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Pose Analysis of Alpha-Carbons in Proteins

School of Mechanical and Aerospace Engineering, Konkuk University, Seoul, Korea

Gregory S. Chirikjian

Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, gregc{at}jhu.edu

In this paper we present a novel method to describe the pose (position and orientation) distribution of amino acid residue pairs within a protein, which are proximal in space and distal in sequence. While the Ramachandran plot provides information of protein conformations using the and angles between sequentially proximal residues, our method can offer six-dimensional relative pose information. Distribution data are visualized in the form of continuous distributions by using Gaussian distribution functions on SO(3) and R3. Hence, we discuss how the classical Gaussian functions can be generalized to capture both positional and orientational data. The method is applied to 168 protein structures in the Protein Data Bank and results are discussed.

Key Words: interaction between residues • 6D relative pose • protein data • data visualization • Gaussian function • axis-angle representation • computational tool • continuous distribution

The International Journal of Robotics Research, Vol. 24, No. 2-3, 183-210 (2005)
DOI: 10.1177/0278364905050353


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