Biplane conformations in the PDB

Part of my thesis involves the scoring of lattice-fit PDB proteins for biplanar conformations. This was a massive computational effort requiring the testing of many possible center cutting planes through the center of the protein (covering the rotational space) so as to find the best biplane alignment. Then all hydrophobic residues found within k lattice distance of the plane were identified and annotated.

When the writing of the thesis was completed, only 59 PDB structures had been scored. At the time, 30 were classified biplanar and the other 29, not biplanar. Upon termination of the automated scorer, 172 PDB structures had been completely scored and are reported on this page.

As described in the thesis, page 28-29, we used the hydrophobic residues in the biplane region to calculate a number of pairwise hydrophobic contacts within the optimal biplane. We partitioned the PDB set by the classifier: biplanar if the number of contacts within the k-distance biplane is greater than or equal to tau times the total number of pairwise hydrophobic contacts. Parameters k=2 and tau=.333 are used. The choice of tau is essential; 1/3 represents our intuition that since contacts are between pairs of amino acids, then tau=1/3 ensures that some quantity greater than 1/2 of the total hydrophobicity lies in the biplane.

In the final 172 PDB set, 70 are found to be significantly biplanar and 102 are not biplanar. This result argues more strongly against the biplane than the original result: the paper reports a ratio of 1:1 whereas the completed set suggests 7:10, with the majority not biplanar.