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.

Cano and Fan BMC Structural Biology 2001 1:2   doi:10.1186/1472-6807-1-2