Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

Table 2 Site pairs with the highest covariation scores.

Domain family Ref. PDB Structure rank	Natural 2H2C		Synthetic PDZ 2H2C		SH3 1N5Z		Kinase 1ATP
	PRD	Peptide	PRD	Peptide	PRD	Peptide	PRD	Peptide
1	Leu60	Trp119	His88	Thr118	Asn71	Leu7	Tyr229	Ile22
2	Val55	Thr117	Ala37	Thr117	Leu34	Leu7	Leu205	Ile22
3	Ala76	Thr117	Ser39	Thr117	Ile73	Leu7	Leu198	Ile22
4	Pro30	Trp119	Leu60	Thr117	Tyr72	Leu7	Lys189	Ile22
5	Ser98	Trp119	Val92	Thr118	Lys35	Leu7	Phe129	Ile22
6	Ala89	Thr117	Ser57	Thr117	Ser44	Leu7	Glu230	Ile22
7	Gln93	Trp119	Asp58	Thr117	Lys61	Leu7	Glu203	Ile22
8	Asp58	Thr117	Phe34	Thr118	Ile68	Leu7	Ile180	Ile22
9	Ala37	Thr117			Leu20	Leu7	Phe187	Arg19
10	Lys103	Trp119			Ala17	Leu7	Cys199	Ile22

For each site on the PRD, only the site on the peptide with the highest score is shown. For synthetic PDZ domains, only ten sites have variations and among them two were filtered, leaving only eight valid sites. All sites are indexed according to their residue numbers in the reference PDB structures.

ISSN: 1741-7007