How does the amino acid sequence affect the stability of an alpha helix?
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Another factor affecting α-helix stability is the total dipole moment of the entire helix due to individual dipoles of the C=O groups involved in hydrogen bonding. Stable α-helices typically end with a charged amino acid to neutralize the dipole moment.
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H-bonds and Steric Factors Determine Helix Stability
The alpha helix also positions the side chains of each amino acid such that they project away from the helix and are kept as far apart as possible to minimize steric repulsive forces. This is clear when the amino acid side chains (R groups) are shown as spacefilling.
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