Is it Ionic interactions (O-N) or hydrogen bonding (O-H2)?
What are the criteria to identify these interactions?
Usually an alkyl amine R-NH2 is ionized in water at a neutral Ph and becomes R-NH3+ positively charged. If the oxygen in question is a carboxyl oxygen (with charge -1) the interaction will be (COO-) ----- (R-NH3+) which can be considered salt bridge (distance < 4 Angstrom). If the oxygen is an hydroxyl group ( Ser, Thr, Tyr) or a carbonyl group (backbone or Gln and Asn), the hydrogen in R-NH3+ can be donated for an hydrogen bond in which is involved the lone pair of the oxygen. Usually the distance between donor and acceptor must be in the range 2.8-3.5 Angstrom to consider the interaction as an HB.
the greater part of the time, the interaction between the two proteins are due to electrostatic interactions between arginine or lysine ( formal charge +1 at physiological pH) and glutamate or aspartate( formal charge -1 at physiological pH).
O=C-O-----H-N O=C-O----- NH3
or sometimes with weaker interactions like hydrogens bond Connections between asparagine or glutamine O = CNH ------ OC = O and aspartate or glutamate.
the best way is to calculate local pKa for determinated which is the protonation state of the considered residus. you can do this with ProPka 3.1 web server.
Usually an alkyl amine R-NH2 is ionized in water at a neutral Ph and becomes R-NH3+ positively charged. If the oxygen in question is a carboxyl oxygen (with charge -1) the interaction will be (COO-) ----- (R-NH3+) which can be considered salt bridge (distance < 4 Angstrom). If the oxygen is an hydroxyl group ( Ser, Thr, Tyr) or a carbonyl group (backbone or Gln and Asn), the hydrogen in R-NH3+ can be donated for an hydrogen bond in which is involved the lone pair of the oxygen. Usually the distance between donor and acceptor must be in the range 2.8-3.5 Angstrom to consider the interaction as an HB.
I'm agree with Davide Pirolli, just one precision, the distance given are between heavy atom ( as CNO ) , H isn't take into account in these distances.
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