H. Torsion Angles and Centers

---

Overview

The database file contains the sidechain torsion angles and one coordinate for the center of the sidechain. This center is the center of mass or the center of the reactive group of the sidechain. The actual specification for each amino acid residue is listed in the following table.

Table 13. Side Chain Torsion Angles and Centers

amino acid	center of mass	chi1	chi2	chi3	chi4	chi5
PRO	Cg	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd
GLY	CA
ALA	CB
VAL	Cg1/Cg2	N-Ca-Cb-Cg1
LEU	Cd1/Cd2	N-Ca-Cb-Cd	Ca-Cb-Cg-Cd1
ILE	Cd	N-Ca-Cb-Cg1	Ca-Cb-Cg1-Cd
MET	Ce	N-Ca-Cb-Cg	Ca-Cb-Cg-Sd	Cb-Cg-Sd-Ce
PHE	CH	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd1
TRP	Ne1	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd1
SER	Og	N-Ca-Cb-Og
THR	Og1	N-Ca-Cb-Og1
ASN	Od1/Nd2	N-Ca-Cb-Cg	Ca-Cb-Cg-Od1
GLN	Oe1/Ne2	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd	Cb-Cg-Cd-Oe1
CYS	Sg	N-Ca-Cb-Sg
TYR	Oz	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd1
ASP	Od1/Od2	N-Ca-Cb-Cg	Ca-Cb-Cg-Od1
GLU	Oe1/Oe2	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd	Cb-Cg-Cd-Oe1
LYS	Nz	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd	Cb-Cg-Cd-Ce	Cg-Cd-Ce-Nz
ARG	NH1/NH2	N-Ca-Cb-Cg	Ca-Cb-Cg-Cd	Cb-Cg-Cd-Ne	Cg-Cd-Ne-Cz	Cd-Ne-Cz-NH1
HIS	Nd1/Cd2	N-Ca-Cb-Cg	Ca-Cb-Cg-Nd1

---

Database file format

This format can be defined by the following FORTRAN specification:

	parameter ( nzres=2000, nzseg=20)
	parameter ( nzlig=200, nzfam=100, nznam=100, nzkey=320)
	character*8 protnm 	! protein name
	integer nlig	! number of ligand records
	integer nrec	! number of analysis records for
		! protein
	integer nxlmol	! number of protein molecules
		! defined in PDB file
	integer nseg	! number of segments
	integer nres	! number of residues
	integer natom	! number of protein atoms
	integer nhetat	! number of non-protein atoms
	integer nhoh	! number of water atoms
	real resol	! resolution of crystal structure
	character*(nzfam)	! protein family
	character*(nznam)	! name of protein
	character*(nzkey) descrip	! keyword description
	character*(nzlig) ligand	! description of ligand
	character*1 segid (nzseg)	! segment name
	integer prsseg (nzseg)	! first residue in segment
	integer nrsseg (nzseg)	! number of residues in segment
	character*5 idres (nzres)	! residue ids
	integer rescode (nzres)	! residue type code
	integer secstr (nzres)	! secondary structure type code
	real x (3,nzres)	! Ca atom coordinates
	real xside (3,nzres)	! `average' side chain coordinate
	real cators (nzres)	! Ca pseudo-torsions
	real phipsi (2,nzres)	! phi/psi torsion angles
	real sidtor (5,nzres)	! side chain torsion angles
c write out the header records describing the protein
	write (file) protnm, nlig, nrec, nxlmol, nseg, nres, natom, 
1		nhetat,nhoh
	write(file) resol, family, name, descrip
c write the description of ligands - NB variable number of records
	do 10 n=1, nlig
10	write (file) ligand(n)
c write the structural description NB not necessarily present for 
c all entries in the database - see the nrec parameter
	write (file) (segid(k), k=1,nseg), (prsseg(k), k=1,nseg),(nrsseg(k), k=1,nseg)
	write (file) (idres(k), k=1,nres)
	write (file) (rescode(k), k=1,nres)
	write (file) (secstr(k), k=1,nres)
	write (file) ((x(j,k), j=1,3), k=1,nres)
	write (file) ((xside(j,k), j=1,3), k=1,nres)
	write (file) (cators(k), k=1,nres)
	write (file) ((phipsi(j,k), j=1,2), k=1,nres)
	write (file) ((sidtor(j,k), j=1,5), k=1,nres)

© 2006 Accelrys Software Inc.