--------------------------------------- SLEUTH Protein Data Bank Abstract Files --------------------------------------- This directory contains a set of descriptive abstracts for many of the Protein Data Bank (PDB) files from the Sept 2001 release. Files are present for the structures from the EMBL 25% sequence similarity list. The current abstract database contains 1641 polypeptide chains for a total of 272472 residues. Each of the abstract files contains: (1) Protein Data Bank 4-Letter Code for the PDB File (2) Name of the Compound as found in the PDB File (3) Number of Amino Acids in the Chain Abstracted (4) Amino Acid Sequence in 3-Letter Code (5) Main Chain and Side Chain Dihedral Angle values for each Residue (phi, psi, omega, chi's) (6) Cartesian Coordinates for each Alpha Carbon Atom (7) Secondary Structure at each Residue as determined by the method of Richards and Kundrot (8) Secondary Structure at each Residue as determined by the method of Kabsch and Sander (DSSP) (9) Amount of Buried Surface Area for each Side Chain, percentage of the Area that is Buried, and the total percentage of Area that is covered by polar atoms When a single PDB file contains multiple chains, the separate chains are abstracted in separate files in this directory; for example, 2bpa.dat, 2bpa.dat_2 and 2bpa.dat_3. The amino acid numbering in the abstract files starts with 1 and moves sequentially to the final residue. Note that this numbering is often different from that used in the original PDB file. In some cases, missing amino acid residues and other types of chain breaks are not handled gracefully by the abstracting program; if in doubt, please consult the original PDB file. For structures determined by NMR and reporting multiple models, only the first model is abstracted. The keys for the two secondary structure analysis methods are as follows: Richards-Kundrot: H alpha helix S sheet T turn C coil 3 3/10 helix P cis peptide bond X chain break or severe irregularity Kabsch-Sander: B residue in isolated beta-bridge E extended strand, participates in beta-ladder G 3-helix (3/10 helix) H 4-helix (alpha-helix) I 5-helix (pi-helix) S bend T hydrogen-bonded turn e extension of beta-strand g extension of 3/10 helix h extension of alpha-helix The values of buried area, percentage buried and percentage of polar coverage are computed in the fashion described by Eisenberg's group for use with the 3-D structure profile method (Science, 253, 164-170, 1991). Software to build the profile database, construct and use individual profiles can be found in the /sleuth/source directory. Also in the /source subdirectory is the abstracting program, as well as the SLEUTH program itself. SLEUTH reads the abstract database and allows searching for hits based on various combinations of data from the abstracts (general sequence patterns, secondary structure, burial, dihedral angles, etc.).