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Interaction geometry involving planar groups in protein–protein interfaces
Author(s) -
Saha Rudra Prasad,
Bhattacharyya Rajasri,
Chakrabarti Pinak
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21244
Subject(s) - hydrogen bond , crystallography , chemistry , protein folding , monomer , folding (dsp implementation) , protein structure , crystal structure , planar , protein–protein interaction , protein crystallization , molecule , crystallization , biochemistry , organic chemistry , computer graphics (images) , computer science , electrical engineering , engineering , polymer
The geometry of interactions of planar residues is nonrandom in protein tertiary structures and gives rise to conventional, as well as nonconventional (XH···π, XH···O, where X = C, N, or O) hydrogen bonds. Whether a similar geometry is maintained when the interaction is across the protein–protein interface is addressed here. The relative geometries of interactions involving planar residues, and the percentage of contacts giving rise to different types of hydrogen bonds are quite similar in protein structures and the biological interfaces formed by protein chains in homodimers and protein–protein heterocomplexes—thus pointing to the similarity of chemical interactions that occurs during protein folding and binding. However, the percentage is considerably smaller in the nonspecific and nonphysiological interfaces that are formed in crystal lattices of monomeric proteins. The CH···O interaction linking the aromatic and the peptide groups is quite common in protein structures as well as the three types of interfaces. However, as the interfaces formed by crystal contacts are depleted in aromatic residues, the weaker hydrogen bond interactions would contribute less toward their stability. Proteins 2007; © 2007 Wiley‐Liss, Inc.