🚀 go-pugleaf

From: Sunil Maulik <MAULIK@BIONET-20.ARPA>


DSSP - DEFINE SECONDARY STRUCTURES OF PROTEINS

   This  program written by Kabsch and Sander defines secondary structures
   of proteins  from  the  patterns  of  hydrogen  bonds  and  geometrical
   features  of  the  backbone  structure.   The program runs on a Protein
   Data Bank file and the output contains up  to  128  characters  in  one
   line.   


OUTPUT
     The following notes are reproduced from the original program.

       # RESIDUE  -  Two  columns  of  residue  numbers.   First  column  is
          DSSP(3)'s   sequential  residue  number,  starting  at  the  first
          residue actually in the data set and including chain breaks;  this
          number  is  used  to  refer to residues throughout.  Second column
          gives crystallographers' residue sequence number,  insertion  code
          and  chain  identifier,  given  for  reference  only  and not used
          further.
       AA - One letter amino acid code, lower case for SS-bridge CYS.
       STRUCTURE - See ANNOT(3) and reference below.
       BP1 BP2 - Residue number of first and second bridge partner  followed
          by one letter sheet label.
       ACC -  Number  of  water  molecules in contact with this residue *10.
          Or residue water exposed surface in angstrom**2.
       N-H-->O etc. - Hydrogen bonds. e.g. -3,-1.4 means:  if  this  residue
          is  residue  I  then  N-H  of  I is H-bonded to C=O of I-3 with an
          electrostatic H-bond energy of -1.4 kcal/mol.
       TCO - Cosine of angle between C=O of residue I  and  C=O  of  residue
          I-1.   For  alpha-helices,  TCO is near +1, for beta-sheets TCO is
          near -1.  Not used for structure definition.
       KAPPA - Virtual bond angle (bend angle) defined by the three  C-alpha
          atoms  of  residues  I-2,  I, I+2.  Used to define bend (structure
          code 'S').
       ALPHA - Virtual torsion angle (dihedral angle) defined  by  the  four
          C-alpha  atoms  of  residues  I-1,  I,  I+1,  I+2.  Used to define
          chirality (structure code '+' OR '-').
       PHI PSI - IUPAC peptide backbone torsion angles.
       X-CA Y-CA Z-CA - Echo of C-alpha atom coordinates.

REFERENCE
     Kabsch, W. and Sander, C.;  Dictionary of protein secondary  structure:
        Pattern  recognition  of  hydrogen-bonded  and geometrical features.
        Biopolymers 22, 2577-2637 (1983).


For more help on the DSSP program, including an annotated example of 
program use and the Brookhaven Protein Databank, enter HELP DSSP at the
@ sign. To run the program, simply enter DSSP at the @ sign. 

For more information on the contributed software available on BIONET, enter
HELP SOFTWARE at the @ prompt. For a guide to the BIONET sytem, enter HELP
ME at the @ prompt.

 
Sincerely,

Sunil Maulik			ARPAnet: Maulik@bionet-20.arpa
Senior Scientific Consultant    BITnet:  Maulik%bionet-20.arpa@wiscvm.bitnet
BIONET
(415)-324-4363
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