Disulfide Bond Analysis
Introduction of disulfide bonds into proteins appears to be an important mechanism by which they have evolved and are evolving.
At the bottom of this page you will find our software for analysing disulfide bonds. Any structure from the PDB can be analysed by entering its PDB identifier. Alternatively, custom PDB files may be uploaded. The analysis can be downloaded as an Excel 97-2003 spreadsheet.
The analysis of the disulfides from all of the PDB, both X-ray and NMR structures (about 60,000 bonds currently), can be directly downloaded. This analysis will be updated every month.
disulfide_analysis_19_Oct_2009.zip
How we performed this analysis and the analysis of this information is described in the following articles.
Schmidt B, Ho L, Hogg PJ. Allosteric disulfide bonds. Biochemistry 45, 7429-33, 2006.
Click here to link to article
Schmidt B, Hogg PJ. Search for allosteric disulfide bonds in NMR structures. BMC Struct Biol 7:49, 2007.
Click here to link to article
| The analysis contains the following features of each disulfide bond. The secondary structure descriptors and solvent accessibility values are from DSSP ( http://swift.cmbi.ru.nl/gv/dssp/).
PDB ID
Header
Compound
Experiment
Cys1 chain
Cys1 residue
Cys1 secondary structure
Cys1 solvent accessibility (~Å^2)
Cys2 chain
Cys2 residue
Cys2 secondary structure
Cys2 solvent accessibility (~Å^2)
Resolution
R-factor
chi1 angle
chi2 angle
chi3 angle
chi2' angle
chi1' angle
Dihedral strain energy (kJ/mol)
Distance between α-carbon atoms of the Cys residues (Å)
Disulfide bond classification
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This web service also provides a remote API for accessing the analysis software. An example of how to do this is below:
where the PDB ID 1cdj maybe replace with any PDB ID in the RCSB Protein Data Bank.
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