PDBGEO is a local program that computes various structural data from PDB-like formatted protein structures. The PDBGEO output contains one data block for each residue in the protein. Each data block includes three sections starting with a "#" character that contains information on the residue as a whole, on individual atoms of the residue, and on contacts with other residues, respectively. NB: areas are given on an arbitrary scale deduced from 66 dots evenly distributed on van der Waals spheres. Description of the residue section (#a): a: Residue type (one letter code) i: Residue number c: Residue chain vdw: van der Waals area acc: Area in contact with solvent C: Area in contact with carbon atoms of other residues N: Area in contact with nitrogen atoms of other residues +: Area in contact with positively charged atoms of other residues O: Area in contact with oxygen atoms of other residues -: Area in contact with negatively charged atoms of other residues S: Area in contact with sulfur atoms of other residues s2: Secondary structure (0= alpha-helix, 1=beta-sheet, 3=coil) d3: Calpha(i)-Calpha(i+3) distance (in Angstroems x 10) d4: Calpha(i)-Calpha(i+4) distance (in Angstroems x 10) d5: Calpha(i)-Calpha(i+5) distance (in Angstroems x 10) d6: Calpha(i)-Calpha(i+6) distance (in Angstroems x 10) d7: Calpha(i)-Calpha(i+7) distance (in Angstroems x 10) phi: Phi backbone dihedral angle psi: Psi backbone dihedral angle chi1: Chi1 side-chain dihedral angle chi2: Chi2 side-chain dihedral angle bur: Area buried by other residues in the protein pol: Percent of total area in contact with solvent or polar atoms pac: Percent of total area in contact with solvent omeg: Omega backbone dihedral angle (CA-C-N-CA) Description of the atom section (# atom) for atom X: vdw, acc, C, N, +, O, -, S: see residue section dcb: distance from the CB atom acb: angle between the CA-CB and the CB-X vectors bcb: dihedral angle X-CB-CA-Z where Z is the gamma atom used in Chi1 determination Description of the contact section (#aa): i: Number (residue in contact) c: Chain (residue in contact) ct: Contact area (residue in contact) dcb, acb, bcb: same as in the atom section with X being the CB atom of the residue in contact dca aca bca: same as above but X is the CA atom of the residue in contact dcm acm bcm: same as above but X is the side-chain centroid of the residue in contact This is followed by all individual atoms of the residue in contact that do contact the reference residue(one atom per line). Each line includes the ct, dcb, acb and bcb atomic data followed by expressions NAME.X.Y where NAME is the name of the atom of the reference residue in contact, X is the distance betwenen atoms in contact (x10) Y is the area of the reference atom in contact