
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   57 (   57),  selected   57 , name T0349TS393_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS393_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    E       3      N       8           #
LGA    L       4      D       9          0.926
LGA    L       5      A      10          0.519
LGA    R       6      V      11          0.498
LGA    T       7      L      12          0.567
LGA    N       8      L      13          0.669
LGA    D       9      S      14          0.420
LGA    A      10      A      15          0.571
LGA    V      11      V      16          0.605
LGA    L      12      G      17          0.982
LGA    L      13      A      18          1.032
LGA    S      14      L      19          1.110
LGA    A      15      L      20          1.136
LGA    V      16      D      21          2.364
LGA    G      17      G      22          2.765
LGA    A      18      A      23          2.583
LGA    L      19      D      24          2.861
LGA    L      20      I      25           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      G      26          2.838
LGA    R      46      H      27           #
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      L      28          4.213
LGA    V      50      V      29          3.338
LGA    -       -      P      45           -
LGA    H      51      R      46           #
LGA    E      52      R      47          5.561
LGA    D      53      -       -           -
LGA    D      54      V      48          5.023
LGA    L      55      L      49          2.706
LGA    A      56      -       -           -
LGA    G      57      V      50          4.016
LGA    A      58      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    -       -      G      57           -
LGA    R      59      A      58           #
LGA    R      60      R      59          1.789
LGA    L      61      R      60          5.292
LGA    L      62      L      61          4.687
LGA    T      63      L      62          1.547
LGA    -       -      T      63           -
LGA    D      64      D      64          3.837
LGA    A      65      A      65          3.486
LGA    G      66      G      66          1.785
LGA    L      67      L      67          2.300
LGA    A      68      A      68           #
LGA    H      69      H      69           -
LGA    E      70      E      70           -
LGA    L      71      L      71           -
LGA    R      72      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   57   57    5.0     31    2.80    41.94     39.753     1.069

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.399062 * X  +  -0.723466 * Y  +   0.563335 * Z  +  -1.802142
  Y_new =   0.901808 * X  +  -0.198579 * Y  +   0.383807 * Z  +   5.557983
  Z_new =  -0.165805 * X  +   0.661183 * Y  +   0.731673 * Z  +   7.146239 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.734833   -2.406760  [ DEG:    42.1028   -137.8972 ]
  Theta =   0.166574    2.975019  [ DEG:     9.5440    170.4560 ]
  Phi   =   1.987407   -1.154186  [ DEG:   113.8700    -66.1300 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0349TS393_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   57   57   5.0   31   2.80   41.94  39.753
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_1-D1
PFRMAT TS
TARGET T0349
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -5.488 -13.381  14.102  1.00 25.00           C
ATOM      2  CA  ARG     2      -5.911 -10.809  11.312  1.00 25.00           C
ATOM      3  CA  GLU     3      -3.362  -9.416   8.820  1.00 25.00           C
ATOM      4  CA  LEU     4      -2.472  -7.411   5.682  1.00 25.00           C
ATOM      5  CA  LEU     5      -5.926  -5.757   5.730  1.00 25.00           C
ATOM      6  CA  ARG     6      -5.476  -4.866   9.428  1.00 25.00           C
ATOM      7  CA  THR     7      -2.038  -3.359   8.672  1.00 25.00           C
