Structural bioinformatics analysis of free cysteines in protein environments

Sheau Ling Ho, Andrew H.J. Wang

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


Cysteine has been considered as a "hydrophilic" amino acid because of its pKa and its ability to form (weak) hydrogen bonds. However, cysteines are found mostly in hydrophobic environments, either in S-S (disulphide) form or in free cysteine form. When free cysteines are found on the surface of proteins, they are often involved in catalytic residues, as in cysteine proteases, P-loop phosphatases, etc. Additionally, a unique property of cysteines is that their side-chain volume is different from all other amino acids. This study is focused on the discrimination between structural versus active free cysteines based on a local environment analysis which does not appear to have been attempted previously. We have demonstrated the corresponding structural positions associated with free cysteines in their three-dimensional localization environment. We examined protein samples including nine, sequenced, coronavirus proteases and cysteine-rich non-membrane proteins. Our present study shows that the sequential environments of free cysteines of coronavirus proteases are rather hydrophobic and that the free cysteines of non-membrane proteases have a higher amount of contacts to hydrophobic residues and lower amount of contacts to polar or charged residues.

Original languageEnglish
Pages (from-to)123-129
Number of pages7
JournalJournal of the Taiwan Institute of Chemical Engineers
Issue number2
Publication statusPublished - Mar 2009
Externally publishedYes


  • Free cysteine
  • Hydrophobic
  • Proteases
  • SH
  • Spatial neighborhood
  • SS
  • Structural bioinformatics
  • Structural preference

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)


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