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    NOTES: dssp

    OCCURRENCE

    ARB_IMPORT

     

    DESCRIPTION

    See NOTES in ´Import Foreign Data(bases)´ for HOWTO reactivate disabled import filters.

    The three filters 'dssp_all.ift', 'dssp_2nd_struct.ift' and 'dssp_sequence.ift' import protein secondary structure information and/or amino acid sequences from DSSP files. In addition, some of the associated information is extracted, too. The following fields are created (see also example below):

    • name: [PDB ID]_[Chain char] (extracted from 'HEADER' and the optional chain character in 'RESIDUE')
    • full_name: [PDB ID] (extracted from 'HEADER') Chain [Chain char] (extracted from the optional chain character in 'RESIDUE'); [Description] (extracted from 'HEADER' and 'COMPND')
    • tax: [Organism description] (extracted from 'SOURCE')
    • author: [Author(s)] (extracted from 'AUTHOR')
    • date: [Date] (extracted from 'HEADER')
    • remark: [Remark] (extracted from headline and 'REFERENCE')
    • ali_[alignment name]/data: [Amino acid sequence or secondary structure] (extracted from 'AA' or 'STRUCTURE')
    • sec_struct: [Secondary structure] (extracted from 'STRUCTURE')

     

    The DSSP code

    • H = alpha helix
    • B = residue in isolated beta-bridge
    • E = extended strand, participates in beta ladder
    • G = 3-helix (3/10 helix)
    • I = 5-helix (pi helix)
    • T = hydrogen bonded turn
    • S = bend

     

    NOTES

    • If a protein consists of several chains these are extracted individually and stored as different species.
    • The filter 'dssp_2nd_struct.ift' fills 'ali_[alignment name]/data' with the protein secondary structure and 'dssp_sequence.ift' as well as 'dssp_all.ift' fill it with the amino acid sequence.
    • The field 'sec_struct' is only used by the filter 'dssp_all.ift'.
    • Gaps-characters ('-') are inserted where no secondary structure is present.
    • The DSSP files are first piped through the script 'format_dssp.pl' (in "$ARBHOME/ARB/PERL_SCRIPTS/ARBTOOLS/IFTHELP") to format the files for use with the filters 'dssp_all2.ift2', 'dssp_2nd_struct2.ift2' and 'dssp_sequence2.ift2'.
    • Reference to DSSP can be found in ´Protein Alignments´ in section 'REFERENCES' [2].

     

    EXAMPLES

    The DSSP format looks like this:

