title: Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences.
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.
authors.affiliation: Department of Pharmacology, University of Massachusetts Medical Center, Worcester 01655.
authors.forename: S
authors.initials: S
authors.lastname: Vazquez
authors.forename: C
authors.initials: C
authors.lastname: Thomas
authors.forename: R A
authors.initials: RA
authors.lastname: Lew
authors.forename: R E
authors.initials: RE
authors.lastname: Humphreys
mesh_terms: D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins