U. C. Davis, Biological Sciences
Molecular and Cellular Biology

Amino Acid Structure/Function


  1. 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.


  2. 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 acid.


  3. Numerical 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).


  4. Chemical 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.

  5. 3-D 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 structures are "live" and can be manipulated with your mouse. Alternative views can be activated through a menu that can be brought up by right-clicking or control-clicking on an image or by mousing down on the "Jmol" in the lower right corner. Brief instructions are also available.


Back to Amino Acid Properties Page

Aliphatic AA

Aromatic AA

Polar but Uncharged AA

G, A, V, L, I, P

F, Y, W

S, T, N, Q

Suflur Containing AA

Charged AA

C, M

D, E, H, K, R

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Copyright© Charles S. Gasser 2010