Table 6

F pocket structures of reference panel alleles.

Residues1

Key residues2

Reference panel allele(s)

Associated supertype(s)

Specificity


DDTLYIIEHYWTKW

DTLH

A*3001

A01 A03

Aromatic and basic

DDTLYIIRDYWTKW

DTLD

A*0301, A*1101

A03

Basic

DDTLYIMQDYWTKW

DTLD

A*3101, A*3301, A*3303, A*7401

A03

Basic

DDTLYIMRDYWTKW

DTLD

A*6801

A03

Basic

DDTLYIRHYYWTKW

DTLY

A*6802

A02

Aliphatic

DDTLYIRQDYWTKW

DTLD

A*6601

A03

Basic

DDTLYLNHDYWTKW

DTLD

B*2703, B*2705

B27

Hydrophobic and basic

DDTLYLNHHYWTKW

DTLH

B*2709

B27

Large hydrophobic

DDTLYLSNYYWTKW

DTLY

B*2707

B27

Large hydrophobic

DDTLYVRHYYWTKW

DTLY

A*6901

A02

Aliphatic

DGNLYWTNFYWTKW

GNLF

B*7301

B27

Large hydrophobic

DNIAYLMHYYWTKW

NIAY

A*2301, A*2402

A24

Large hydrophobic

DNIAYLNHDYWTKW

NIAD

B*2702

B27

Large hydrophobic

DNTAYLSNYYWTKW

NTAY

B*0802

B08

Hydrophobic

DNTLYIIEHYWTKW

NTLH

A*3002-4

A01

Aromatic

DNTLYIIRDYWTKW

NTLD

A*0101

A01

Aromatic

DNTLYIMRDYWTKW

NTLD

A*2902

A01 A24

Aromatic and large hydrophobic

DNTLYIRQDYWTKW

NTLD

A*2601

A01

Aromatic

DNTLYIRQNYWTKW

NTLN

A*2602

A01

Aromatic

DSIAYIMQDYWTKW

SIAD

A*3201

A01

Aromatic

DSNLYLRDSYWTKW

SNLS

B*4601

B62

Large hydrophobic

DSNLYLRNFYWTKW

SNLF

B*3901-2, B*3909, B*6701

B07 B27

Hydrophobic

DSNLYLSDYYWTKW

SNLY

B*0702-3

B07

Hydrophobic

DSNLYLSNYYWTKW

SNLY

B*0705, B*0801, B*4201

B07

Hydrophobic

DSNLYLWNFYWTKW

SNLF

B*1402

B27

Hydrophobic

DSNLYWTNLYWTKW

SNLL

B*5401, B*5501-2, B*5601

B07

Small hydrophobic

DSNLYWTNYYWTKW

SNLY

B*7801

B07

Hydrophobic

DSTLYLNDYYWTKW

STLY

B*2706

B27

Large hydrophobic

DSTLYLNHDYWTKW

STLD

B*2704

B27

Large hydrophobic

HDTLYIRQDYWTKW

DTLD

A*2603

A01

Aromatic

HDTLYLMHYYWTKW

DTLY

A*0217

A02

Aliphatic

HDTLYLRHYYWTKW

DTLY

A*0202, A*0205, A*0214

A02

Aliphatic

HDTLYVMHYYWTKW

DTLY

A*0204

A02

Aliphatic

HDTLYVRHYYWTKW

DTLY

A*0201, A*0203, A*0206-7

A02

Aliphatic

YDTLYIRNFYWTKW

DTLF

B*3701

B44

Hydrophobic

YNIAYIRDSYWTKW

NIAS

B*1513, B*5301, B*5801

B07 B58 B62

Large hydrophobic

YNIAYIVDSYWTKW

NIAS

B*5701

B58

Large hydrophobic

YNIAYIVNYYWTKW

NIAY

B*5702

B58

Large hydrophobic

YNIAYLRHDYWTKW

NIAD

B*1517

B58

Large hydrophobic

YNIAYLRNFYWTKW

NIAF

B*3801

B27

Large hydrophobic

YNIAYLWDSYWTKW

NIAS

B*5802

B58

Large hydrophobic

YNIAYWRDSYWTKW

NIAS

B*1516

B58

Large hydrophobic

YNIAYWTNYYWTKW

NIAY

B*5101-3, B*5201

B07 B62

Large hydrophobic

YNTAYIRDDYWTKW

NTAD

B*4402-3

B44

Hydrophobic

YSNLYIRDFYWTKW

SNLF

B*3503

B07

Hydrophobic

YSNLYIRDSYWTKW

SNLS

B*1502, B*3501

B07 B62

Hydrophobic

YSNLYLRDSYWTKW

SNLS

B*1501, B*1503, B*1508, B*1512, B*1518, B*1801

B07 B27 B44 B62

Large hydrophobic

YSNLYLRDYYWTKW

SNLY

B*1510

B27

Hydrophobic

YSNLYLRNYYWSKL

SNLY

B*4001

B44

Hydrophobic

YSNLYLRNYYWTKW

SNLY

B*1509

B27

Hydrophobic

YSNLYLSNYYWSKL

SNLY

B*4801

B27

Hydrophobic

YSNLYLSNYYWTKW

SNLY

B*4002

B44

Hydrophobic

YSNLYWRNLYWTKW

SNLL

B*4501

B44

Small hydrophobic

YSNLYWTNYYWTKW

SNLY

B*4006

B44

Hydrophobic


1. Based on data presented in Saper et al, and Madden (see Methods), the MHC residues utilized as constituting the F pocket are: 74, 77, 80, 81, 84, 95, 97, 114, 116, 123, 133, 143, 146, and 147. Key residues are those in positions 77, 80, 81, and 116.

2. The key residue pockets DTLD, DTLH and DTLY are each associated with two different, although overlapping, specificity descriptions. In each case, one description is associated with HLA B27 alleles, and in the other with HLA A alleles. In assigning key residue matches, matches were assigned on the basis of corresponding locus.

Sidney et al. BMC Immunology 2008 9:1   doi:10.1186/1471-2172-9-1

Open Data