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Table 3 Amino acid propensities for interacting with lipids from crystal structures and MD trajectories, and lipophilicity scales

From: Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

  Propensity from crystal structuresa Propensity from MD trajectories Lipophilicity scaleb
  Head group Tail group Head group Tail group POPC octanol
TRP 2.41 (1.04) 3.25 (0.63) 5.44 4.38 -1.85 -2.09
PHE 1.55 (0.50) 1.96 (0.43) 0.97 1.97 -1.13 -1.71
TYR 2.17 (0.57) 1.15 (0.26) 2.12 1.45 -0.94 -0.71
LEU 0.75 (0.17) 1.60 (0.23) 0.80 1.70 -0.56 -1.25
ILE 0.47 (0.09) 1.46 (0.27) 0.48 1.41 -0.31 -1.12
CYS 0.47 (0.32) 1.16 (0.93) 0.06 1.68 -0.24 -0.02
MET 0.96 (0.25) 1.47 (0.38) 1.01 1.56 -0.23 -0.67
GLY 0.53 (0.20) 0.43 (0.13) 0.42 0.42 0.01 1.15
VAL 0.60 (0.18) 1.24 (0.41) 0.40 1.23 0.07 -0.46
SER 0.68 (0.20) 0.89 (0.25) 0.73 0.44 0.13 0.46
THR 0.82 (0.25) 0.76 (0.15) 0.43 0.35 0.14 0.25
ALA 0.54 (0.15) 0.92 (0.19) 0.22 0.66 0.17 0.50
HIS 1.99 (0.39) 0.53 (0.09) 1.35 0.88 0.17 0.11
ASN 1.92 (0.47) 0.43 (0.13) 1.57 0.31 0.42 0.85
PRO 0.56 (0.37) 0.35 (0.12) 0.77 0.65 0.45 0.14
GLN 1.69 (0.98) 0.51 (0.26) 1.26 0.25 0.58 0.77
ARG 2.42 (0.65) 0.27 (0.21) 3.85 0.43 0.81 1.81
LYS 1.64 (0.58) 0.23 (0.09) 3.26 0.55 0.99 2.80
ASP 0.51 (0.32) 0.06 (0.04) 0.61 0.00 1.23 3.64
GLU 0.56 (0.57) 0.30 (0.13) 0.93 0.12 2.02 3.63
  1. The amino acids are sorted in the ascending order of the lipophilicity scale for POPC interface.
  2. a Values in parentheses represent the estimated standard error of correlation. The average of the standard error is 0.41 for lipid head and 0.27 for tail groups.
  3. b The oxidation state of HIS has been taken as neutral. All ARG and LYS are taken as positively and all ASP and GLU are taken as negatively charged.