Abstract
Knowledge about protein function is essential in understanding the biological processes. A specific class or family of protein shares common structural and chemical properties amongst its member sequences. The set of properties that display its unique characteristics for clearly classifying a protein sequence into its corresponding protein family needs to be studied. Our study of these important properties conducted on four major classes of proteins namely Globins, Homeoboxes, Heat Shock proteins (HSP) and Kinase have shown that frequency of twenty naturally occurring amino acids, hydrophobic content of protein, molecular weight of protein, isoelectric point of protein, secondary structure composition of amino acid residues as helices, coils and sheets and the composition of helices, coils and sheets in the secondary structure topology plays a significant role in correctly classifying the protein into its corresponding class or family as indicated by the overall efficiency of Nearest Neighbor Classifier as 84.92%.