Figure 6

Smoothing positions of PPI regions. Amino acid sequence is represented as a bit string in which 1 indicates those residue positions that are involved in PPI, and 0 – those that are not. Subsequently smoothing is conducted such that contact segments separated by spacers shorter than N residues are merged, and then the segments shorter than M are deleted. In this example a sequence fragment of the human importin β-chain (PDB code 1ibr; residue positions from 7 to 77) is shown which interacts with the GTP-binding nuclear protein RAN. The interaction involves residues situated on one side of two α-helices. After smoothing with N = 5 and M = 1 entire helices are considered interacting regions.