alexa Geometry of interplanar residue contacts in protein structures.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Proteomics & Bioinformatics

Author(s): Brocchieri L, Karlin S

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Abstract The relative spatial disposition of interacting side-chain planar groups (aromatic, guanidinium, amide, carboxyl, imidazole) is analyzed for 186 non-homologous well-resolved protein structures. The dihedral angle of amide or carboxyl planar groups with other planar groups accords with a random distribution of planes. By contrast, the dihedral angle of the planes between close aromatic rings or of the histidine ring interacting with aromatic residues is significantly nonrandom, showing an approximately uniform distribution. Our results indicate that edge-to-edge and edge-to-center spatial dispositions of residue planar sections are prevalent, while complete stacking configurations are uncommon. The hypothesis that electrostatic forces are a major determinant of the geometry of interactions between side-chain planar groups is discussed.
This article was published in Proc Natl Acad Sci U S A and referenced in Journal of Proteomics & Bioinformatics

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