Hello Vivek, As Brian has mentioned, the angle is an important aspect, but most people consider distances of 2.4 to 3.2 (although there is some variability here to go slightly longer/ shorter, say 2.3 to 3.3) Angstrom to be a hydrogen bond distance between two 'heavy' atoms like oxygen and nitrogen. If you are interested in 'seeing' the hydrogens, you can add these to your model to see where they are automatically placed. >From your figure, your density is not perfect and I suggest that you drop the >last digit (2.61 should be 2.6) as you have at least 0.1 Angstrom error in >these positions. On first inspection without knowing anything other than the >figure you sent, it looks like it is a likely hydrogen bond distance and a >likely pair of side chains that are positioned to make that hydrogen bond.
Best of luck, tom Tom Peat, PhD Proteins Group Biomedical Program, CSIRO 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of vivek sharma <rviveksharm...@gmail.com> Sent: Monday, June 7, 2021 6:05 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] H-bond modelling Dear all, How does one validate if 2 atoms (non-hydrogen) which are close enough, actually participate in H-bonding? I have a recent data that i am currently working on, the NH2 of ARG is at 2.61A from ligand's oxygen atom (refer to attached image), since there is no electron density for hydrogens, how can i be sure if i am modelling ligand correctly? thanks ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
