Do we see what we should see? Describing non-covalent interactions in protein structures including precision

Manickam Gurusaran, Mani Shankar, Raju Nagarajan, John R. Helliwell, Kanagaraj Sekar
  • IUCrJ, December 2013, International Union of Crystallography
  • DOI: 10.1107/s2052252513031485

Estimating the atomic coordinate errors of atoms in proteins is important.

What is it about?

The power of X-ray crystal structure analysis as a technique is to ‘see where the atoms are’. The results are extensively used by a wide variety of research communities. However, this ‘seeing where the atoms are’ can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace.

Why is it important?

The end point of protein structure model refinement requires a knowledge of the individual atomic position errors. A Salt Bridges in Protein Structures (SBPS) webtool ( has been designed and created to help to understand the nature and geometry of the ion pairs found in protein structures. Also an online computing server to estimate the atomic coordinate errors for all the atoms in any protein structure is at the URL All this is important because until now the errors on each of the the atomic coordinates in biological structures have not not been individually displayed and a false precision often assumed including in widely used molecular graphics tools.

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The following have contributed to this page: Professor John Richard Helliwell, Mr Gurusaran Manickam, and Professor Kanagaraj Sekar