Chemistry Reference
In-Depth Information
Table 9.1
Solvent accessible
surface area of bovine
recoverin computed with
different probe-sphere radii
Solvent accessible surface area (Å
2
)
Probe sphere radius (Å)
1.0
10104.96
1.4
9470.86
1.8
9280.83
2.2
9290.03
Fig. 9.1
Fragment of solvent accessible surface area per residue computed for bovine recoverin
using GETAREA webserver
When solvent accessible surface area per residue is computed, the contributions from
backbone and side chain are emphasized and solvent exposed (o) and buried residues
(i) are revealed, as it is presented in Fig.
9.1
.
Residues are considered to be exposed or buried depending on the ratio of side-
chain surface area to “random coil” value per residue. The “random coil” value
is a constant computed for every residue as the average solvent-accessible surface
area of this residue (X) in the tripeptide Gly-X-Gly in an ensemble of 30 random
conformations (Fraczkiewicz and Brown
1998
), If this ratio exceeds 0.5 the residue
is considered to be exposed and if it is less than 0.2 the residue is considered to
be buried. Information about exposed and/or buried residues is important when
analyzing putative protein-ligand and protein-protein interactions.
