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*A scale combining hydrophobicity and hydrophilicity of R groups; it can be used to measure the tendency of an amino acid to seek an aqueous environment (- values) or a hydrophobic environment (+ values). See Chapter 11. From Kyte, J. & Doolittle, R.F (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.

*A scale combining hydrophobicity and hydrophilicity of R groups; it can be used to measure the tendency of an amino acid to seek an aqueous environment (- values) or a hydrophobic environment (+ values). See Chapter 11. From Kyte, J. & Doolittle, R.F (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.

fAverage occurrence in more than 1,150 proteins. From Doolittle, R.F (1989) Redundancies in protein sequences. In Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G.D., ed.), pp. 599-623, Plenum Press, New York.

Amino Acids Can Be Classified by R Group

Knowledge of the chemical properties of the common amino acids is central to an understanding of biochemistry. The topic can be simplified by grouping the amino acids into five main classes based on the properties of their R groups (Table 3-1), in particular, their polarity, or tendency to interact with water at biological pH (near pH 7.0). The polarity of the R groups varies widely, from nonpolar and hydrophobic (water-insoluble) to highly polar and hydrophilic (water-soluble).

The structures of the 20 common amino acids are shown in Figure 3-5, and some of their properties are listed in Table 3-1. Within each class there are gradations of polarity, size, and shape of the R groups.

Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and hydrophobic. The side chains of alanine, valine, leucine, and isoleucine tend to cluster together within proteins, stabilizing protein structure by means of hydrophobic interactions. Glycine has the simplest structure. Although it is formally nonpolar, its very small side chain makes no real contribution to hydrophobic interactions. Methionine, one of the two sulfur-containing amino acids, has a nonpolar thioether group in its side chain. Proline has an

Nonpolar, aliphatic R groups

COO-

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