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torsion along the polypeptide chain is limited to the C
α
- C
′
bond and the C
α
- N bond of
each residue, the angles of rotation referred to as
respectively (figure 1). By
convention
φ
and
ϕ
are set to zero when the C
α
-N bond is trans to the carbonyl bond and
C
α
-C
φ
and
ϕ
is trans to the amide group [4] Looking down the dipeptide from N- to C-terminal,
clockwise rotation is defined as positive and anti clockwise defined as negative.
′
Figure 1. Ball and stick model of a peptide bond showing φ and ϕ angles. The space
filling surface shows characteristics mentioned in the text.
Figure 2 Amide tautomers
The backbone conformation is also limited by steric constraints illustrated by the
spacefilling surface superimposed on the ball and stick model in Figure 1. Ramachandran
et al. [5] calculated the allowed conformations from Van der Waals contact distances and
displayed them on a plot of
known as the Ramachndran map (figure 3). The
patterned areas represent allowed regions and the grey areas represent outlying regions for
which the contact distances were reduced on the basis of empirical data available at the
time. The map has been revised a number of times to coincide with accumulated data and
quantum mechanical calculations which demonstrate that increased stability due to good
hydrogen bond alignment compensates for single steric clashes between hydrogen atoms
creating the diagonal distribution shown in figure 4 [6].
φ
versus
ϕ
