Biomedical Engineering Reference
In-Depth Information
A major consideration in defining bond and torsion angles is whether to use the traditional Cartesian
coordinate system or internal coordinates. The Cartesian coordinate system, with origin 0 and three
orthogonal axes, commonly labeled x, y, and z, is used by the major protein databases, including the
PDB (see
Figure 9-15
). For example, the first atom in the sequence for Deoxy Human Hemoglobin,
PDB entry 1A3N, contributes to the first amino acid in the sequence, Valine (VAL). The coordinates
for the first atom, a Nitrogen atom (N), are 10.720 (x) 19.523 (y), and 6.163 (z). Also listed are the
occupancy (21.36), the frequency with which the atom is present in the protein, and temperature
(1.00), which is a measure of the uncertainty in the position of the atom in the crystalline protein.
The listing also indicates the role of each atom in the sequence. For example, the second atom is an
alpha carbon, while the fifth atom is a beta carbon.
Figure 9-15. PDB Entry for Deoxy Human Hemoglobin, PDB ID 1A3N. It
shows Cartesian coordinates for the first amino acid (Valine) in the
sequence.
