CONNECTION TOPOLOGY OF PROTEINS

One-dimensional amino acid sequences and three-dimensional folded poly peptide chains were modelled as non-directed graphs in which nodes cor responded to amino acids and arcs represented connections between them . In the case of folded chains, non-backbone connections were assigned to amino acid pairs if their distance was lower than a threshold. Two topological indices, the connectedness number and the effective chain length were devised to compare folding topologies. Loops created by n on-backbone connections in the structure graphs were studied by simple graphical representations, revealing the hierarchy in native protein structures.