
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0335TS307_4u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_4u-D1.T0335_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    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      A       5          2.157
LGA    N      11      K       6          1.306
LGA    E      12      I       7          1.121
LGA    L      13      A       8          0.745
LGA    A      14      R       9          0.541
LGA    A      15      I      10          0.477
LGA    K      16      N      11          0.609
LGA    A      17      E      12          0.372
LGA    K      18      L      13          0.386
LGA    A      19      A      14          1.328
LGA    I      22      A      15          2.202
LGA    T      23      K      16          2.111
LGA    E      24      A      17          1.090
LGA    E      25      K      18          3.104
LGA    E      26      A      19          3.722
LGA    K      27      G      20           #
LGA    -       -      V      21           -
LGA    A      28      I      22          3.949
LGA    -       -      T      23           -
LGA    E      29      E      24          4.159
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    Q      30      K      27          3.625
LGA    Q      31      A      28          1.428
LGA    K      32      E      29          3.244
LGA    L      33      Q      30          2.507
LGA    -       -      Q      31           -
LGA    R      34      K      32          5.911
LGA    Q      35      L      33           -
LGA    E      36      R      34           -
LGA    Y      37      Q      35           -
LGA    L      38      E      36           -
LGA    K      39      Y      37           -
LGA    G      40      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   36    5.0     22    2.57     9.09     46.962     0.825

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.594381 * X  +   0.606164 * Y  +   0.528466 * Z  +  -4.164252
  Y_new =   0.433926 * X  +  -0.795018 * Y  +   0.423857 * Z  +  -2.243740
  Z_new =   0.677066 * X  +  -0.022617 * Y  +  -0.735574 * Z  +  -1.859492 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.110854    0.030738  [ DEG:  -178.2388      1.7612 ]
  Theta =  -0.743769   -2.397824  [ DEG:   -42.6148   -137.3852 ]
  Phi   =   0.630608   -2.510984  [ DEG:    36.1312   -143.8688 ]
 
# 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: T0335TS307_4u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_4u-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   36   5.0   22   2.57    9.09  46.962
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_4u-D1
PFRMAT   TS
TARGET   T0335
MODEL    4  UNREFINED
PARENT   2co5_A
ATOM      1  N   LYS     6       5.319  -1.766 -15.413  1.00 53.96           N  
ATOM      2  CA  LYS     6       4.190  -2.484 -14.765  1.00 50.66           C  
ATOM      3  C   LYS     6       4.731  -3.569 -13.841  1.00 51.97           C  
ATOM      4  O   LYS     6       5.886  -3.990 -13.938  1.00 48.63           O  
ATOM     10  N   ILE     7       3.879  -3.998 -12.923  1.00 51.68           N  
ATOM     11  CA  ILE     7       4.258  -4.959 -11.909  1.00 52.65           C  
ATOM     12  C   ILE     7       3.271  -6.104 -11.946  1.00 53.43           C  
ATOM     13  O   ILE     7       2.217  -6.003 -12.583  1.00 53.07           O  
ATOM     22  N   ALA     8       3.627  -7.200 -11.285  1.00 53.82           N  
ATOM     23  CA  ALA     8       2.708  -8.325 -11.121  1.00 53.49           C  
ATOM     24  C   ALA     8       1.436  -7.824 -10.419  1.00 52.16           C  
ATOM     25  O   ALA     8       1.530  -7.093  -9.430  1.00 52.39           O  
ATOM     30  N   ARG     9       0.267  -8.208 -10.947  1.00 52.09           N  
ATOM     31  C   ARG     9      -1.298  -7.971  -9.025  1.00 51.76           C  
ATOM     32  O   ARG     9      -1.965  -7.200  -8.340  1.00 51.79           O  
