Table 3

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

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


The amino acids are sorted in the ascending order of the lipophilicity scale for POPC interface.

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.

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.

Morita et al. BMC Biophysics 2011 4:21   doi:10.1186/2046-1682-4-21

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