Side chains numeration of proteins (example Cytochrome C)

[Lindsayyyy]

Hi everybody,

I hope I'm in the right forum. I have a question concerning the side chain numeration. I was reading the following paper

http://www.ncbi.nlm.nih.gov/pubmed/22927377

and they used the some of the following names for the side chains: M65, H33 etc.

What does that mean? What does the M stand for in M65? At first I thought its the one letter code for amino acids, but I'm wrong. Can anyone help me out with this? I'm quite new to the subject. I tried to google it, but I failed.

Thanks for your help

 

[Ygggdrasil]

You are correct about the letters standing for the one letter amino acid codes (so M65 is the methionine at position 65, H33 is the histidine at position 33). I think what's throwing you off is the numbering. Some people count the initial methionine in the sequence as amino acid #1, but often this methionine gets removed during post-translational processing of the protein. In these cases, scientists will often take amino acid number 1 as the amino acid following the initiator methionine (in the case of the horse cytochrome c used in the paper, this would be G1, glycine-1).

In case it's helpful, you can find the amino acid sequence for horse cyt c here (although the numbering system is off by one from the numbering system used by the paper you reference):

http://www.uniprot.org/uniprot/P00004#section_seq