
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL242_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_1-D1.T0363_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    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    Q      31      N      14          2.342
LGA    V      32      I      15          3.457
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    D      33      V      32          1.198
LGA    E      34      D      33          3.984
LGA    -       -      E      34           -
LGA    G      35      G      35          3.522
LGA    I      36      I      36          3.811
LGA    -       -      T      37           -
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    T      37      T      40          0.926
LGA    V      38      A      41          3.333
LGA    Q      39      I      42          4.431
LGA    T      40      T      43          4.567
LGA    A      41      Q      44          4.740
LGA    I      42      S      45          2.775
LGA    T      43      G      46          3.163
LGA    Q      44      -       -           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    I      47      I      47          2.211
LGA    L      48      L      48          2.983
LGA    S      49      S      49          3.551
LGA    Q      50      Q      50          5.048
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    F      51      E      53          2.375
LGA    P      52      I      54          0.906
LGA    E      53      D      55          2.275
LGA    I      54      L      56          3.919
LGA    D      55      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26   46    5.0     21    3.33    38.10     26.560     0.612

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.758821 * X  +  -0.624418 * Y  +   0.185184 * Z  +  30.113428
  Y_new =   0.636165 * X  +   0.771535 * Y  +  -0.005261 * Z  +  14.654055
  Z_new =  -0.139591 * X  +   0.121799 * Y  +   0.982690 * Z  +   8.942812 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.123316   -3.018277  [ DEG:     7.0655   -172.9345 ]
  Theta =   0.140048    3.001544  [ DEG:     8.0242    171.9758 ]
  Phi   =   0.697698   -2.443895  [ DEG:    39.9751   -140.0249 ]
 
# 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: T0363AL242_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   46   5.0   21   3.33   38.10  26.560
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_1-D1
REMARK Aligment from pdb entry: 1f0z_A
ATOM     41  N   GLN    31      18.764  12.121   5.255  1.00  0.00              
ATOM     42  CA  GLN    31      18.441  10.803   5.859  1.00  0.00              
ATOM     43  C   GLN    31      19.483   9.803   5.380  1.00  0.00              
ATOM     44  O   GLN    31      19.634   9.537   4.204  1.00  0.00              
ATOM     45  N   VAL    32      20.212   9.286   6.298  1.00  0.00              
ATOM     46  CA  VAL    32      21.302   8.313   5.966  1.00  0.00              
ATOM     47  C   VAL    32      21.282   7.097   6.896  1.00  0.00              
ATOM     48  O   VAL    32      20.276   6.765   7.491  1.00  0.00              
ATOM     49  N   ASP    33      22.396   6.420   6.989  1.00  0.00              
ATOM     50  CA  ASP    33      22.492   5.203   7.836  1.00  0.00              
ATOM     51  C   ASP    33      22.863   5.534   9.283  1.00  0.00              
ATOM     52  O   ASP    33      24.015   5.758   9.598  1.00  0.00              
ATOM     53  N   GLU    34      21.907   5.539  10.169  1.00  0.00              
ATOM     54  CA  GLU    34      22.229   5.825  11.596  1.00  0.00              
ATOM     55  C   GLU    34      23.282   4.843  12.103  1.00  0.00              
ATOM     56  O   GLU    34      23.243   3.662  11.814  1.00  0.00              
ATOM     57  N   GLY    35      24.216   5.328  12.857  1.00  0.00              
ATOM     58  CA  GLY    35      25.283   4.456  13.403  1.00  0.00              
ATOM     59  C   GLY    35      26.486   4.489  12.464  1.00  0.00              
ATOM     60  O   GLY    35      27.567   4.051  12.799  1.00  0.00              
ATOM     61  N   ILE    36      26.301   5.019  11.290  1.00  0.00              
ATOM     62  CA  ILE    36      27.421   5.100  10.314  1.00  0.00              
ATOM     63  C   ILE    36      28.315   6.308  10.640  1.00  0.00              
ATOM     64  O   ILE    36      27.843   7.416  10.702  1.00  0.00              
ATOM     65  N   THR    37      29.590   6.123  10.862  1.00  0.00              
ATOM     66  CA  THR    37      30.443   7.306  11.188  1.00  0.00              
ATOM     67  C   THR    37      30.269   8.403  10.156  1.00  0.00              
ATOM     68  O   THR    37      29.430   8.356   9.286  1.00  0.00              
ATOM     69  N   VAL    38      31.134   9.360  10.247  1.00  0.00              
ATOM     70  CA  VAL    38      31.169  10.490   9.292  1.00  0.00              
ATOM     71  C   VAL    38      31.759  10.000   8.003  1.00  0.00              
ATOM     72  O   VAL    38      31.159  10.062   6.957  1.00  0.00              
ATOM     73  N   GLN    39      32.932   9.422   8.095  1.00  0.00              
ATOM     74  CA  GLN    39      33.534   8.837   6.888  1.00  0.00              
ATOM     75  C   GLN    39      32.450   7.967   6.293  1.00  0.00              
ATOM     76  O   GLN    39      32.356   7.759   5.098  1.00  0.00              
ATOM     77  N   THR    40      31.584   7.508   7.163  1.00  0.00              
