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. Author manuscript; available in PMC: 2008 Nov 9.
Published in final edited form as: J Mol Biol. 2007 Aug 23;373(5):1123–1140. doi: 10.1016/j.jmb.2007.07.079

Table 1.

Violations of NMR constraints for the central four base pairs

Violations Total
Constraints
Base-Base
Protons		 Base-Pucker Protons Total
Violations
CP-DNA
(171) 		Interstrand 1 0 1 18
Intrastrand 1 1 2 43
Same
Nucleotide 		0 2 2 110
OX-DNA
(160) 		Interstrand 0 0 0 18
Intrastrand 1 1 2 44
Same
Nucleotide 		0 0 0 98

Inter-proton differences averaged from the final 6 ns of the simulation trajectories were compared to the NOE derived inter-proton differences for CP-DNA and OX-DNA30,33 as described in Methods. All average inter-proton distances from the MD simulations trajectories which differed from the NOE inter-proton distance constraints by more than 0.5 Å were considered violations. The total number of inter-proton distance constraints for the central four base pairs is reported in parentheses in the first column. Restraints are reported according to category in the last column. The middle columns give the number of violations between base and base protons or between base and sugar pucker protons, and the total number of violations in each category.