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. 2008 Oct 14;3:42. doi: 10.1186/1745-6150-3-42

Table 3.

Selected alleles, their representative peptides and motifs

Peptide       Sequence and motif      allele
          1xx4x6xx9          
CLIP peptide 81–104 LPKPPKPVSKMRMATPLLMQALPM      DR3
MET proto-oncogene 724–735           LKIDLANRETSI        DR3
HSP70 M leprae 261–280     DSDKNPLFLDEQLIRAEFQR      DR3
HSP70 M leprae 408–427        QPSVQIQVYQGEREIASHNK   DR3
SSX2 37–51        WEKMKASEKIFYVYM        DR3
Tetanus toxin 830–843         QYIKANSKFIGITE        DR3
Preproinsulin 78–88         QPLALEGSLQK           DR4
ER-60 protease       TEDEFKKFISDKDASVVG      DR4
14-3-3 epsilon 57–71        RASWRIISSIEQKEE        DR4
GAD65 274–286         IAFTSEHSHFSLK         DR4
GAD65 471–490  VDKCLELAEYLYNIIKNREG         DR4
Aminopeptidase 462–475           FELFPSLSHNLLVD      DR4
β2 microglobulin 64–78          LYYTEFTPTEKDEY       DR0405
der pII 58–73        IDGLEVDVPGIDPNA        DR0405
HSP90 beta 68–81       KELKIDIIPNPQER          DR0405
Fel d1 22–37      EQVAQYKALPVVLENA         DR0405
Integrin β3 24–39          AWCSDEALPLGSPRCD     DR52a
AChR alpha 144–163      MKLGTWTYDGSVVAINPESD     DR52a
AChR epsilon 201–219       ENGEWAIDFCPGVIRRHHG     DR52a
Lol p1 101–120         APYHFDLSGHAFGSMAKKG   DR52a
Influenza A HA 306–324         PKYVKQNTLKLATGMRNVP   DR7
HSP70 M Leprae 241–260       AKIELSSSQSTSVNLPYITV    DR7
HIV-1 RT 326–345           FRKQNPDIVIQYMDDLYVG DR7
HLA class I α52–60           IEQEGPEYW           DQ2
Flu NP 265–278          IASNENMDAMESSTL      DQ2
M leprae 18 kD 31–43          DAWREGEEFVVEF        DQ2
Rabies virus NP 11–24        NNQVVSLKPEIIVDQ        DQ2
Thyroid peroxidase 632–645        IDVWLGGLAENFLP         DQ2
Thyroid peroxidase 632–645          IDVWLGGLAENFLP       DQ8
Trail receptor 2 364–380       GRFTYQNAAAQPETG         DQ8
Cyclophilin R 325–340       VDQWSTETIASHEDIE        DQ8
Cathepsin D 65–77        EPVSELLKNYLDA          DQ8
E25B protein 112–126       YQTIEENIKIFEEDA         DQ8
I-A2B 644–658      GGDPGADATAAYQEL          DQ8
I-A2B 762–776         KNRSLAVLTYDHSRV       DQ8
GAD65 121–140      YVVKSFDRSTKVIDFHYPNE     DQ8
GAD65 231–250   PGGSGDGIFSPGGAISNMYA        DQ8
GAD65 248–259          NYAMMIARFKMF         DR3
GAD65 250–273     AMMIARFKMFPEVKEKGMAALPRL  DQ8
GAD65 471–490   VDKCLELAEYLYNIIKNREG        DR4
I-A2 961–979         FEFALTAVAEEVNAIL      DQ8
I-A2 961–979          FEFALTAVAEEVNAIL     DQ8
ICA69 33–50       TKQAFIKATGKKEDEHVV      DQ8
Insulin B:9–23       SHLVEALYLVCGERG         DQ8
Insulin B:24-C:4          FFYTPKTRREAED        DQ8

Epitopes of several class II MHC molecules are aligned manually according to their pocket motif. The major diabetes susceptibility molecules DR3, DR4. DR405 and DQ8 show a strong preference for polar residues at position P9. Acidic residues such as Asp and Glu are common at this position but there are also basic and other polar residues. In contrast alleles that are neutral (DR7 and DR52a) show a preference for aliphatic and hydrophobic residues at P9. DQ2 shows no preference for acidic residues at P9 that characterize diabetogenic molecules. Sequence information comes from several sources including [46].