AW: Histidine

Dear Meena,
 the way I do this is to inspect each HIS residue manually and have a look on
 the surrounding amino acids in terms of ionization state and hydrogen bond
 donor/acceptor capabilities. In many cases you get a good hint about where
 to put the proton, especially if you have a GLU or an ASP in hydrogen
 bonding distance, there is a good chance, that the HIS will form a salt
 bridge, hence it carries protons on both nitrogens. In analogy you can make
 a decision to put the proton on N(delta) or N(epsilon) depending on the
 closeness of HB donors/acceptors. In cases, where I can not make a clear
 estimate, I arbitrarily put the proton on N(delta).
    Dr. Christian Pilger
    Dept. Chemical Research / Structural Research
    Boehringer Ingelheim Pharma KG
    D-88397 Biberach/Germany
    Phone: 07351-545749
    Fax:     07351-5497924
    mailto: christian.pilger { *at * }