Small molecule studies indicate that C-H...X interactions (X: O,N) constitu
te weak H-bonds. We have performed a comprehensive analysis of their occurr
ence and geometry in RNA structures. Here, we report on statistical propert
ies of the total set of interactions identified and discuss selected motifs
. The distance/angle distribution of all interactions exhibits an excluded
region where the allowed C--H...X angle range increases with an increasing
H...X distance. The preferred short C--H...X interactions in RNA are backbo
ne-backbone contacts between neighbour nucleotides. Distance/angle distribu
tions generated for various interaction types can be used for error recogni
tion and modelling. The axial C2'(H)...O4' and C5'(H)...O2' interactions co
nnect two backbone segments and form a seven-membered ring that is specific
for RNA. An AA base pair with one standard H-bond and one C-H...N interact
ion has been identified in various structures. Despite the occurrence of sh
ort C--H...X contacts their free energy contribution to RNA stability remai
ns to be assessed.