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Structure and hydrogen bonding
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The following 4 scenes are inspired by a nice set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly). In an alpha helix, the main chain arranges in a with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by from amino acid n to n+4. There are . In space filling depiction, you can see how the main chain is (no space in the middle).
Which amino acids are found in alpha helices?
Proline is a helix breaker because its main chain nitrogen is not available for hydrogen bonding.
Alpha helices in soluble (globular) proteins
Example: myoglobin
Example: DNA binding
Alpha helices in transmembrane proteins
opioid receptors: http://pdb101.rcsb.org/motm/217
Alpha helices in filamentous proteins
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Experimental evidence
a) CD spectroscopy
b) NMR chemical shifts
c) Fiber diffraction
Role of alpha helices in the history of structural biology
a) Pauling predicts it http://onlinelibrary.wiley.com/doi/10.1111/febs.12796/full
b) Determination of hand: There are several methods in X-ray crystallography where crystallographers obtain an electron density, but don't know whether it or its mirror image is correct. Historically, finding electron density that fits a helix was used to break this ambiguity. If the helix was right-handed, the electron density was used as is, but if the helix was left-handed, the mirror image was used.
c) Tracing the chain: When building a model into electron density, the first step was to place continguous C-alpha atoms into the density (with proper spacing). To see in which direction an alpha helix goes, you look at the side chain density. If it points up, the N-terminus is on top, otherwise on the bottom.
References