ATOM     33  CA  ARG     9      -1.021  -7.657 -10.487  1.00 50.86           C  
ATOM     41  N   ILE    10      -0.799  -9.099  -8.538  1.00 53.16           N  
ATOM     42  CA  ILE    10      -1.064  -9.469  -7.159  1.00 52.78           C  
ATOM     43  C   ILE    10      -0.642  -8.347  -6.190  1.00 49.11           C  
ATOM     44  O   ILE    10      -1.254  -8.190  -5.139  1.00 51.83           O  
ATOM     49  N   ASN    11       0.380  -7.568  -6.562  1.00 51.58           N  
ATOM     50  CA  ASN    11       0.836  -6.421  -5.758  1.00 50.11           C  
ATOM     51  C   ASN    11      -0.257  -5.363  -5.627  1.00 49.61           C  
ATOM     52  O   ASN    11      -0.482  -4.800  -4.557  1.00 47.67           O  
ATOM     57  N   GLU    12      -0.925  -5.095  -6.742  1.00 50.83           N  
ATOM     58  CA  GLU    12      -2.052  -4.172  -6.791  1.00 49.80           C  
ATOM     59  C   GLU    12      -3.152  -4.605  -5.806  1.00 49.90           C  
ATOM     60  O   GLU    12      -3.646  -3.796  -5.014  1.00 48.82           O  
ATOM     69  N   LEU    13      -3.495  -5.886  -5.832  1.00 48.95           N  
ATOM     70  CA  LEU    13      -4.532  -6.428  -4.955  1.00 49.96           C  
ATOM     71  C   LEU    13      -4.155  -6.287  -3.469  1.00 49.87           C  
ATOM     72  O   LEU    13      -4.992  -5.897  -2.646  1.00 45.50           O  
ATOM     81  N   ALA    14      -2.902  -6.604  -3.142  1.00 48.10           N  
ATOM     82  CA  ALA    14      -2.418  -6.564  -1.762  1.00 47.53           C  
ATOM     83  C   ALA    14      -2.442  -5.133  -1.230  1.00 48.65           C  
ATOM     84  O   ALA    14      -2.844  -4.903  -0.096  1.00 48.76           O  
ATOM     89  N   ALA    15      -2.022  -4.179  -2.057  1.00 49.61           N  
ATOM     90  CA  ALA    15      -2.055  -2.761  -1.689  1.00 49.59           C  
ATOM     91  C   ALA    15      -3.478  -2.294  -1.344  1.00 49.41           C  
ATOM     92  O   ALA    15      -3.718  -1.730  -0.275  1.00 49.54           O  
ATOM     97  N   LYS    16      -4.415  -2.549  -2.246  1.00 49.25           N  
ATOM     98  CA  LYS    16      -5.817  -2.175  -2.024  1.00 50.40           C  
ATOM     99  C   LYS    16      -6.411  -2.882  -0.806  1.00 48.60           C  
ATOM    100  O   LYS    16      -7.143  -2.274  -0.031  1.00 51.30           O  
ATOM    105  N   ALA    17      -6.079  -4.158  -0.631  1.00 48.53           N  
ATOM    106  CA  ALA    17      -6.568  -4.944   0.507  1.00 50.04           C  
ATOM    107  C   ALA    17      -6.080  -4.362   1.833  1.00 49.75           C  
ATOM    108  O   ALA    17      -6.859  -4.230   2.770  1.00 50.10           O  
ATOM    114  N   LYS    18      -4.796  -4.021   1.908  1.00 50.95           N  
ATOM    115  CA  LYS    18      -4.225  -3.449   3.133  1.00 49.73           C  
ATOM    116  C   LYS    18      -4.871  -2.106   3.464  1.00 48.61           C  
ATOM    117  O   LYS    18      -5.072  -1.783   4.636  1.00 47.69           O  
ATOM    121  N   ALA    19      -5.202  -1.332   2.432  1.00 49.00           N  
ATOM    122  CA  ALA    19      -5.929  -0.077   2.621  1.00 48.54           C  
ATOM    123  C   ALA    19      -7.346  -0.332   3.117  1.00 49.31           C  
ATOM    124  O   ALA    19      -7.797   0.325   4.060  1.00 50.44           O  
ATOM    129  N   ILE    22      -8.039  -1.291   2.506  1.00 46.84           N  
ATOM    130  CA  ILE    22      -9.401  -1.622   2.934  1.00 49.92           C  
ATOM    131  C   ILE    22      -9.425  -2.099   4.389  1.00 49.84           C  
ATOM    132  O   ILE    22     -10.220  -1.610   5.191  1.00 54.63           O  
ATOM    136  N   THR    23      -8.542  -3.035   4.729  1.00 52.28           N  
ATOM    137  CA  THR    23      -8.388  -3.502   6.114  1.00 51.93           C  
ATOM    138  C   THR    23      -8.147  -2.347   7.092  1.00 51.02           C  
ATOM    139  O   THR    23      -8.577  -2.412   8.237  1.00 48.78           O  
