After the calculation begins, ConSurf produces a status page indicating the computation parameters along with the different stages of the server activity. The main result of a ConSurf calculation is under the link ‘View ConSurf Results with Protein Explorer’, which leads to the graphic visualization of the query protein, color coded by conservation scores, through the Protein Explorer interface (9 (link)). The continuous conservation scores of each of the amino acid positions are available under the link ‘Amino Acid Conservation Scores’, along with the color grades and additional data. The script command for viewing the 3D structure of the query protein, color coded by conservation scores, is available under the link ‘RasMol coloring script source’. This file can be downloaded and used locally with the RasMol program (10 (link)), thus producing the same color-coded scheme generated by the server. A PDB file, in which the conservation scores are specified in the temperature (B) factor field, can be downloaded through the link: ‘The PDB file updated with the conservation scores in the tempFactor field’. Thus, any 3D protein viewer, such as the RasMol program (10 (link)), which is capable of presenting the B factors, is suitable for mapping the conservation scores on the structure.
The ConSurf output also includes links to the PSI-BLAST results, the homologous sequences along with a link to their SWISS-PROT entry page, the MSA and the phylogenetic tree used in the calculation.
As an example, we provide in Figure 2 the main output of a ConSurf run of the Kcsa potassium-channel (11 (link)), a transmembrane protein from Streptomyces Lividans. Kcsa is a homotetramer with a 4-fold symmetry axis about its pore. The ConSurf calculations demonstrate the high level of conservation of the pore region as compared with the rest of the protein. The pore architecture provides the unique stereochemistry which is required for efficient and selective conduction of potassium ions (11 (link)). The biological importance of this stereochemistry is reflected by a strong evolutionary pressure to resist amino acid replacements in the pore. In contrast, the regions that surround the pore and face the extracellular matrix are highly variable.