Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences.

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Abstract
Hydrophobic amino acids of the group Leu, Ile, Val, Phe, and Met (LIVFM) are distributed in favored or suppressed patterns within protein sequences. The frequencies of all five-position combinations of [symbol: see text] = LIVFM and [symbol: see text] = non-LIVFM residues were analyzed in 48 proteins of known crystallographic structure. Some motifs were strongly preferred or suppressed; e.g., [symbol: see text] was favored (z = 3.5), while [symbol: see text] was suppressed (z = -3.4). In longer patterns, [symbol: see text] followed by [symbol: see text] and one [symbol: see text] was favored ([symbol: see text], z = 5.1), while conversion of the single hydrophobic residue to a pair was not ([symbol: see text], z = 0.8). Distributions of certain non-LIVFM amino acids around [symbol: see text] positions in strongly favored patterns were also favored or disfavored (Asp, Glu, Lys, Arg, Asn, Cys, Tyr, and Pro; for each magnitude of z > 2.0). While the strongly favored pattern [symbol: see text] was found in both alpha-helical and beta-strand sequences, it associated significantly with alpha-helices (z = 3.6 for the second-position alpha-helical phi and psi angles) but not with beta-strands (z = -1.1). Certain motifs of LIVFM and non-LIVFM residues might be selected if they lead efficiently to the local nucleations hypothesized to characterize molten globule intermediates in the folding of proteins.