HA sequencing numbering

Confusingly, HA protein sequences are numbered a variety of different ways in the literature. There are historical reasons for these different numbering schemes (see here for a partial explanation).

For the plots shown on this website, site refers to H3 numbering, which numbers the H5 HA ectodomain in a way that puts its sites into correspondence with the H3 HA ectodomain. Note that in many cases, mousing over points also shows their number in other numbering schemes.

Click here for a file that intra-converts the various numbering schemes for the H5 HA used in our experiments (the sequence of that HA protein is here). The different numbering schemes in that file are as follows:

• sequential_site: sequential 1, 2, ... numbering of the H5 HA protein starting with 1 at the N-terminal methionine.
• reference_site: numbering using the widely used H3 numbering scheme, which puts sites into alignment with the mature ectodomain of the H3 subtype HA. Because H3 was the first HA studied in detail using structural methods, this is the most widely used scheme and all of the interactive plots on this webpage use this numbering scheme for the default site number.
• reference_H1_site: numbering using the H1 numbering scheme which puts sites into alignment with the mature ectodomain of the H1 subtype HA.
• mature_H5_site: numbering with 1 starting with the first amino acid of the mature H5 HA ectodomain (after cleavage of the signal peptide) and then continuing sequentially. Sites in the signal peptide get negative numbers.
• HA1_HA2_H5_site: sequential numbering as for the sequential_site scheme but starting with 1 for the HA1 domain, and then starting again with 1 for the HA2 domain.