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Open Access Research article

Relationship between chemical shift value and accessible surface area for all amino acid atoms

Wim F Vranken1* and Wolfgang Rieping2

Author Affiliations

1 Protein Databank Europe, European Bioinformatics Institute, Cambridge, UK

2 Department of Biochemistry, University of Cambridge, Cambridge, UK

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BMC Structural Biology 2009, 9:20  doi:10.1186/1472-6807-9-20

Published: 2 April 2009

Abstract

Background

Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes.

Results

We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA) in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html webcite.

Conclusion

Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.