Coil Library File Formats
There are two file formats used in the Protein Coil Library. The first is a simplified version of the PDB file format (described at the RCSB) which uses only SEQRES, ATOM, TER, and END records. These files end with the extension ".pdb.gz." The other file format used is the torsion angle file format, which is described below. Torsion angle files contain information about the phi, psi, omega, and chi backbone torsions and end with the extension ".tor.gz."
| Line 1: | This line describes how many chains are stored in this torsion file. In the Coil Library, this is always 1. | ||
| Column | C Format | Description | |
| 0:8 | %8i | Integer number of chains | |
| Line 2: | For the first chain, this line gives the chain identifier as well as number of residues listed for this particular chain. | ||
| Column | C Format | Description | |
| 0:2 | %-2s | The chain identifier. | |
| 3:10 | %7i | Integer number of residues in this chain | |
| Line 3: | (Additionally, subsequent lines, one line for each residue given in line 2.) This line describes the torsion angles and residue information for a particular residue. | ||
| Column | C Format | Description | |
| 0:8 | %8i | Integer that describes the residue index, from the originating PDB file. | |
| 9 | %1s | The one-letter code for insertion of residues. Can be a space. | |
| 11:14 | %3s | The three-letter amino acid code for this residue | |
| 15:25 | %10.4f | The backbone φ torsion, defined for residue i as the torsion angle between Ci-1-Ni-CAi-Ci. | |
| 26:36 | %10.4f | The backbone ψ torsion, defined for residue i as the torsion angle between Ni-CAi-Ci-Ni+1 | |
| 37:47 | %10.4f | The backbone ω torsion, defined for residue i as the torsion angle between CAi-1-Ci-1-Ni-CAi. | |
| 48:58 | %10.4f | The backbone χ1 torsion, if it exists. If it does not exist, this column contains 999.9900. It is guaranteed that, if χ1 is defined, it will be within the range [-180.0, 180.0). The atom definitions used to calculate χ1 torsions are given here. | |
| 59:69 | %10.4f | The backbone χ2 torsion, if it exists. If it does not exist, this column contains 999.9900. It is guaranteed that, if χ2 is defined, it will be within the range [-180.0, 180.0). The atom definitions used to calculate χ2 torsions are given here. | |
| 70:80 | %10.4f | The backbone χ3 torsion, if it exists. If it does not exist, this column contains 999.9900. It is guaranteed that, if χ3 is defined, it will be within the range [-180.0, 180.0). The atom definitions used to calculate χ3 torsions are given here. | |
| 81:91 | %10.4f | The backbone χ4 torsion, if it exists. If it does not exist, this column contains 999.9900. It is guaranteed that, if χ4 is defined, it will be within the range [-180.0, 180.0). The atom definitions used to calculate χ4 torsions are given here. | |
| 92 | %1s | The one-letter mesostate code, as defined in Srinivasan, R. and Rose, G. "A Physical Basis for Protein Secondary Structure." PNAS 96 (25):14258-63. This code designates a region in φ-ψ that is used to define secondary structure. "*" designates a residue whose ω torsion deviates over 90 degrees from planarity. | |
| 94 | %1s | The one-letter secondary structure code, using the backbone-torsion angle method described in Srinivasan, R. and Rose, G. "A Physical Basis for Protein Secondary Structure." PNAS 96 (25):14258-63. E indicates β-strand, H indicates α-helix, P indicates polyproline-II helix, T indicates turn, and C indicates coil. This secondary structure code is included for compatibility purposes only. It is not used in generating the coil library. | |
| 96:98 | %2s | The two-letter mesostate code, as defined on the methods page. This code designates a region in φ-ψ that is used to define secondary structure. "**" designates a residue whose ω torsion deviates over 90 degrees from planarity. | |
| 99 | %1s | The one-letter secondary structure code, as defined on the methods page. This secondary structure code is the code actually used to determine whether the fragment is or is not coil. Typically it is identical to the previous secondary structure definition. E indicates β-strand, H indicates α-helix, P indicates polyproline-II helix, T indicates turn, and C indicates coil. | |
In addition to having entries for each non-helix, non-strand residue, torsions files also contain at most a two residue buffer on either side of the coil fragment. This provides some idea of the context of the fragment in question when the fragment is flanked by helical or strand residues.
Because the Protein Coil Library is derived from the PDB, all files should adhere to the formats described above. If you identify a file that does not conform to this standard, please contact the maintainers