    ==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=27-JUN-2003     .
    REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
    HEADER    RNA BINDING PROTEIN                     22-NOV-99   1DG1                                                             .
    COMPND   2 MOLECULE: ELONGATION FACTOR TU;                                                                                     .
    SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                                                                              .
    AUTHOR    K.ABEL,M.YODER,R.HILGENFELD,F.JURNAK                                                                                 .
    ...
    ...
      #  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA
        1    9 G K              0   0  143      0, 0.0    65,-0.2     0, 0.0    64,-0.1   0.000 360.0 360.0 360.0 143.2   13.7   48.3  -15.2
        2   10 G P        -     0   0   38      0, 0.0    65,-2.6     0, 0.0     2,-0.6  -0.404 360.0-137.6 -64.4 148.4   12.2   51.7  -14.1
        3   11 G H  E     -a   67   0A  88     63,-0.2     2,-0.3   191,-0.1    65,-0.2  -0.949  24.0-180.0-114.6 117.8   10.1   51.4  -10.9
        4   12 G V  E     -a   68   0A   0     63,-2.0    65,-2.3    -2,-0.6     2,-0.5  -0.855  18.2-141.7-116.0 149.5    6.8   53.4  -10.8
        5   13 G N  E     +a   69   0A  36     -2,-0.3    86,-2.5    63,-0.2    87,-1.2  -0.949  31.8 154.0-113.1 127.7    4.2   53.5   -8.0
        6   14 G V  E     -ab  70  92A   0     63,-2.5    65,-2.0    -2,-0.5     2,-0.3  -0.820  16.5-171.5-139.8-179.7    0.5   53.6   -8.8
        7   15 G G  E     -ab  71  93A   0     85,-0.5    87,-2.2    63,-0.3     2,-0.3  -0.969  28.1-103.8-167.9 164.5   -2.7   52.6   -7.2
        8   16 G T  E     + b   0  94A   0     63,-1.9    65,-0.4    -2,-0.3     2,-0.3  -0.735  37.7 175.7 -97.6 147.4   -6.4   52.2   -7.9
        9   17 G I  E     + b   0  95A   3     85,-1.9    87,-2.6    -2,-0.3     2,-0.2  -0.962  21.1  98.6-147.2 156.0   -8.8   54.9   -6.7
       10   18 G G        -     0   0    0     -2,-0.3    87,-0.1    85,-0.2    97,-0.1  -0.829  69.1 -41.6 148.3 177.9  -12.6   55.4   -7.1
       11   19 G H  S >  S-     0   0   35     85,-0.4     3,-1.4    -2,-0.2     5,-0.3  -0.330  72.6 -81.6 -74.1 153.0  -15.9   54.9   -5.4
       12   20 G V  T 3  S+     0   0   58      1,-0.2    -1,-0.1     2,-0.1    94,-0.1  -0.094 111.7  15.7 -52.8 150.0  -16.8   51.7   -3.5
       13   21 G D  T 3  S+     0   0  145      1,-0.1    -1,-0.2    -3,-0.1    -2,-0.1   0.575  91.3 115.4  59.3  12.4  -17.9   48.6   -5.4
       14   22 G H  S <  S-     0   0    4     -3,-1.4    -2,-0.1    82,-0.1    85,-0.1   0.789  92.2 -97.1 -80.7 -25.6  -16.7   50.1   -8.6
       15   23 G G  S  > S+     0   0   11     -4,-0.2     4,-2.5    81,-0.1     5,-0.2   0.577  75.0 138.4 123.2  16.6  -14.0   47.5   -9.1
       16   24 G K  H  > S+     0   0   12     -5,-0.3     4,-2.7     1,-0.2     5,-0.1   0.931  82.3  40.1 -55.3 -48.3  -10.7   48.7   -7.8
       17   25 G T  H  > S+     0   0   17      2,-0.2     4,-2.3     1,-0.2    -1,-0.2   0.887 114.0  51.1 -70.8 -40.4   -9.8   45.4   -6.2
       18   26 G T  H  > S+     0   0   30      2,-0.2     4,-2.4     1,-0.2    -1,-0.2   0.899 113.8  47.6 -64.1 -39.4  -11.1   43.1   -9.0
       19   27 G L  H  X S+     0   0    0     -4,-2.5     4,-2.6     2,-0.2    -2,-0.2   0.955 107.8  53.8 -66.2 -49.6   -9.1
    ...
    ...

    The extracted ARB database entry looks like this (for alignment with the name 'ali_prot' and imported with 'dssp_all.ift'):

    name            S6: 1DG1_G
    full_name       S0: 1DG1 Chain G; RNA BINDING PROTEIN; MOLECULE: ELONGATION FACTOR TU
    tax             S0: ORGANISM_SCIENTIFIC: ESCHERICHIA COLI
    author          S0: K.ABEL,M.YODER,R.HILGENFELD,F.JURNAK
    date            S0: 22-NOV-99
    ali_prot        %0:
    ali_prot/data   S0: KPHVNVGTIGHVDHGKTTL...
    sec_struct      S0: --EEEEEEE-STTSSHHHH...
    remark          S0: === Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=22-FEB-2008
                        DSSP program by: W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637
    ...
    ...
     

    WARNINGS

    None

     

    BUGS

    No bugs known