Obtaining MHC peptide binding groove protein sequences

Question

[krc3004]

Hi all,

I am trying to obtain the protein sequences of the peptide binding grooves of MHC class I and class II alleles, but am unsure how to go about it. We know that for class I, the peptide binding groove is exons 2 and 3, and for class II the binding groove is exon 2, but I'm not sure how to extract these from the allele sequences.

The protein sequences for all HLA alleles are easily obtainable from IMGT, i.e. https://www.ebi.ac.uk/ipd/imgt/hla/download.html. But it is not clear how to extract the protein sequences of the indicated exons. Perhaps there is a way using bioconductor and annotations from ensembl, or someone has already compiled these?

Would greatly appreciate any tips. Thanks!