Cysteine has a hydropathy score that reflects its overall preference for non-polar environments compared to some other polar amino acids, meaning it can be somewhat hydrophobic. Its positive hydropathy index value suggests that it has some hydrophobic qualities, making it more favorable in non-polar environments compared to very polar amino acids.
Dear Homasadat Esfahani You stumbled on the shortcoming of every individual hydrophobicity scale (which is behind every bioinformatics method that can predict the hydrophobicity).
In general the overall 'consensus is that cysteine is (moderate) hydrophobic.
See for example: Data keller3biotech2015suppl.docx
where a comparison between some of the most frequently used scales is made.See also https://en.wikipedia.org/wiki/Cysteine (scroll to "Roles in protein structure") which indicates quite accurately the nuanced view on this matter (there is for example a big difference whether you consider the individual AA or look at the amino acid in the context of the protein and/or when the protein is in its 'natural environment').
Best regards.
Dear Rob Keller ,
Thank you so much for your insightful comments regarding the hydrophobicity scales and the role of cysteine. I appreciate you pointing out the nuances involved and providing additional resources for further reading. It's always valuable to have such depth of understanding in discussions about protein structure.
Best regards, Homasadat Esfahani
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