I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy).
How can I identify donor and acceptor atoms in a chain?
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Sign up to join this communityI know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy).
How can I identify donor and acceptor atoms in a chain?
A hydrogen bond donor heavy atom is one that is protonated, while the acceptor has a lone pair. If you talking about amino acids, then it's simple as they are fixed.
atom name | description | role | note |
---|---|---|---|
N |
backbone nitrogen | donor | SS |
CA |
backbone Cα | apolar | |
C |
backbone carboxyl C | sterically hindered and electrophilic | nucleophilic attack |
O |
backbone carboxyl O | acceptor | SS |
CB etc. |
sidechain carbons | apolar | |
OXT |
C-terminal oxygen | acceptor | may be protonated especially if a membrane embedded C-terminus |
Serine's OG / Threonine's OG1 |
sidechain hydroxyl | donor | SS: may form ST turns. Fairly uncommon: may be a donor |
Asp OD1 /OD2 /Asn OD1 |
sidechain carboxyl/amide O | acceptor | SS: may form Asx turns |
Glu OG1 /OG2 /Gln OG1 |
sidechain carboxyl/amide O | acceptor | |
Lysine NZ |
sidechain amine | donor | |
Asn ND2 / Gln NG2 |
terminal admide N | donor | the direction of an Asn/Gln may be accidentally filled if manually assigned as N/O have the same density in X-ray crystals |
Water can be both a donor and an acceptor. Two charged residues form a salt bridge more so than a hydrogen bond, because the interaction is driven by the Coulomb electrostatic forces of the two heavy atoms.
Atom
object? I mean, can I test or search it using BioPython?
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Oct 28, 2021 at 10:49
Atom
instance is a graph network node representation of any atom. It may be a hydrogen —_in silico_ protonated, neutron diffraction or 1H NMR. Technically to the most pedantically punctilious level, it could be virtual (e.g. Drude particle)...
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Oct 28, 2021 at 10:57