Based on traditional definitions of nucleotide conformations, their
symbolic characterization takes place on two levels. The first one is
the position of the furanose ring atoms relative to the general plane
of the ring, which determines the sugar puckering mode. The values of
the pseudorotation phase angle for furanose rings described by Altona
et al. [1] are divided into the ten classes shown in
Table 3.2. The second is the orientation of the
nitrogen base relative to the sugar, which can be determined by the
angle around the glycosyl bond, , defined by the atoms O4', C1',
N9 and C4 for purines and the atoms O4', C1', N1 and C2 for
pyrimidines. As accepted by the IUPAC-IUB
commision [12], values of
in the range
indicate a syn orientation whereas other
values indicate a trans orientation. Since the other parts of a
nucleotide are mostly rigid, the two above properties represent a fair
qualitative description of nucleotide conformations. The class of a
nucleotide conformation can thus be defined by its sugar puckering
mode and nitrogen base orientation around the glycosyl bond. The
corresponding symbols assigned by MC-Annotate are summerized in
Table 3.2.
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The distance,
, between two nucleotide
conformations,
and
, can be defined by
the root mean square deviation (RMSD) between the heavy atoms in the
backbone of the two nucleotides, a posteriori of optimal
superimposition of their local referentials in 3-D space
[9]. Our metric is in good correlation with the more
standard all-atom superposition and RMSD metric,
, performed using the analytical
method described by Kabsch [13,14] and places the
emphasis on the backbone atom positions and orientation relative to
the nitrogen base.