ATOM     78  CA  THR    40      30.437   6.686   6.699  1.00  0.00              
ATOM     79  C   THR    40      29.319   7.628   6.253  1.00  0.00              
ATOM     80  O   THR    40      28.640   7.393   5.273  1.00  0.00              
ATOM     81  N   ALA    41      29.138   8.711   6.967  1.00  0.00              
ATOM     82  CA  ALA    41      28.082   9.694   6.593  1.00  0.00              
ATOM     83  C   ALA    41      28.478  10.381   5.292  1.00  0.00              
ATOM     84  O   ALA    41      27.785  10.312   4.303  1.00  0.00              
ATOM     85  N   ILE    42      29.604  11.030   5.295  1.00  0.00              
ATOM     86  CA  ILE    42      30.081  11.727   4.075  1.00  0.00              
ATOM     87  C   ILE    42      30.075  10.772   2.897  1.00  0.00              
ATOM     88  O   ILE    42      29.474  11.027   1.874  1.00  0.00              
ATOM     89  N   THR    43      30.738   9.670   3.042  1.00  0.00              
ATOM     90  CA  THR    43      30.765   8.685   1.925  1.00  0.00              
ATOM     91  C   THR    43      29.343   8.266   1.562  1.00  0.00              
ATOM     92  O   THR    43      29.008   8.128   0.403  1.00  0.00              
ATOM     93  N   GLN    44      28.493   8.070   2.535  1.00  0.00              
ATOM     94  CA  GLN    44      27.099   7.675   2.204  1.00  0.00              
ATOM     95  C   GLN    44      26.459   8.794   1.400  1.00  0.00              
ATOM     96  O   GLN    44      25.859   8.577   0.365  1.00  0.00              
ATOM     97  N   SER    45      26.616   9.998   1.866  1.00  0.00              
ATOM     98  CA  SER    45      26.060  11.162   1.147  1.00  0.00              
ATOM     99  C   SER    45      26.742  11.271  -0.209  1.00  0.00              
ATOM    100  O   SER    45      26.235  11.915  -1.099  1.00  0.00              
ATOM    101  N   GLY    46      27.907  10.655  -0.327  1.00  0.00              
ATOM    102  CA  GLY    46      28.732  10.681  -1.582  1.00  0.00              
ATOM    103  C   GLY    46      29.748  11.807  -1.466  1.00  0.00              
ATOM    104  O   GLY    46      30.107  12.449  -2.431  1.00  0.00              
ATOM    105  N   ILE    47      30.209  12.049  -0.273  1.00  0.00              
ATOM    106  CA  ILE    47      31.198  13.135  -0.066  1.00  0.00              
ATOM    107  C   ILE    47      32.456  12.544   0.571  1.00  0.00              
ATOM    108  O   ILE    47      32.385  11.618   1.352  1.00  0.00              
ATOM    109  N   LEU    48      33.603  13.066   0.245  1.00  0.00              
ATOM    110  CA  LEU    48      34.856  12.522   0.840  1.00  0.00              
ATOM    111  C   LEU    48      35.500  13.580   1.743  1.00  0.00              
ATOM    112  O   LEU    48      34.967  13.917   2.783  1.00  0.00              
ATOM    113  N   SER    49      36.629  14.116   1.361  1.00  0.00              
ATOM    114  CA  SER    49      37.281  15.156   2.205  1.00  0.00              
ATOM    115  C   SER    49      38.169  16.054   1.341  1.00  0.00              
ATOM    116  O   SER    49      37.831  17.186   1.055  1.00  0.00              
ATOM    117  N   GLN    50      39.305  15.563   0.923  1.00  0.00              
ATOM    118  CA  GLN    50      40.210  16.398   0.081  1.00  0.00              
ATOM    119  C   GLN    50      40.648  17.621   0.856  1.00  0.00              
ATOM    120  O   GLN    50      41.110  18.595   0.294  1.00  0.00              
ATOM    121  N   PHE    51      40.483  17.595   2.135  1.00  0.00              
ATOM    122  CA  PHE    51      40.865  18.774   2.930  1.00  0.00              
ATOM    123  C   PHE    51      39.599  19.388   3.521  1.00  0.00              
ATOM    124  O   PHE    51      39.290  20.536   3.285  1.00  0.00              
ATOM    125  N   PRO    52      38.842  18.629   4.265  1.00  0.00              
ATOM    126  CA  PRO    52      37.584  19.188   4.833  1.00  0.00              
ATOM    127  C   PRO    52      37.436  18.861   6.313  1.00  0.00              
ATOM    128  O   PRO    52      37.789  17.792   6.768  1.00  0.00              
ATOM    129  N   GLU    53      36.855  19.761   7.047  1.00  0.00              
ATOM    130  CA  GLU    53      36.595  19.514   8.486  1.00  0.00              
ATOM    131  C   GLU    53      35.095  19.726   8.702  1.00  0.00              
ATOM    132  O   GLU    53      34.436  20.297   7.862  1.00  0.00              
ATOM    133  N   ILE    54      34.530  19.235   9.769  1.00  0.00              
ATOM    134  CA  ILE    54      33.055  19.397   9.955  1.00  0.00              
ATOM    135  C   ILE    54      32.696  19.474  11.444  1.00  0.00              
ATOM    136  O   ILE    54      33.402  18.954  12.286  1.00  0.00              
ATOM    137  N   ASP    55      31.594  20.099  11.775  1.00  0.00              
ATOM    138  CA  ASP    55      31.193  20.171  13.212  1.00  0.00              
ATOM    139  C   ASP    55      29.848  19.475  13.395  1.00  0.00              
ATOM    140  O   ASP    55      28.850  19.882  12.837  1.00  0.00              
ATOM    141  N   LEU    56      29.798  18.429  14.171  1.00  0.00              
ATOM    142  CA  LEU    56      28.488  17.743  14.359  1.00  0.00              
ATOM    143  C   LEU    56      27.925  18.090  15.738  1.00  0.00              
ATOM    144  O   LEU    56      28.634  18.098  16.719  1.00  0.00              
END
