Biology Reference
In-Depth Information
129
The bond angles are:
As discussed later, these values are very similar to those for a standard
peptide unit. In fact, since most of the X-ray diffraction studies of protein
three-dimensional structures do not have enough resolution to locate the
positions of atoms, the standard peptide unit is used to construct the final
atomic model.
RAMACHANDRAN
PLOT AND STERIC HINDRANCE
Based on quantum mechanical calculations (see, for example, Schiff, 1955),
electron density distributions around hydrogen atoms are relatively diffused.
Therefore, hydrogen atoms are usually not “visible” in X-ray diffraction
studies. However, based on hard-sphere approximation or various empirical
interactions between non-bounded atoms, hydrogen atoms play an extremely
important role in determining whether a certain configuration is sterically
allowed. Ramakrishnan and Ramachandran (1965) made an exhaustive
study of such configurations for amino acid residues, based on and
angles as defined above. They introduced the Ramachandran plot,
although they used an angle designated as which was different from
Hard-spheres are usually assumed for non-bounded atoms, with a minimum
contact distance allowed between any two atoms as listed in Table 5-4.
