Highly restricted distributions of hydrophobic and charged amino acids in longitudinal quadrants of α-helices

Helix formation in folding proteins is stabilized by binding of recurrent Hydrophobic side chains in one longitudinal quadrant against the locally most hydrophobic region of the protein. To test this hypothesis, we fitted sequences of 247 α-helices of 55 proteins to the circular (infinite) template □ ○ △ ○ □ ○ ○ □ ○ △ ○ □ ○ ○ □ ○ △ ○ to maximize the strip-of-helix hydrophobicity index (the mean hydrophobicity of residues in □ positions). These template-predicted configurations closely matched crystallographic structures in 87% of four- or five-turn helices compared. We determined the longitudinal quadrant distributions of amino acids in the template-fitted, sheet projections of α-helices with respect to the best longitudinal, hydrophobic strip on each helix and to the N and C termini, interiors, and entire helices. Amino acids Leu, Ile, Val, and Phe were concentrated in one longitudinal quadrant (p < 0.001). Lys, Arg, Asp, and Glu were not in the quadrant of Leu, Ile, Val, and Phe (p < 0.001). Significant quadrant distributions for other amino acids and for termini of the helices were also found.