Table 3

Seven 2009-H1N1 T cell epitope candidates that could be cross-reactive with 2004-H5N1 T cell responses.

2009_H1N1

position

Strain

Sequence

MHC-bound predicted score

Docked to HLA-B*4405

Docked to DM1-TCR


Energy

Energy


50

2009-H1N1

LE

    D
KHNGKL

1.0508

-661.4

-552.1

2004-H5N1

LE

    KT
HNGKL

1.1478

-715.0

-682.2

412

2009-H1N1

    K
EFNHLEKR

0.9764

-599.5

-737.2

2004-H5N1

    R
EFNNLEKR

0.9949

-638.9

-640.8

446

2009-H1N1

LENERTLD

    Y

1.1929

-603.1

-621.1

2004-H5N1

    M
ENERTLDF

1.5813

-563.5

-667.2

493

2009-H1N1

MESVKNGTY

1.73

-543.0

-645.0

2004-H5N1

MESV

    R
NGTY

1.6645

-595.0

-667.5

421

2009-H1N1

IENLNKK

    V
D

0.8563

-464.6

-666.0

2004-H5N1

IENLNKKME

0.7968

-466.1

-642.0

475

2009-H1N1

KE

    I
GNGCFE

0.9892

-519.6

-715.4

2004-H5N1

KE

    L
GNGCFE

0.8258

-548.9

-733.8

482

2009-H1N1

FEFYHKCDN

1.1128

-846.8

-743.9

2004-H5N1

FEFYHKCDN

1.1129

-846.8

-743.9


*Different residues are underlined. The residues that interacted with DM1-TCR are highlighted in bold.

Two significant changes in TCR binding energy are marked in bold.

Su et al. BMC Bioinformatics 2013 14(Suppl 2):S21   doi:10.1186/1471-2105-14-S2-S21

Open Data