ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

Abstract

Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf (http://consurf.tau.ac.il/) is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.

Figure 1

A flow chart of a ConSurf calculation.

Figure 2

A ConSurf analysis of the Kcsa potassium channel. The tetrameric channel, which is viewed along the pore from the extracellular end, is presented using a space-filled model. The amino acids are colored by their conservation grades using the color-coding bar, with turquoise-through-maroon indicating variable-through-conserved. Amino acid positions, for which the inferred conservation level was assigned with low confidence, are marked with light yellow. The potassium ion at the channel pore is colored green. Conservation scores, which were calculated for one of the channel's subunits, were projected on the homotetrameric structure. The run was carried out using PDB code 1bl8 (11) and default ConSurf parameters. The picture was generated using MOLSCRIPT (21) and Raster3D (26).