Conformational attractors 
on the 
Ramachandran map.

Dirk Walther & Fred E. Cohen

 Department of Cellular and Molecular Pharmacology
University of California, San Francisco

 Acta Crystallographica Section D 55: 506-517


 

WWW Service:

    WebMol (Option 'Rama', map type: 'df/dRes')

Supplementary material:
 
 

  •     Protein data set

    •         (Note: only 880 structures of this list of 897 protein chains met the DSSP quality requirements)
            Listed are the PDB ID, chain ID (0=all chains), and the resolution at which the protein was determined.
     
     
  •     Differential Ramachandran maps for individual amino acid types

    •         'r'- correlation coefficient for the linear correlation between fractional occurences of
            phi/psi bins and crystallographic resolutions.

            gif-format:
                Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu,
                Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr
            postscript format:
                Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu,
                Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr
     

    Note/ Correction:

        In the concluding remarks of chapter 3.1 we state that "the fractional
        content of any secondary structural type defined in DSSP was observed to
        be uncorrelated with resolution with corresponding correlation
        coefficients of r<0.03 for each secondary structural type including
        random coil interpreted as a separate structural category. Thus, the
        frequency shifts observed in Figure 1B did not originate from an
        unbalanced data set."
     
        We note that the reported maximal absolute value of 0.03 actually was
        obtained for the regression slopes and not the correlation coefficients
        r.
     
        For the correlation coefficients we find |r|<0.05 for all secondary
        structural states defined in DSSP except for r=-0.19 for Turns (designated 'T') and
        r=-0.11 for isolated beta-bridges (designated 'B'). The conclusion in our original paragraph remains
        unchanged. However, the significant correlation coefficient for Turns
        (increased frequencies at higher resolution) shows the tendency towards
        all satisfied hydrogen bonds in high-resolution protein structures.
     
     


    Last modified: Thu Aug 20 14:33:11 PDT