S. Vazquez et al., FAVORED AND SUPPRESSED PATTERNS OF HYDROPHOBIC AND NONHYDROPHOBIC AMINO-ACIDS IN PROTEIN SEQUENCES, Proceedings of the National Academy of Sciences of the United Statesof America, 90(19), 1993, pp. 9100-9104
Hydrophobic amino acids of the group Leu, Ile, Val, Phe, and Met (LIVF
M) are distributed in favored or suppressed patterns within protein se
quences. The frequencies of all rive-position combinations of lozenge
= LIVFM and lozenge = non-LIVFM residues were analyzed in 48 proteins
of known crystallographic structure. Some motifs were strongly preferr
ed or suppressed; e.g., lozenge was favored (z = 3.5), while lozenge w
as suppressed (z = -3.4). In longer patterns, lozenge followed by loze
nge and one lozenge was favored (lozenge, z = 5.1), while conversion o
f the single hydrophobic residue to a pair was not (lozenge, z = 0.8).
Distributions of certain non-LIVFM amino acids around lozenge positio
ns in strongly favored patterns were also favored or disfavored (Asp,
Glu, Lys, Arg, Asn, Cys, Tyr, and Pro; for each Absolute value of z >
2.0). While the strongly favored pattern lozenge was found in both alp
ha-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 LI
VFM and non-LIVFM residues might be selected if they lead efficiently
to the local nucleations hypothesized to characterize molten globule i
ntermediates in the folding of proteins.