Table 2 Summary of the analysis performed on cladograms for the whole groove and five sub-pockets. For a pair of different alleles, the pair of molecules obtaining high PM₁₃ Score on whole groove or sub-pocket comparison is presented. Literature citation for other independent work supporting the observation is also provided wherever possible. The examples shown here refer to different alleles that appear in the same branch of the clustergarm computed either by using the whole grooves or by their individual sub-pockets as indicated in each row.

DQB1*0602-DQB1*0302

(1UVQ, 1JK8)

whole

0.83

The involvement of the two alleles DQB1*0602 and DQB1*0302, negatively and positively associated with Type 1 diabetes is reported by Siebold and co-workers [22]

(1UVQ, 2NNA)

0.75

(1UVQ, 2NNA)

P4

0.74

(1UVQ, 1JK8)

P7

0.71

DQB1*0201, 2-DRB1*1501

(1S9V, 1BX2)

P7

0.4

DQB1*0201, 2-DRB1*1501

(1S9V, 1BX2)

P9

0.08

DRB1*0401-DRB1*0101

(2SEB, 2FSE)

P9

0.61

(1J8H, 2IPK)

0.85

The study by Rosloniec and co-workers [13] indicate the association of the two alleles are known to be associated with RA.

DRB1*1501-DRB1*0101

(2WBJ, 1LO5)

P9

0.69

These observations agree with the study by Smith and co-workers [23] that reports the similarity of the P9 sub-pocket. Study by Drouin and co-workers [24] refer to the association of the two alleles with antibiotic-refractory arthritis.

(1YMM, 1KLU)

0.59

(1YMM, 2IAM)

0.66

DRB1*1501-DRB1*0301

(1BX2, 1A6A)

whole

0.80

Both alleles came in two branches under a common root which is in accordance with a study by Zivadinov and co-workers [25] that associates the two alleles to Multiple sclerosis.

DRB3*0101-DRB1*0101

(2Q6W, 1HXY)

P1

0.66

DRB3*0101-DRB1*0301

(2Q6W, 1A6A)

P4

0.54

The two molecules are grouped together. Though the score is only 0.54, there are no other molecules they could come similar to with matching allele types. The study by Parry and co-workers [26] indicate the expected similarity in the P4 sub-pocket and correlate the differences in other subpockets and the differences in P4 itself to difference between the two alleles in susceptibility to Type 1 diabetes.

DRB3*0301-DRB1*0401

(3C5J, 1J8H)

P6

0.43

(3C5J, 2SEB)

0.37

(3C5J, 2SEB)

P7

0.77

DRB5*0101-DRB1*0101

(1HQR, 1PYW)

whole

0.78

(1HQR, 2G9H)

P1

0.9

Meinl and co-workers [27] also report similarity between the two allele types in recognition of myelin basic protein. The P1 similarity between the two alleles is reported by Jurcevic and co-workers [28].

(1H15, 1DLH)

whole

0.8

(1H15, 1LO5)

P1

0.73

(1ZGL, 1JWM)

P1

0.8

DRB5*0101-DRB1*0301

(1FV1, 1A6A)

P1

0.81

Though P1 score is high, the other subpocket scores are low (less than 0.34) which is in accordance with study by Texier and co-workers [29] that reports difference between the two alleles in their peptide binding properties.

P9

0.56

(1FV1, 1R5W)

P9

0.6

(2Q6W, 3C5J)

P9

0.84

This similarity of P9 is a known feature [30] for the two, DR52a and DR52c alleles which are encoded by the DR3 gene whose alleles are all associated with autoimmune diseases.

DQB1*0602-H2-Aa, H2-Ab1

(1UVQ, 1IAK)

P6

0.64

Orthologous alleles from human and mouse [31].

(1UVQ, 1JL4)

P9

0.71

(1UVQ, 2IAD)

P9

0.75

DQB1*0201-H2-Aa, H2-Ab1

(1S9V, 2PXY)

whole

0.73

(1S9V, 2Z31)

0.79

(1S9V, 3CUP)

0.78

(1S9V, 1MUJ)

P1

0.57

DRB1*0101-H2-Aa, H2-Ab1

(1AQD, 1K2D)

P1

0.52

(1D9K, 1SJE)

P9

0.46

(1D9K, 1SJH)

P9

0.53

DRB1*0301-H2-Aa, H2-Ab1

(1A6A, 1LNU)

whole

0.83

(1A6A, 1IAO)

0.83

DRB1*1501-H2-Aa, H2-Ab1

(2WBJ, 1IAO)

P7

0.42

(2WBJ, 1LNU)

0.57

DRB1*1501-H2-Ea, H2-Eb1

(1R5V, 1BX2)

P6

0.65

Orthologous alleles from human and mouse.