Backbone-backbone geometry of tertiary contacts between alpha-helices

Knowledge about how secondary-structure elements combine together to form the tertiary structure is crucial for understanding protein folding. We have examined packing solutions for alpha-helices by performing a crystal survey of the underlying backbone-backbone inter-geometry of tertiary contacts. The information content is different from, and complementary to, the results of side-chain to side-chain crystal surveys and studies of helix-helix-crossing angles. Six geometry descriptors were recorded from each tertiary contact in nonredundant data sets of globular and transmembrane proteins. The descriptors included distances, angles, and dihedral angles that together describe completely the underlying geometry of each contact. From the results it is possible to identify differences in the geometry requirements of tertiary contacts between alpha-helices in general and transmembrane alpha-helices. The differences become more apparent when the correlation between the different geometry descriptors is analyzed. The results are compared with those of other types of secondary structure. Finally, an investigation of how the geometry of tertiary contacts changes with the amino-acid types involved in the contact is performed using multivariate techniques. The results of this study provide a well-defined overview of the underlying structural framework of tertiary contacts between alpha-helices, in both globular and TM environments, that will have valuable implications for predicting protein tertiary structure.