Spectral Analysis of Amino Acid Sequence. II. Characterization of α-Helices by Local Periodicity

Abstract

The average hydrophobicity as well as the helix periodicity in the amino acid sequence were compared among filamentous proteins, α-type globular proteins and intrinsic membrane proteins, in order to study the correlation between the side chain arrangement and the environmental conditions around helices. Although the helix content of those proteins is equally high, the average hydrophobicity and the power spectral density at the helix period (3.6 residues per a turn) changed systematically among three kinds of proteins, revealing the systematic distribution of two types of helical segments: hydrophobic and amphiphilic helices. The analysis of partial sequences showed that the amphiphilic helix occurs at the interface between polar and nonpolar environment, while the hydrophobic helixis found in the interior of protein complex or membranes.