Solvent accessibility is calculated from the 'solvent accessible' surface we saw in the last section. The area described by the centre of the probe as it travels across the protein surface is assigned to the adjacent atoms giving an atomic solvent accessibility.
From the atomic solvent accessibility, a residue solvent accessibility can be calculated, by summing the component atomic accessibilities.
Standard accessibility values can be calculated for each amino acid type in an extended conformation as part of an Ala-X-Ala tripeptide. By expressing a residue accessibility as a percentage of the standard accessibility, one can obtain a relative accessibility.
View this structure (lysozyme, 7lyz, 1.4A relative accessibility) using RasMol. The PDB file has been modified by placing the relative solvent accessibility (calculated with a 1.4A probe) in the column in the file normally used to store the temperature factor (this is a measure of mobility of an atom).
RasMol allows you to colour the structure by temperature factor. Parts of the protein that are 'cold' (relatively immobile) are blue ranging through green, yellow and orange to red for the 'hot' (most mobile) parts of the structure.
From the RasMol menus, choose
You are now viewing the lysozyme using a thick wire-frame view and have coloured the residues by their relative accessibility. As you rotate the structure, you will see the residues buried in the middle of the protein are blue and those on the surface are green, yellow or red. Only the most exposed residues with sidechains extended away from the protein are coloured red.
Now, from the RasMol menus, choose
The space-filling representation shows even more clearly the fact that the buried residues are dark blue.
Carefully note which residues are shown in red.
View this structure (lysozyme, 7lyz, 1.4A residue accessibility) using RasMol. This time the total residue accessibility (1.4A probe) is patched into the PDB file instead of the relative accessibility.
From the RasMol menus, choose
Again note which residues are shown in red. You will see that two completely different residues are identified:
View this structure (lysozyme, 7lyz, 0.4A residue accessibility) using RasMol. This time the total residue accessibility was calculated with a 0.4A probe.
As before, from the RasMol menus, choose
Again note which residues are shown in red. You will see that a lot more residues are shown in red and orange.
This is because the smaller probe is able to slip between the atoms and a lot more of the structure has high accessibility.