U. C. Davis, Biological Sciences

Amino Acid Structure/Function

Footnotes

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. pK_a'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 pK_a 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. To view 3-D structures you need the Chime plug-in which is available from MDL Information Systems, Inc. 3-D Images can be rotated (mouse down on the structure and pull to rotate on a Mac, use the Left mouse button on a Windows computer) or altered (mouse down on an image on the Mac and wait for the menu, use the right mouse button in Windows, the menu can also be brought up by clicking on the "MDL" at the lower right corner of the structure). You can zoom in and out on the image ("Shift" and use the mouse on the Mac, "Shift" and and use the left mouse button in Windows). More information is available on the Chime FAQ page.

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Copyright© Charles S. Gasser 1996