Dedicated to the memory of Prof. G.N. Ramachandran on the 50th anniversary of the appearance of the seminal paper on the Ramachandran map.
Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps
Article first published online: 18 DEC 2013
© 2013 Wiley Periodicals, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 82, Issue 7, pages 1101–1112, July 2014
How to Cite
Kalmankar, N. V., Ramakrishnan, C. and Balaram, P. (2014), Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps. Proteins, 82: 1101–1112. doi: 10.1002/prot.24384
The entire work was performed at Indian Institute of Science, Bangalore, India.
- Issue published online: 11 JUN 2014
- Article first published online: 18 DEC 2013
- Accepted manuscript online: 12 AUG 2013 04:23AM EST
- Manuscript Accepted: 25 JUL 2013
- Manuscript Revised: 20 JUL 2013
- Manuscript Received: 7 MAY 2013
- DST project at the National Centre for Biological Sciences (to NVK) and DBT-IISc partnership program grant of the Department of Biotechnology
- Ramachandran map;
- protein conformation;
- secondary structural motifs;
- amino acid conformational propensities;
- Type II′ β turn
The Ramachandran map clearly delineates the regions of accessible conformational (φ–ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely “arid”, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ–ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II′ β turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II′ β turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in β hairpins. The β strand–helix motif with the Type II′ β turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101–1112. © 2013 Wiley Periodicals, Inc.