Fig. 6. Modeling of Class II bHLH structures place subclass-specific amino acids residues on an external surface of the dimer. (A) Alignment of amino acid residues from the bHLH domain of neural bHLH factors and MyoD. A representative from mouse for each neural sub-class is shown; Mash1, the Achaete-scute family; Math1, the Atonal family; Ngn1, the Neurogenin family; Nscl1, the Nscl family; NeuroD, the NeuroD family. Residues in red highlight the residues conserved between all Class II bHLH factors. Residues in blue are conserved within members of a specific sub-family but are unique between the sub-families. (B) Mash1 bHLH monomer modeled onto the crystal structure of MyoD. The interfaces between the E-protein heterodimer partner and DNA are shown. Note the residues conserved between all Class II bHLH factors provide these interfaces (red). The residues unique to each sub-family (blue) provide surfaces for additional interactions.