Biology Reference
In-Depth Information
Table 3.1
Network Parameters Concerning the Dark and MII Rhodopsin States
Dark
MII
Imin
a
4.33
3.98
Nodes
b
230
226
CommNodes
b
84.35
85.84
Links
c
250
235
CommLinks
c
53.60
57.02
Hubs
d
37
35
CommHubs
d
45.95
48.57
Hlinks
e
131
121
CommHLinks
e
39.69
42.98
Paths
f
13,828
9476
RET
g
10,006
5638
RET%
g
72.36
59.50
MaxLen
h
24 (4%)
31 (2%)
AvgLen
i
10.73
11.77
MaxScr
j
1.00 (30%)
1.00 (25%)
AvgScr
k
0.31
0.28
Hubs50
l
7084 (51.23%)
2927 (30.89%)
AvgMSDF
m
0.0004
0.0007
a
Imin cutoff.
b
Total number of nodes and fraction (%) of nodes shared with the other functional state.
c
Total number of links and fraction (%) of links shared with the other functional state.
d
Total number of hubs and fraction (%) of hubs shared with the other functional state.
e
Number of hub-mediated links and fraction (%) of hub-mediated links sharedwith theother functional state.
f
Total number of shortest pathways.
g
Number of pathways passing through the retinal and fraction (%) of such retinal-mediated paths over
the total number of paths.
h
Maximal path length (i.e., excluding the two extremities); the number in parenthesis indicates the
fraction of paths over the total holding such length.
i
Average path length.
j
Maximal correlation score (i.e., number of internal nodes correlated with at least one extremity node,
divided by path length); the number in parenthesis indicates the fraction of paths over the total holding
such correlation score value.
k
Average correlation score.
l
Number of paths, in which
50% of nodes are hubs: the number in parenthesis indicates the fraction of
paths over the total holding such node composition.
m
Average MSDF index.
(4.5
˚
);
N
i
and
N
j
are normalization factors for residue types
i
and
j
, which account
for the differences in size of the amino acid side chains and their propensity to make
the maximum number of contacts with other amino acids in protein structures. The
normalization factors for the 20 amino acids were derived from the work by
Kannan
and Vishveshwara (1999)
. The normalization index for retinal (i.e., 170.13) was
computed as the average number of contacts done by the molecule in a dataset of
83 crystallographic structures concerning the different photointermediate states of
