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Calculation of the solvent-accessible surface area

SG Sigrid Gouma
TV Tessa Vermeire
SG Steven Van Gucht
LM Lennart Martens
VH Veronik Hutse
JC Jeroen Cremer
PR Paul A. Rota
GL Geert Leroux-Roels
MK Marion Koopmans
RB Rob van Binnendijk
EV Elien Vandermarliere
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The absolute solvent-accessible surface area (aSAS), the area of a residue that is accessible by a water molecule (radius of 1.4 Å), was calculated with the aid of DSSP52,53. The relative solvent-accessible surface (rSAS) area was then obtained by calculation of the ratio of the aSAS of the amino acid as present in the protein to the aSAS of the residue in the tripeptide G-X-G54,55. A residue is said to be surface-accessible (solvent exposed) if the relative SAS is >25%, otherwise a residue is said to be buried56,57. A surface exposed residue can be targeted by other molecules, such as antibodies. The RMSD of the homology model and the experimentally defined structure of the HN protein was calculated by using the Align command in PyMol (The PyMOL Molecular Graphics System, Version 1.1r1, Schrödinger, LLC).

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