A geometric and algebraic view of MHC-peptide complexes and their binding properties

BMC Structural Biology

Table 4 Distance between logical combinations of HLA and peptide sequence properties.

MHC	HLA sequence variables	Peptide sequence variables	Similarity index
pocket class			(distance)
P2-I.1	Hp = 9, Haa = Y	Pp = 2, Paa = P	0.90
	Hp = 66, Haa = I
	Hp = 67, Haa = Y or F
P2-III.1	Hp = 45, Haa = D or E	Pp = 2, Paa = R or H or K	0.73
P2-IV.1	Hp = 45, Haa = M	Pp = 2, Paa = L or I or M	0.63
	Hp = 63, Haa = E
	Hp = 66, Haa = K
	Hp = 67, Haa = V
P2-IV.2	Hp = 45, Haa = M or T	Pp = 2, Paa = V or S or T	0.48
	Hp = 66, Haa = N
	Hp = 67, Haa = V or M
P2.-V.1	Hp = 9, Haa = S or V	Pp = 2, Paa = Y or F or W	0.85
	Hp = 63, Haa = E or Q
	Hp = 66, Haa = K or R
PΩ-I	Hp= 116, Haa = Y or F or L	Pp = 9, Paa = I or M or L or V	0.59
PΩ-II.1	Hp= 116, Haa = D	Pp = 9, Paa = K or R	0.73
	Hp = 74, Haa = D
	Hp = 77, Haa = D
PΩ-II.2	Hp = 116, Haa = D	Pp = 9, Paa = K or R	0.63
	Hp = 74, Haa = D
PΩ-III	Hp = 116, Haa = D or S	Pp = 9, Paa = Y or F or W or L or I or M	0.19
	Hp = 74, Haa = D or Y
PΩ-III	Hp = 116, Haa = D or S	Pp = 9, Paa = K or R or Y	0.63
	Hp = 74, Haa = D or Y

HLA molecule.- Hp: position number; Haa: amino acid. Peptide.- Pp: position number, Paa: amino acid. For the similarity index (Ochiai index), '1' means total similarity and '0' total absence of similarity; in our study only 4% of distance measurements between isolated sequence variables had an index greater than 0.2, 1% had an index greater than 0.4, 0.1% had an index greater than 0.6, and only in 0.03% of measurements the index was greater than 0.8.

ISSN: 1472-6807