The Miyazawa-Jernigan Contact Energies Revisited

Hui Zeng, Ke-Song Liu, Wei-Mou Zheng*
Institute of Theoretical Physics, Academia Sinica, Beijing 100190, China

© 2012 Zeng et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Institute of Theoretical Physics, Academia Sinica, Beijing 100190, China; Tel: 86-10-62541820; Fax: 86-10-62562587; E-mail:


The Miyazawa-Jernigan (MJ) contact potential for globular proteins is a widely used knowledge-based potential. It is well known that MJ’s contact energies mainly come from one-body terms. Directly in the framework of the MJ energy for a protein, we derive the one-body term based on a probabilistic model, and compare the term with several hydrophobicity scales of amino acids. This derivation is based on a set of native structures, and the only information of structures manipulated in the analysis is the contact numbers of each residue. Contact numbers strongly correlate with layers of a protein when it is viewed as an ellipsoid. Using an entropic clustering approach, we obtain two coarse-grained states by maximizing the mutual information between coordination numbers and residue types, and find their differences in the two-body correction. A contact definition using sidechain centers roughly estimated from Cα atoms results in no significant changes.

Keywords: Protein contact energies, Protein potential function.