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Table 4 Sub-pocket similarities. (A) Sub-pocket similarities between a pair of alleles HLA-DR4.1 [PDB:1J8H] and HLA-DR4.2 (model) are shown. The residues of the peptide are shown on the left most column. Residue numbers 311 and 314 correspond to P4 and P7 respectively. The low PM13Scores are shown in boldface. (B) Variation of the P4 similarity scores among HLA-DRB1*0101 [PDB:1DLH], HLA-DR4.1 [PDB:1J8H], HLA-DR4.4 and HLA-DR4.2 are shown. (C) Variation in P7 similarities are shown for proteins mentioned under (B).

From: An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

(A) - HLA-DR4.1(1J8H-abc) and HLA-DR4.2(model)

Pocket

Residue

PMSMin

PMSMax

P1

Tyr308

0.85

0.91

P4

Gln311

0.79

0.85

P6

Thr313

0.89

0.89

P7

Leu314

0.53

0.71

P9

Leu316

1.0

1.0

(B) - P4 (Gln311)-similarity

PDB/MODEL

PDB/MODEL

PMSMin

PMSMax

1DLH

1J8H

0.56

0.60

1DLH

HLA-DR4.2

0.53

0.53

1DLH

HLA-DR4.4

0.63

0.68

1J8H

HLA-DR4.2

0.79

0.85

1J8H

HLA-DR4.4

0.86

0.86

HLA-DR4.2

HLA-DR4.4

0.74

0.79

(C) - P7 (Leu314)-similarity

PDB/MODEL

PDB/MODEL

PMSMin

PMSMax

1DLH

1J8H

0.44

0.58

1DLH

HLA-DR4.2

0.50

0.50

1DLH

HLA-DR4.4

0.67

0.67

1J8H

HLA-DR4.2

0.53

0.71

1J8H

HLA-DR4.4

0.60

0.81

HLA-DR4.2

HLA-DR4.4

0.57

0.57