FIGURE 4.

Comparisons of surface burial calculated from the T. thermophilus S-domain structure and structural mapping, which records the difference between the I and the N states. (A) Plot of C4′ burial and normalized hydroxyl radical protection factors (normalized PF = PF − 1; red and blue squares). Red nucleotides have a better correlation than blue nucleotides. Hydroxyl radical data are from Krasilnikov et al. (2004) and Loria and Pan (1996). (B) Plot of whole nucleotide burial and normalized T1 nuclease protection factors (red squares). (C) Plot of normalized hydroxyl radical protection factors for T. thermophilus (red) and E. coli (black) S-domains. Regions of significant differences are indicated by red bars and are illustrated within the structure of the T. thermophilus S-domain in D.