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The first three residues at the N-terminus of the
alpha-helix are called N1, N2 and N3. We surveyed 2102
N-termini of alpha-helices in 298 high resolution,
non-homologous protein crystal structures for N1, N2 and
N3 side chain rotamer preferences and hydrogen bonding
We find strong structural preferences that are unique to
these sites. The rotamer distributions as a function of amino
acid identity and position in the helix are often explained in
terms of hydrogen bonding interactions to the free N-cap,
N1, N2 and N3 backbone NH groups. Notably, the "good
N2" amino acids Gln, Glu, Asp, Asn, Ser and Thr
preferentially form (i, i) or (i+1, i) hydrogen bonds to
the backbone, though this is hindered by good N-caps (Asp,
Asn, Ser, Thr and Cys) which compete for these hydrogen
The strong energetic and structural preferences found for N1, N2 and N3, which differ greatly from positions within helix interiors, suggest that these sites should be treated explicitly in any consideration of helical structure in peptides or proteins. Keywords : alpha-helix, rotamer, hydrogen bonding, stability, protein design, N-cap. Side Chain Structures in the First Turn of the Alpha-Helix S. Penel, E. Hughes & A.J. Doig 1999 J. Mol. Biol. 287, 127-143.