Residues in the longitudinal, hydrophobic strip-of-helix relate to terminations and crossings of alpha-helices.
An alpha-helix terminates when the virtual extension of its most hydrophobic, longitudinal strip containing Leu, Ile, Val, Phe, and Met lacks those residues. In each of 247 helices a template was fitted to maximize the mean hydrophobicity of  positions forming a longitudinal strip-of-helix. The template was then extended into sequences beyond the ends of the helices. Leu, Ile, Val, Phe, and Met occurred in  positions in the longitudinal strip-of-helix at an increased frequency (p less than 0.001), but in the first and second  positions beyond either end of each true helix, they occurred at the same frequency as for their empirical distribution over all the proteins. Excesses of Asp and Glu were found in the N-terminal loop, and of Arg, His, and Lys in specific positions about the C terminus of helices. The longitudinal hydrophobic strip, the smallest amino acid in that strip, and charged amino acids in that strip, related to rotational and longitudinal orientation of alpha-helices in 15 proteins. Adjacent helices generally crossed through their longitudinal hydrophobic strips. They usually crossed through the smallest residue in the strip. Charged residues, when they occurred in the strips, were excluded from the crossing regions.
Vazquez
S R
SR
Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655.
Kuo
D Z
DZ
Bositis
C M
CM
Hardy
L W
LW
Lew
R A
RA
Humphreys
R E
RE
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D003574:Cytochrome c Group / Q000737:chemistry; D045362:Cytochromes c2; D008969:Molecular Sequence Data; D011487:Protein Conformation
D000596:Amino Acids; D003574:Cytochrome c Group; D045362:Cytochromes c2