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Residue–Residue Contacts: Application to Analysis of Secondary Structure Interactions

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 932)

Abstract

Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom–atom and residue–residue contacts is described and applied to analysis of protein–protein interactions in dimeric β-sandwich proteins.

Key words

Contact surface area Protein structure analysis Protein structure prediction Force field Protein–protein interactions 
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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Department of BiologyMITCambridgeUSA
  2. 2.Department of Plant SciencesWeizmann Institute of ScienceRehovotIsrael

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