Database name: Smotifs_redundant_01282011 Table names: loop_descriptors clusters motif_clusters loops2geom loops2geom_2_30_30_45 loops2geom_tailored pdb2phipsi Table Descriptions: loop_descriptors: contains the unique identifier, pdb information, sequence, dssp secondary structure and geometry description of each Smotif fields: nid - unique numerical identifier for discrete Smotif pdbid - pdb structure id from which Smotif is derived chain - chain within pdb structure from which Smotif is derived type - secondary structure content of Smotif (HH=helix-loop-helix, HE=helix-loop-strant, EH=strand-loop-helix, JA=hairpin/strand-loop-strand, AR=arch/strand-loop-strand) start - initial pdb residue of Smotif length - loop length, in number of residues, of Smotif ss1length - N-terminal secondary structure length, in number of residues, of Smotif ss2length - C-terminal secondary structure length, in number of residues, of Smotif seq - amino acid sequence of Smotif ss - dssp defined secondary structure of Smotif acc - internal letter code describing each residue of the Smotif phi/psi location on the Ramachandran plot cadist - distance (A) between Calpha atoms of loop stem residues (residues immediately preceding and following the loop) of Smotif ndist - distance (A) between N atoms of loop stem residues of Smotif cdist - distance (A) between C atoms of loop stem residues of Smotif mediadist - median distance of Ca, N, and C distance of Smotif continuous - indicates whether the Smotif is continuous (1) in the PDB structure or has an unresolved region (2), which usually occurs in the loop clusters: contains a unique integer id for each RMSD-based Smotif cluster fields: cluster_id - unique integer identifier for the RMSD-based Smotif cluster (used internally in the mysql database) cluster_name - unique cluster name for the RMSD-based Smotif cluster motif_clusters: contains the integer cluster id (internal id) for each Smotif fields: cluster_id - unique integer identifier for the RMSD-based Smotif cluster (used internally in the mysql database) nid - unique numerical identifier for discrete Smotif loops2geom: contains the 4-parameter geometry of each Smotif (see ref Oliva B et al (1997) An automated classification of the structure of protein loops. J Mol Biol 266: 814) fields: nid - unique numerical identifier for discrete Smotif d - "distance" measure for Smotif delta - "delta" angle measure for Smotif theta - "theta" angle measure for Smotif rho - "rho" angle measure for Smotif loops2geom_2_30_30_45: contains the 4-dimension geometrical groups that each Smotif belongs to where bin intervals are regular measures bin intervals: d=2angstroms, theta=30degrees, delta=30degrees, rho=45degrees fields: nid - unique numerical identifier for discrete Smotif dbinned - "distance" bin value for Smotif deltabinned - "delta" bin value for Smotif thetabinned - "theta" bin value for Smotif rhobinned - "rho" bin value for Smotif loops2geom_tailored: contains the 4-dimension geometrical groups that each Smotif belongs to where bin intervals are based on the distribution of each parameter in the initial Smotif set bin intervals: d=4angstroms, delta=60degrees, theta=60degrees, rho=90degrees fields: nid - unique numerical identifier for discrete Smotif dtailoredbin - "distance" tailored bin value for Smotif deltatailoredbin - "delta" tailored bin value for Smotif thetatailoredbin - "theta" tailored bin value for Smotif rhotailoredbin - "rho" tailored bin value for Smotif pdb2phipsi: contains the dssp-defined phi/psi angles of each residue of each Smotif in the library fields: pdb - pdb structure in which the Smotif residue occurs chain - chain within the pdb structure in which the Smotif residue occurs resnum - resnum of the Smotif residue phi - phi angle measure of the Smotif residue psi - psi angle measure of the Smotif residue