DEFINE_S uses CA - CA distances to determine the secondary structure of a protein. The output is both graphical and in ASCII format.

The ASCII output lists the definitions in varous formats. For instance by distance criteria DEFINE_S categorizes residues 6-25 as three contiguous beta strand segments with bends that create angles of 20-34 degrees between the segments:

 SECND :      START       END  LENGTH STRUCTURE WITH_AXIS

 SECND :          6        13       8    B         34.
 SECND :         13        20       8    B         23.
 SECND :         21        25       5    B         20.

and it defines the geometrical relationship between the strands that make up the central sheet, e.g.,

 SSS   : ANGLES FOR STRAND-STRAND PAIRS
 SSS   :                                                        FRACTIONAL DISTANCE
 SSS   :                                                        FROM N TERM. POINT 
 SSS   :                   MIN     ATOMS AT   A1-A2      AXIAL  TO MIN SEPN. POINT
 SSS   : STRND 1  STRND 2  DIST    MIN DIST   ANGLE      SEPN.  STRND 1  STRND 2

 SSS   :  13- 20  103-110   4.4     14  105   -172.      4.1     -0.7      1.1

Below is a portion of the graphical output:

Here the beta strand from residues 10-19 seen in the RIBBONS image is broken up into two separate beta regions (6-13 & 13-20) with a slight crossing angle indicated by :

And the beta strands formed between residues (6-13,14-20) and (97-102,103-110) is indicated by:

Other icon definitions can be found in the DEFINE_S description.

Return to Post-structure Analysis

Revised: Thursday, 22-Oct-1998 11:32:04 EDT