Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study

BMC Structural Biology

Table 3 Pair energies in peptide binding pocket 1

DP chain	position	aa	peptide position	aa	E_total	E_atr	E_rep	E_sol	E_hbnd
A	9	Tyr	1	Phe	0.02	−0.4	0	0.41	0
A	24	Phe	1	Phe	−0.46	−0.45	0	−0.01	0
A	32	Phe	1	Phe	−1.69	−1.64	0	−0.05	0
A	43	Trp	1	Phe	−0.01	−0.13	0	0.12	0
A	52	Phe	1	Phe	−0.39	−0.42	0	0.04	0
A	53	Ser	1	Phe	−0.88	−0.50	0	0.33	−0.71
A	54	Phe	1	Phe	−0.75	−1.50	0.41	0.34	0
A	55	Glu	1	Phe	0.01	−0.01	0	0.02	0
B	80	Asn	1	Phe	−0.12	−1.52	0.03	1.38	0
B	83	Leu	1	Phe	−0.11	−0.15	0	0.04	0
B	84	Gly	1	Phe	−0.17	−0.21	0	0.04	0
sum					−4.55	−6.93	0.44	2.66	−0.71

Polymorphic residues are given in bold. E_tot corresponds to the sum of all energies between the pair residues; E_atr and E_rep are the Lennard – Jones attractive and repulsive energies, respectively; E_sol – the solvatation energy; E_hbnd – energy of hydrogen bonding per residue; E_pair – statistics-based pair term.

ISSN: 1472-6807