The protein chain is represented by all heavy atoms - no hydrogen atoms (either polar or nonpolar)
are included. Additionally, a pseudo-atom, situated at the centroid of each six-membered
ring, is appended to the aromatic residues phenylalanine, tyrosine and tryptophan. This pseudoatom
is used when calculating the contact energy but ignored when determining steric clashes.
Bond lengths and bond angles are held fixed at ideal values, with the exception of the
tau-angle (N-CA -C), which is allowed to vary in the range 108 to 114 °.
Atom radii are as follows: carbon
with double bond character = 1.50 Å all other carbon = 1.65 Å nitrogen = 1.35 Å oxygen
= 1.35 Å cysteinyl sulfur = 1.85 Å, methionyl sulfur = 1.80 Å and the aromatic pseudo-atom
= 0.0 Å.