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

From: A geometric and algebraic view of MHC-peptide complexes and their binding 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   
  1. 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.