The ConSurf webserver
HANDS-ON ConSurf!
Web-Server: http://consurf.tau.ac.il/
The ConSurf webserver
Essential input (BLAST, MSA and tree by ConSurf):
• ConSurf mode: PDB ID\PDB file\model-structure and
chain
• ConSeq mode: a single fasta sequence
Essential and optional input:
1. PDB ID\PDB file\model-structure and chain
2. Constructed MSA, with the query sequence included
3. Phylogenetic tree
The ConSurf webserver
http://consurf.tau.ac.il/
http://consurf.tau.ac.il/results/1322930641/output.php
The ConSurf webserver
The ConSurf webserver
http://consurftest.tau.ac.il/•
The ConSurf webserver
The ConSurf webserver
The ConSurf webserver
MSA colored by conservation
ConSurf for pymol
BLAST & sequences
MSA
Phylogenetic tree
Jmol- Easy web-based viewer
View scores
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View phylogenetic tree
Search sequence
Change presentation
Summary- ConSurf
• Before using ConSurf, it is recommended to
install MDL chime on your computer for the
Protein Explorer web-viewer.
• It is highly recommended to install RasTop
or PyMol as well.
Summary- ConSurf
MSA Quality
• ConSurf is dependent on the quality of the MSA.
• When an MSA is not given by the user, sequences
are automatically gathered by PSI-BLAST and
aligned by CLUSTALW with default parameters.
• Even though these alignments are usually good, it is
highly recommended to inspect the alignment
manually (use BioEdit) and with other tools in order
to improve the quality of the evolutionary data .
Summary- ConSurf
A caveat: In some cases the functionally
important region may not be conserved at
all
The peptide-binding
groove of the MHC
class I heavy chain.
PDB id : 2vaa
ConSurf-DB
Pre-calculated conservation scores
http://consurfdb.tau.ac.il/
• Creates MSAs for all proteins in the PDB using a
methodology developed from our experience with
building MSAs.
• This process is important to ensure
conservation scores can be reliably utilized.
that
the
• The database is updated and is extremely userfriendly and easy to use.
Goldberg et al., 2008
ConSurf-DB
Goldberg et al., 2008
ConSurf-DB
Main Characteristics:
1.Maximum 300 sequences
2.Homologues obtained from SwissProt if there are enough hits,
otherwise collected from a clean version of UniProt.
3.MSA performed using MUSCLE
4.Fragments excluded
5.Redundant sequences filtered
Goldberg et al., 2008
ConSurf-DB
Example: Cytochrome C
• Panels A&B- ConSurf
calculation via the ConSurfDB (A) and the server with
default parameters (B).
• Panels C&D- conservation
calculated via Evolutionary
Trace Viewer Wizard and the
SiteFiNDER|3D server,
respectively.
Goldberg et al., 2008
ConSurf-DB
PDB id
Or protein sequence
A list of PDBs
ConSurf-DB
Select chain
ConSurf-DB
View via FirstGlance in Jmol
Results similar to the
ConSurf webserver
Producing images
Producing images
High quality via PyMol
• Open the PDB file downloaded from the PyMol
instructions (“File  Open…”)
• Open the script “consurf_new.py“ downloaded from the
PyMol instructions (“File  Run…”)
• Write “colour_consurf” in the command line
• Create the image “ray [x] [y]” in the command line
• Save the image “File  Save image”
Producing images
Press
Download!
Producing images
Producing images
Producing images
Producing images
Producing images