Home
This programme allows the number of neighbours of each residue in the 3D structure of a protein to be determined. It is based partly on the Atomic Density Calculation programme in Krane and Raymer (2003) (page 270). For each residue it reports the number of non-hydrogen atoms within a threshold distance (default 3.6 Angstroms), excluding the neighbouring atoms in the primary structure (default 3 on each side). Hydrogen atoms are excluded from calculations, so distances are measured between non-hydrogen atoms.
The programme is written in perl, and can be run under Unix, including MacOSX. Use the command line:
perl dist6.pl xxx.pdb
where xxx.pdb is the name of the appropriate pdb file, available in the same folder.
The threshold value (default 3.6 Angstroms) and the number of neighbours excluded (default 3) can be changed by editing the appropriate lines near the start of the programme.
On running the programme you should get an on-screen indication of progress (run-time). On completion a list of residues, in each case with the number of 'hits' (Count) appears on screen. But the main output will be in a file called 'theresult'. Change the name of this to avoid overwriting. This file contains
(1) a table listing residues in order in the sequence, with the number of 'hits' (i.e. the number of non-hydrogen atoms within the threshold distance) against each.
(2) a table showing the same data but in order of hits, and with a value for Count/aa size (the Count divided by the number of non-hydrogen atoms in that residue) in each case.
(3) The same data, ordered by Count/aa size.
The programme as it stands will probably not deal satisfactorily with a protein comprising more than one chain. It is advisable to check that the programme is working as expected by checking the hit value for a few residues using a molecular modelling programme such as Rasmol. For example the RasMol command :
"select within(3.6, 114) and not 111-117"
should give the same number of hits for residue 114 as dist6.pl.
dist6.pl can be obtained HERE .
Reference
Krane DE & Raymer ML (2003) Bioinformatics Benjamin Cummngs, San Francisco