Accessible Surface of Folded Structures

The contact surface of a protein molecule is designated as those parts of the van der Waals surface that comes in contact with a rolling chemical probe, typically a water molecule (approximated as a spherical probe). When the water molecule is simultaneously in contact with more than one protein atom, its border surface defines the re-entrant surface, which is the area described by the center of a spherical water molecule of radius Rw (taken as 1.4 A). The contact surface and the re-entrant surface combined trace a continuous surface known as the (molecular) accessible surface. The accessible surface area (Aj) in of a 

TABLE 5.10 Some naturally occurring circular proteins 

Antibacterial protein consists of five a helices connected by short turns that enclose a hydrophobic core. 

Macrocyclic polypeptides with 30 amino acids with six conserved Cys that form three knotted disulfide bonds with uterotonic activity. 

Six conserved Cys (3 knotted disulfides) with trypsin inhibitory activity. Small triple stranded 3 sheet is associated with cyclic cysteine knot motif. 

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