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. 2011 Feb 18;39(11):4553–4563. doi: 10.1093/nar/gkr070

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Analysis of bHLH residue/DNA-contact frequency. (a) Canonical structure of a bHLH monomer contacting the CANNTG E-box. The E-box nucleotides on each DNA strand are indicated in blue, the bHLH basic region is shown in green and bHLH helices 1 and 2 are indicated in red and cyan, respectively. Residues 1, 15 and 50 indicate the start of the basic region, helices 1 and 2, respectively. (b) Plot indicating the frequency of contacts between bHLH residues and the bases in or flanking the E-box based on seven co-crystal structures. (c) As in (b) but indicating contacts between bHLH residues and the DNA backbone. P, phosphate; dR, deoxyribose. bHLH residue consensus numbering scheme based on Atchley et al. (33).