Welcome to CCR XP:
Explorer for clusters of conserved residues in protein structures
Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein-protein and protein-DNA complexes. Number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing out to a crucial role that these clusters play in protein function, specially protein-protein and protein-DNA interactions. [See references]
CCRs in DNA-binding proteins have been shown to be distributed in protein-DNA or protein-protein interfaces based on their overall physical properties. For example, most positively charged clusters are in protein-DNA interface. Therefore a detailed structure analysis of CCRs is very useful in understanding protein-DNA interactions and to a certain extent, predicting interfaces from structures.
However, finding such clusters is time consuming and requires several computational steps, specially if a certain critereon on selecting residues, based on their structural or physical charachterstics is implemented. An objective protocol and tool to determine CCRs is therefore needed.
CCR XP tries to automate the detection and analysis of such clusters in protein structures.
CCR XP is made of two input modules. CCR XP lite can be accessed directly (see query form on top), by uploading a PDB coordinate data or entering a PDB code and CCRs using default parameter settings for all protein chains in the coordinate file will be returned. The server will automatically (1) Extract fasta file from atom records (2) Find aligned sequences and calculate conservation scores (3) Cluster conserved residues and (4) Report several other structural properties of each residue as well as whole clusters, including their solvent accessibility that will allow to distinguish potential interface clusters from stabilizing core residues.