ATOM      8  CA  ASN     8      -3.541  -1.302   5.813  1.00 25.00           C
ATOM      9  CA  ASP     9      -6.317  -0.053   8.137  1.00 25.00           C
ATOM     10  CA  ALA    10      -3.709   0.926  10.765  1.00 25.00           C
ATOM     11  CA  VAL    11      -1.699   2.809   8.104  1.00 25.00           C
ATOM     12  CA  LEU    12      -4.865   4.646   6.976  1.00 25.00           C
ATOM     13  CA  LEU    13      -5.635   5.597  10.606  1.00 25.00           C
ATOM     14  CA  SER    14      -2.062   6.900  11.048  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.392   8.968   7.841  1.00 25.00           C
ATOM     16  CA  VAL    16      -5.711  10.416   9.088  1.00 25.00           C
ATOM     17  CA  GLY    17      -4.087  11.316  12.439  1.00 25.00           C
ATOM     18  CA  ALA    18      -1.192  13.025  10.604  1.00 25.00           C
ATOM     19  CA  LEU    19      -3.680  15.003   8.468  1.00 25.00           C
ATOM     20  CA  LEU    20      -5.570  16.078  11.620  1.00 25.00           C
ATOM     21  CA  ASP    21      -2.286  17.198  13.238  1.00 25.00           C
ATOM     22  CA  GLY    22      -2.773  17.153  17.037  1.00 25.00           C
ATOM     23  CA  ALA    23      -6.506  16.564  16.720  1.00 25.00           C
ATOM     24  CA  ASP    24      -6.498  14.122  19.624  1.00 25.00           C
ATOM     25  CA  ILE    25      -5.845  11.305  17.206  1.00 25.00           C
ATOM     26  CA  GLY    26      -8.983  11.284  15.076  1.00 25.00           C
ATOM     27  CA  HIS    27     -10.320  11.328  11.459  1.00 25.00           C
ATOM     28  CA  LEU    28     -12.666  10.044   8.713  1.00 25.00           C
ATOM     29  CA  VAL    29     -11.814   6.783   7.028  1.00 25.00           C
ATOM     45  CA  PRO    45      -6.410  12.499   1.436  1.00 25.00           C
ATOM     46  CA  ARG    46      -8.846   9.573   0.803  1.00 25.00           C
ATOM     47  CA  ARG    47     -10.671   7.506  -1.873  1.00 25.00           C
ATOM     48  CA  VAL    48      -7.478   6.766  -3.859  1.00 25.00           C
ATOM     49  CA  LEU    49      -5.747   3.766  -5.380  1.00 25.00           C
ATOM     50  CA  VAL    50      -3.594   0.963  -3.956  1.00 25.00           C
ATOM     51  CA  HIS    51      -0.748   2.383  -6.088  1.00 25.00           C
ATOM     52  CA  GLU    52       3.034   2.057  -6.238  1.00 25.00           C
ATOM     53  CA  ASP    53       4.296   5.616  -5.599  1.00 25.00           C
ATOM     54  CA  ASP    54       1.051   6.461  -3.748  1.00 25.00           C
ATOM     55  CA  LEU    55       1.418   3.302  -1.614  1.00 25.00           C
ATOM     56  CA  ALA    56       5.037   4.248  -0.792  1.00 25.00           C
ATOM     57  CA  GLY    57       3.915   7.772   0.204  1.00 25.00           C
ATOM     58  CA  ALA    58       1.189   6.295   2.452  1.00 25.00           C
ATOM     59  CA  ARG    59       3.759   3.979   4.091  1.00 25.00           C
ATOM     60  CA  ARG    60       6.095   6.953   4.690  1.00 25.00           C
ATOM     61  CA  LEU    61       3.215   8.931   6.258  1.00 25.00           C
ATOM     62  CA  LEU    62       2.381   5.964   8.529  1.00 25.00           C
ATOM     63  CA  THR    63       6.053   5.710   9.588  1.00 25.00           C
ATOM     64  CA  ASP    64       6.114   9.460  10.363  1.00 25.00           C
ATOM     65  CA  ALA    65       2.923   9.104  12.451  1.00 25.00           C
ATOM     66  CA  GLY    66       3.223   5.514  13.781  1.00 25.00           C
ATOM     67  CA  LEU    67       4.231   1.832  13.780  1.00 25.00           C
ATOM     68  CA  ALA    68       6.931   1.196  16.378  1.00 25.00           C
ATOM     69  CA  HIS    69      10.470   1.547  17.590  1.00 25.00           C
ATOM     70  CA  GLU    70      10.216   2.581  21.202  1.00 25.00           C
ATOM     71  CA  LEU    71       6.731   1.065  21.406  1.00 25.00           C
ATOM     72  CA  ARG    72       6.561  -0.131  25.014  1.00 25.00           C
TER
END
