Abstract: Finding different clusters in sequence plays major role in the computational biology, which could help as evidence of structural and functional conservation, as well as of evolutionary relations among the sequence. Functionally related genes often appear in other’s neighborhood on the genome. However, the order of the genes may not be at the same. These groups or clusters of genes may have an ancient evolutionary origin or may signify some other critical phenomenon and may also serve in function prediction. Similarly, cluster of protein domains as appearing in different orders in the protein sequence and suggests more functional parts. Proteins are the large organic compounds made of amino acid in a linear fashion. The side chains of these amino acids are chemically different from one another in some respect can be classified broadly two ways hydrophobic and hydrophilic. Carbon content in these side chains makes the amino acids. It is easily demonstrable that the linear amino acid sequence completely specifies the three dimensional shapes. The study is carried out for prediction of possible cluster in carbon atom rich and low amino acids using permutation method. It is interesting to observe that permutations involving as many as large hydrophobic residues or clusters.