Table 1

The letter and secondary structural element (SSE) frequency distributions and 2-sample T-tests of first-and second-shell amino acid residues vs. all amino acid residues in the Mg2+-proteins

1st-shell vs. all residues
 2nd-shell vs. all residues
Letter, xa
 νx,1/νx, allb
 T-testc
 p-valuec,d
 νx,2/νx, alle
 T-testc
 p-valuec,d
a
 1.47
 1.4037
 0.0802
 0.57
 2.4731
 0.0067
b
 1.86
 2.7909
 0.0027
 1.20
 1.2200
 0.1113
c
 0.56
 2.0160
 0.0219
 0.50
 4.3510
 <0.0001
d
 1.23
 1.7376
 0.0412
 1.23
 3.1829
 0.0008
e
 1.46
 1.0111
 0.1560
 2.03
 4.1825
 <0.0001
f
 1.47
 1.9389
 0.0263
 1.70
 5.4060
 <0.0001
g
 1.15
 0.2494
 0.4015
 1.18
 0.5381
 0.2953
h
 5.29
 9.3752
 < 0.0001
 1.19
 0.7921
 0.2142
i
 0
 1.8928
 0.0292
 1.34
 1.1910
 0.1168
j
 2.21
 1.6156
 0.0531
 1.54
 1.3401
 0.0901
k
 1.40
 1.4992
 0.0669
 1.60
 4.1820
 <0.0001
l
 0.76
 0.9209
 0.1786
 1.08
 0.5978
 0.275
m
 0.52
 2.9377
 0.0017
 0.74
 5.2192
 <0.0001
n
 0.53
 1.1306
 0.1291
 0.88
 0.5208
 0.3013
o
 1.52
 1.4066
 0.0798
 0.35
 3.3637
 0.0004
p
 0
 3.1174
 0.0009
 0.77
 1.3204
 0.0934
SSE, x





Loop
 1.56
 2.5575
 0.0053
 1.47
 2.1874
 0.0144
β-strands
 1.30
 1.0780
 0.1405
 1.34
 1.2170
 0.1118
α-helices
 0.47
 3.6454
 0.0002
 0.51
 3.3621
 0.0004

a16-letter structural alphabet defined by de Brevern and co-workers (see Methods and original reference) [6]. bThe ratio of the letter/SSE 'x' frequency of first-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins. cThe statistical analyses were carried out using the package, SAS/STAT version 8 (SAS Institute, NC). dP-values <0.05 are highlighted in bold. eThe ratio of the letter/SSE 'x' frequency of second-shell amino acid residues to that of all amino acid residues in the 70 Mg2+ proteins.

Dudev and Lim BMC Bioinformatics 2007 8:106   doi:10.1186/1471-2105-8-106