The accessible molecular surface is calculated, relative to what the accessibility would be in vacuum. See chapter 9 of the WHAT IF writeup.
The accessibility is calculated twice. Once just normal for the protein you
submitted to the server, and once for every residue with the conformation it
has in the molecule, but all the rest of the molecule except the backbone of its
two direct neighbours (if available) removed.
The accessible molecular surface calculated by WHAT IF comes within 5%
of the well known Connolly surface area; the difference being that WHAT IF
does not take the so-called reentrant surface into account. The surface is
reported in squared Ångstroms. WHAT IF uses
the following Van der Waals radii: C:1.8 Ångstrom;
O:1.4 Ångstrom; N:1.7 Ångstrom; S:2.0 Ångstrom.
If you have detected any error, or have any question or suggestion,
please send an Email to Gert Vriend.
Roland Krause, Maarten L Hekkelman, Jens E Nielsen,