- Hydrophobicities are a measure of how
strongly the side chains are pushed out of water. The more
positive a number is the more the amino acid residue will have a
tendency NOT to be in an aqueous environment. Negative
numbers indicate hydrophilic side chains, with more negative
numbers indicating greater affinity for water. Numbers from
Eisner, D. et al (1982) Hydrophobic moments in protein
structure. Faraday Symp. Chem. Soc. 17:109-120.
- pKa's listed are for the alpha amino group
(N), the alpha carboxy group (C) and the side chain (R, for
R-group) for free amino acids. The pKa of an R-group
can be altered by the local environment when the amino acid is
part of a protein or peptide. pI's are for the entire free amino
values for protein structure indicate relative frequencies
of occurance of the amino acid in each of the three main protein
structural motifs &endash; alpha helix (a), ß-sheet
(ß) and turn (t). The numbers are corrected for the overall
frequency of the amino acid in proteins. A score of 1.0 indicates
a random occurance of the amino acid residue in that structural
motif. Numbers less than 1 indicate lower than random frequency
(and hence a tendency NOT to promote that structure) and numbers
greater than 1 indicate higher than random frequency (and hence a
tendency to promote that structure).
structures are presented as the predominant form at pH 7.0.
The common part of the amino acids (alpha carbon, alpha amino and
alpha carboxy groups - in the zwitterion form) are outlined in
violet and the R-groups are outlined in white.
structures are presented using the JSmol (HTML5) version of the Jmol Java applet. Structures should display in any modern browser, even those on mobile devices using iOS, Android,
or Windows phone or RT. If you can't see the structures then you are not using a modern HTML5 compatible browser.
To activate them download a newer browser or a different browser. The
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instructions are also available.
Polar but Uncharged AA
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