Appendix B - PDB Atom Definitions

PDB Designation of Amino Acid Structure

This is the standard backbone labelling for an amino acid. Note that OXT will only appear on the C-terminal amino acid

The 20 side chains are labeled as follows

PDB Designation of Nucleotide Structure

The following scheme for labeling the sugar phosphate backbone of polynucleotides is constant, with only the structure of the base, B, varying. Note that O2* only exists in ribonucleic acid structures and that O3P only exists at the 5' end of the polynucleotide strand.

The following schemes apply to the five naturally occurring bases