Relationship between chemical shift value and accessible surface area for all amino acid atoms.
Vranken, Wim F
BMC Struct Biol
Springer Science and Business Media LLC
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Vranken, W. F., & Rieping, W. (2009). Relationship between chemical shift value and accessible surface area for all amino acid atoms.. BMC Struct Biol https://doi.org/10.1186/1472-6807-9-20
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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. 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.
External DOI: https://doi.org/10.1186/1472-6807-9-20
This record's URL: http://www.dspace.cam.ac.uk/handle/1810/237637
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Rights Holder: Vranken et al.; licensee BioMed Central Ltd.
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