Anti glycosidic conformation (source code)

= Anti glycosidic conformation

An \b[anti glycosidic conformation] is a base–sugar orientation in the anti region of the <glycosidic torsion angle> $\chi$. Under the IUPAC-IUB atom convention, this region is centered at $180^\circ$ and extends90degrees on either side. Equivalently, for an angle reported in $[0^\circ,360^\circ)$, the broad anti region lies between90 and270degrees.<Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains>[Section2.3, note(a), anti region]{ref}

For a <purine> nucleoside, $\chi$ uses O4′–C1′–N9–C4; for a <pyrimidine>, it uses O4′–C1′–N1–C2. The ordered atoms specify the <dihedral angle>. An angle reported using different outer atoms cannot be assigned to this region by its numerical value alone.<Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains>[Section2.3, definition and note(b)]{ref}

For an original example, $\chi=-160^\circ$ and $\chi=200^\circ$ describe the same orientation modulo one full turn, and both are anti. Moving to $\chi=60^\circ$ changes the orientation into the <syn glycosidic conformation> region while retaining the base–sugar bond connectivity. Conformational change and a change in covalent constitution are different descriptions.

The word anti here does not describe how two bases pair with one another. <RNA base-pair geometry> can separately classify the relative orientations of two <glycosidic bonds>. Nor does a single anti torsion determine the entire <nucleotide> or <RNA> structure: sugar geometry and the other backbone angles remain to be specified.