There are two types of available molecular surface area calculations, van der Waals (vdW) and solvent accessible (SA). The calculation method is based on Ferrara et al.
Fig. 1 Van der Waals surface area calculation results
Fig. 2 Solvent-accessible surface area calculation results
The calculation and the display options can be set in the Molecular Surface Area (3D) Options panel:
Decimal places: sets the number of decimal places for the result values.
Van der Waals: calculates the van der Waals surface of the molecule (in Å2).
Solvent Accessible: calculates the solvent accessible surface of the molecule (in Å2).
Solvent radius: sets the radius of the solvent molecule (by default water, 1.4 Å).
Show surface area increments: if set, atomic increments are shown.
Take major microspecies at pH: the surface area of the major microspecies present at the given pH is calculated.
Fig. 3 Options panel
The values indicated in the text field of solvent accessible surface area calculation are the following (all in Å2):
ASA: solvent accessible surface area calculated using the radius of the solvent (1.4 Å for the water molecule)
ASA+: solvent accessible surface area of all atoms with positive partial charge (strictly greater than 0)
ASA-: solvent accessible surface area of all atoms with negative partial charge (strictly less than 0)
ASA_H: solvent accessible surface area of all hydrophobic (|qi|<0.125) atoms (|qi| is the absolute value of the partial charge of the atom)
ASA_P: solvent accessible surface area of all polar (|qi|>0.125) atoms (|qi| is the absolute value of the partial charge of the atom)