Dismiss Notice
Join Physics Forums Today!
The friendliest, high quality science and math community on the planet! Everyone who loves science is here!

Side chains numeration of proteins (example Cytochrome C)

  1. Jan 7, 2014 #1
    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


    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
  2. jcsd
  3. Jan 7, 2014 #2


    User Avatar
    Science Advisor
    2017 Award

    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):

Share this great discussion with others via Reddit, Google+, Twitter, or Facebook