Amino acid neighbours and detailed conformational analysis of cysteines inproteins

Here we present an investigation of the contacts that cysteines make with r esidues in their three-dimensional environment and a comprehensive analysis of the conformational features of 351 disulphide bridges in 131 non-homolo gous single-chain protein structures. Upstream half-cystines preferentially have downstream neighbours, whereas downstream half-cystines have mainly u pstream neighbours. Non-disulphide bridged cysteines (free cysteines) have no preference for upstream or downstream neighbours. Free cysteines have mo re contacts to non-polar residues and fewer contacts to polar/charged resid ues than half-cystines, which correlates with our observation that free cys teines are more buried than half-cystines. Free cysteines prefer to be loca ted in a-helices while no clear preference is observed for half-cystines, H istidine and methionine are preferentially seen nearby free cysteines, Tryp tophan is found preferentially nearby half-cystines, We have merged sequent ial and spatial information, and highly interesting novel patterns have bee n discovered. The number of cysteines per protein is typically an even numb er, peaking at four. The number of residues separating two half-cystines is preferentially 11 and 16, Left-handed and right-handed disulphide bridges display different conformational parameters. Here we present side chain tor sion angle information based on a 5-12 times larger number of disulphide br idges than has previously been published. Considering the importance of cys teines for maintaining the 3D-structural scaffold of proteins, it is essent ial to have as accurate information as possible concerning the packing and conformational preferences. The present work may provide key information fo r engineering the protein environment around cysteines.