Å, is stored. |
| File | confc_all.zip (14.2 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| confID | ID of this table |
| classID | ID including structural change class information |
| index | Record Index |
| pdbIDA | PDB ID compared protein structure A |
| pdbIDB | PDB ID compared protein structure B |
| pdbChainA | PDB chain ID compared protein structure A |
| pdbChainB | PDB chain ID compared protein structure B |
| confDatafile | Link to conformation analysis file (zip) |
| confClass | Binding molecular type |
| confName | Name of binding molecules |
| dmax | Maximum distance between Cα atoms of superimposed protein structures |
| rmsd | RMSD of distance between Cα of superimposed protein structures |
| identity | Protein sequence identity |
2.3 Supplement data for conformation changes by some binding
| Data name | Supplement data for conformation changes by some binding |
| Description of data contents | The distance values of φ and ψ between the superimposed protein structures of each residues are calculated, and the Z score of distance is computed.The information about a regions of structural change sekected with the Z score is stored. |
| File | confc_part.zip (231 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| confID | ID of ConfAll table |
| siteNo | Site number in residue number order |
| siteStart1 | Dihedral angle number at the start of the site in the structure 1 (numbering starts at the second visible residue) |
| siteStartR1 | Residue number at the start of the site in the structure 1 |
| siteEnd1 | Dihedral angle number at the end of the site in the structure 1 |
| siteEndR1 | Residue number at the end of the site in the structure 1 |
| siteLength1 | The longest site length in the structure 1 |
| siteStart2 | Dihedral angle number at the start of the site in the structure 2 (numbering starts at the second visible residue) |
| siteStartR2 | Residue number at the start of the site in the structure 2 |
| siteEnd2 | Dihedral angle number at the end of the site in the structure 2 |
| siteEndR2 | Residue number at the end of the site in the structure 2 |
| siteLength2 | The longest site length in the structure 2 |
| phiMax | Maximum value of φchange |
| psiMax | Maximum value of ψchange |
2.4 Data of evolutionary structure change
| Data name | Data of evolutionary structure change |
| Description of data contents | The information about a regions of structural change by mutation, insersion and/or deletion is stored. |
| File | confc_ev.zip (373 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| confEVID | ID of this table |
| pdbIDA | PDB ID of compared protein structure A |
| pdbIDB | PDB ID of compared protein structure B |
| pdbChainA | PDB chain ID of compared protein structure A |
| pdbChainA | PDB chain ID of compared protein structure B |
| identity | Sequence identity |
| indelSize | Number of indels analyzed |
| alignment | Sequence alignment |
| indel | Analysis of indels |
2.5 Data of structural flexibility
| Data name | Data of structural flexibility |
| Description of data contents | The regions of structural flexibility are selected with the Z score of temperature factor (B-factor) values by Cα atom of each residue in PDB. |
| File | confc_disorder.zip (3.7 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| confID | ID of this table |
| classID | ID of structural change class |
| pdbID | PDB ID |
| pdbChain | PDB chain ID |
| method | Experimental technique used for the structure determination |
| program | Refinement program |
| temperature | Temperature at experiment |
| resolution | Resolution |
| Rfactor | R-factor |
| depositDate | Deposition date |
| depositDateClass | Date format |
| ECnumber | EC number |
| SCOPID | SCOP ID |
| domainNumber | Number of domains |
| complex | Type of complex |
| SEQRESLength | SEQRES Length |
| ATOMLength | ATOM Length |
| REMARK465 | Whether REMARK 465 (describing missing residues) is used |
| disorderNumber | Number of disorder regions |
| disSumLength | Total number of disordered residues |
| maxDisLength | Maximum length of disorder region |
| minDisLength | Minimum length of disorder region |
| disSeqresPosition | Position of disorder regions by SEQRES |
| disAtomPosition | Position of disorder regions by ATOM |
| temperatureFactorAve | Average of temperature factor |
| temperatureFactorStddev | Standard deviation of temperature factor |
| checkOccupy | Whether OCCUPANCY less than 1.00 is used |
| modelNumber | Whether MODEL NUMBER is used |
2.6 Conformation analysis
| Data name | Conformation analysis |
| Description of data contents | Results of conformation analysis for PDB files (raw data) Each result is linked from "Data of conformation changes by some binding" table. |
| File | confc_datafile.zip (63.9 MB) |
2.7 Protein structure image
| Data name | Protein structure image |
| Description of data contents | Structure images of the protein which has structural flexibility. Each image is linked from "Data of structural flexibility" table. |
| File | confc_structure_image.zip (1.3 GB) |
3. License
Last updated : 2016/09/20
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "ConfC © Tamotsu Noguchi (National Institute of Advanced Industrial Science and Technology) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
Tamotsu Noguchi
Tel: 042-495-8736
E-mail: noguchit[at]my-pharm[dot]ac[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2016/09/20 | ConfC English archive site is opened. |
| 2005/05/01 | ConfC (http://mbs.cbrc.jp/ConfC/) is opened. |
5. Literature
-6. Contact address
When you have any question about "ConfC", contact the following:
Tamotsu Noguchi
Tel: 042-495-8736
E-mail: noguchit[at]my-pharm[dot]ac[dot]jp