In the alpha helix, the amino acids arrange in a helical formation, with 3.6 amino acid residues per turn of the helix. The carbonyl oxygen of each peptide is hydrogen bonded to the hydrogen of the amino group of an amino acid four residues away. The hydrogen bonds run almost parallel to the axis of the helix. Interactions between amino acid side chains can either stabilize or destabilize the helix. Positively charged amino acids are found 3 residues away from negatively charged ones resulting in the formation of an ion pair. Aromatic residues give rise to hydrophobic interactions. There is a net dipole along the helix due to the cumulative effect of each small dipole moment of each peptide. Negatively charged residues are found near the amino terminal where they interact with the positive charge of the helix. Positively charged residues are found at the carboxyl end where they stabilize the negative end of the helix’s dipole.

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