Figure 5
From: Probabilistic grammatical model for helix‐helix contact site classification
An average parse tree of van der Waals‐based grammar of class 2 (Eq.27). Lengths of branches express expected level of van der Waals volume. Terminal symbols on the tree branches represent residues of two helix pairs from: (A,B) glutamate transporter from P.horikoshii (PDB code: 1XFH) and (C) calcium ATPase from O.cuniculus (PDB code: 1SU4). The residues expected to be the smallest in the left‐hand‐side helix, according to the grammar, are shown in cyan. The residues expected to be the largest in the right‐hand‐side helix, according to the grammar, are shown in green. Note, that the helix contact in (C) is disturbed by the presence of another helix (drawn in magenta).