Amino Acid Physicochemical and Structural Features

A large number of chemical and physical properties, manifest in the amino acid side chains, have been thoroughly examined by many investigators. Attempts have been made to correlate these properties with their relatedness among protein sequences. What is most relevant is how these side chains interact with the backbone and with one another and what roles they each play within particular types of secondary and tertiary structure. The parametric description of residue environments with the help of solvent accessibility, secondary structure, backbone torsion angles, pairwise residue-residue distances, or Ca positions is the comparison between amino acid types at protein sequence positions and residue locations in structural templates. A recent review has evaluated and quantified the extent to which the amino acid type-specific distributions of commonly used environment parameters discriminate with respect to the 20 amino acid types (Sunyaev et al., 1998). Some of the important amino acid properties and residue environments are discussed below. 

Hydrophobicity is believed to play a major role in organizing the self-assembly of protein molecules. Patterns of hydrophobic versus hydrophilic side chains are very in predicting secondary and tertiary structure simply by virtue of their preferential occurrence on the inside versus outside of various structural features. Those hydrophobicity patterns 

Amino Acid Residues (3-, 1-letter code) Chemical Property Volume (A3) Mass (daltons) HP Scale K D Surface 2D Structure Propensity Area a-heiix P-strand Turn  

Volume = Volume enclosed by van der Waals radii Mass = molecular weight of nonionized amino acid minus that of water both adopted from Creighton (1993) HP scale = degree of hydrophobicity of amino acid side chains, based on Kyte Doolittle (1982) Surface Area = mean fraction buried, based on Rose et al. (1985) and Secondary structure propensity = the normalized frequencies for each conformation, adopted from Creighton (1993), is the fraction of residues of each amino acid that occurred in that conformation, divided by this fraction for all residues. 

Some other physicochemical and structural properties include polarity, volume, bulkiness, and refractivity. 

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