An Algebro-Topological Description of Protein Domain Structure
Figure 9
Fatgraphs corresponding to the common secondary structures.
(a) alpha helix, (b) parallel beta sheet, and (c) anti-parallel beta sheet. Each boundary component (dashed red line) passes through four peptide units; the alpha helix is local in that it connects only closely situated peptide units whereas the beta sheet also connects peptide units potentially far away from each other. The number of components depends on the length of the structure. The less frequently occurring -helices and
-helices give rise to similar pictures as (a), the only difference is that hydrogen bonds connect stubs three and five peptide units apart instead of four. The backbone of an
-helix is a string of untwisted alpha carbon linkages, whereas for the
-sheets these are twisted.