Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects

BMC Chemical Biology

Table 3 Correlations between electronic properties and folding preferences^a.

Index	HN_NMR	σ_I	σ_R	σ_α	σ_F	A_I	C_αMULL
Kyte-Doolittle	-0.8**	0	0	-0.2	0.3	-0.5*	0.4
Water vapor	0.8**	0.2	0.2	0.1	-0.6*	0.5*	-0.4
Bulk	-0.3	-0.1	-0.2	0.9**	0	0.2	-0.4
Gyration	-0.2	0	-0.2	0.9**	0	0.3	-0.5*
α-helix	-0.1	0.3	0.1	0.2	-0.2	0.6**	-0.7**
β-strand	-0.8**	-0.2	-0.1	0.3	0.3	-0.4	0.2
coil	0.7**	0.1	0.4	-0.3	-0.4	0.3	-0.3
e_σ	-0.1	-0.9**	-0.9**	0.3	0.7**	-0.6**	0.4
pKa	-0.1	0.3	0.3	-0.3	0.1	0	0
σ_I	0.2
σ_R	0.2	0.8**
σ_α	-0.4	-0.1	-0.2
σ_F	-0.4	-0.8**	-0.9**	0
A_I	0.5*	0.7**	0.5*	0	-0.6**
C_αMULL	-0.2	-0.6*	-0.4	-0.2	0.5*	-0.8**

^aLinear regression analysis was performed to determine possible correlations between the various electronic scales presented here. The first 2 indices of hydrophobicity were taken from Kyte and Doolittle [46], the bulk scale was from Kidera et al. [38], and the gyration scale is that of Levitt [39]. The secondary structure preferences and e_σ scales were described previously [8]. The r values from the analysis are presented here and directions of the slope are indicated by the signs. Statistical analysis of the data revealed significant correlations: *p < 0.05, **p < 0.01.