CCRXP ADV: User selected parameters (Definitions are provided here. For detailed effect on CCR analysis, click here)Critereon to determine residue positions in space:
Before clustering, CCRXP assign a single geometric position to each residue. This position will be used to reduce a residue to single point and the density of resulting points will be used as packing density (first sub-selection) and clustering residue (second sub-selection). Currently two methods of selecting this position are available. Choosing "ca", uses atomic coordinates of C-alpha position in the PDB. Choosing geometric center, CCRXP will calculate the center of mass for all atoms in the ATOM records of that residue. Both these methods in either combination can be used to define packing density as well as clustering. Defaule for CCRXP_lite is C-alpha for packing density and geometric center for clustering.
Packing density range:
Packing density is defined as the number of residues (points, as defined above), within a given distance. This distance is called PD Range. Default for CCRXP_lite is 7A.
Distance range for clustering residues:
Clusters are formed using single linkage hierarchical approach, by starting seeds at every residue point. If no linkage is found between two evolving clusters at a distance cutoff, clusters are counted as separate. Default for CCRXP_lite is 5A.
Maximum number of aligned sequences:
During BLAST search, many sequences may be found to be similar to the query sequence. Only top "N" sequences are used for calculating multiple alignments and conservation score. N can be selected by users. Default value is 50.
Conservation score cutoff to include in clustering:
Conservation score is calculated in 0 to 1 scale units. Default cutoff is 0.7.
ASA cutoff (% exposed units):
Some times, only clusters on surface need to be found. Residues less than a given relative solvent accessibility can be filtered here. Default is "no filtering".
Minimum number of residues in a cluster:
Sometimes only large clusters are required and singlets may be filtered, by chosing a minimum size of a cluster. Default minimum size set at 2.
CCRXP: Explanation of outputsTwo output files are generated by CCRXP. First is the result of clustering for each protein chain within the uploaded file and other is a tabulated data of basic structural properties, considered relevant for hot spot analysis.
Explanation for clusters output (Results are repeated for each chain in the following order). CCR ID: All clusters of conserved residues are assigned numerical index, starting from 1. Numbers are restarted for each chain.
Size: This is the number of residues in the corresponding cluster.
Members: This contains the list of residues in the given cluster. Residue ID in one letter code, and residue numbering in PDB file are separated by ":" within the name of each member in the list.
Positive charge: This is simply the number of positively charged residues in the cluster (only Arg and Lys are assigned +1 charge).
Negative charge: This is simply the number of negatively charged residues in the cluster (only Asp and Glu are assigned -1 charge).
Dipole moment: Only the residues within the cluster are considered and assigned a position, as defined in clustering options. Charges are assigned as above. Reference is the geometric center of the cluster and measurements are in atomic units.
Average conservation: Conservation scores of all residues within the cluster are averaged.
Average packing density: Packing density of all residues (as defined above) within the cluster are averaged.
Helical residue count: Number of residues from the given cluster in helical conformation.
Strand residue count: Number of residues from the given cluster in strand conformation.
Coil residue count: Number of residues from the given cluster in coil conformation.
Average ASA: Relative solvent accessibility of all residues of the cluster (in % units) is averaged.