ATOM    144  N   GLU    24      -7.462  -1.298   6.641  1.00 51.55           N  
ATOM    145  CA  GLU    24      -7.190  -0.125   7.483  1.00 52.06           C  
ATOM    146  C   GLU    24      -8.194   1.022   7.320  1.00 50.28           C  
ATOM    147  O   GLU    24      -7.861   2.181   7.566  1.00 51.23           O  
ATOM    152  N   GLU    25      -9.423   0.701   6.923  1.00 50.18           N  
ATOM    153  CA  GLU    25     -10.475   1.710   6.778  1.00 51.62           C  
ATOM    154  C   GLU    25     -10.262   2.675   5.622  1.00 50.43           C  
ATOM    155  O   GLU    25     -10.653   3.844   5.700  1.00 50.25           O  
ATOM    156  N   GLU    26      -9.638   2.179   4.556  1.00 49.98           N  
ATOM    157  CA  GLU    26      -9.391   2.938   3.317  1.00 51.82           C  
ATOM    158  C   GLU    26      -8.462   4.153   3.472  1.00 50.73           C  
ATOM    159  O   GLU    26      -8.387   5.000   2.579  1.00 48.95           O  
ATOM    162  N   LYS    27      -7.742   4.212   4.593  1.00 52.63           N  
ATOM    163  CA  LYS    27      -6.767   5.270   4.860  1.00 52.01           C  
ATOM    164  C   LYS    27      -5.529   4.642   5.496  1.00 52.71           C  
ATOM    165  O   LYS    27      -5.641   3.727   6.315  1.00 53.25           O  
ATOM    173  N   ALA    28      -4.352   5.137   5.119  1.00 51.74           N  
ATOM    174  CA  ALA    28      -3.099   4.661   5.699  1.00 51.34           C  
ATOM    175  C   ALA    28      -1.965   5.613   5.357  1.00 49.56           C  
ATOM    176  O   ALA    28      -1.901   6.135   4.248  1.00 48.42           O  
ATOM    181  N   GLU    29      -1.079   5.848   6.321  1.00 51.34           N  
ATOM    182  CA  GLU    29       0.118   6.650   6.075  1.00 51.18           C  
ATOM    183  C   GLU    29       0.988   5.909   5.070  1.00 50.08           C  
ATOM    184  O   GLU    29       1.221   4.711   5.219  1.00 50.71           O  
ATOM    190  N   GLN    30       1.448   6.626   4.048  1.00 50.16           N  
ATOM    191  CA  GLN    30       2.259   6.046   2.973  1.00 50.00           C  
ATOM    192  C   GLN    30       3.468   5.265   3.500  1.00 49.71           C  
ATOM    193  O   GLN    30       3.782   4.192   2.988  1.00 51.42           O  
ATOM    199  N   GLN    31       4.125   5.797   4.527  1.00 47.68           N  
ATOM    200  CA  GLN    31       5.318   5.162   5.106  1.00 49.76           C  
ATOM    201  C   GLN    31       5.033   3.834   5.797  1.00 49.97           C  
ATOM    202  O   GLN    31       5.933   3.012   5.938  1.00 51.13           O  
ATOM    208  N   LYS    32       3.794   3.629   6.236  1.00 51.68           N  
ATOM    209  CA  LYS    32       3.422   2.407   6.956  1.00 51.08           C  
ATOM    210  C   LYS    32       2.932   1.274   6.048  1.00 51.76           C  
ATOM    211  O   LYS    32       2.636   0.179   6.536  1.00 53.61           O  
ATOM    219  N   LEU    33       2.842   1.518   4.745  1.00 51.21           N  
ATOM    220  CA  LEU    33       2.275   0.521   3.828  1.00 51.41           C  
ATOM    221  C   LEU    33       3.109  -0.769   3.802  1.00 51.24           C  
ATOM    222  O   LEU    33       2.574  -1.873   3.940  1.00 49.47           O  
ATOM    227  N   ARG    34       4.416  -0.617   3.648  1.00 48.07           N  
ATOM    228  CA  ARG    34       5.317  -1.751   3.594  1.00 47.57           C  
ATOM    229  C   ARG    34       5.254  -2.598   4.863  1.00 50.03           C  
ATOM    230  O   ARG    34       5.143  -3.823   4.784  1.00 52.26           O  
ATOM    238  N   GLN    35       5.336  -1.935   6.022  1.00 48.45           N  
ATOM    239  CA  GLN    35       5.220  -2.588   7.331  1.00 47.82           C  
ATOM    240  C   GLN    35       3.873  -3.273   7.533  1.00 47.42           C  
ATOM    241  O   GLN    35       3.811  -4.376   8.076  1.00 48.18           O  
ATOM    244  N   GLU    36       2.797  -2.600   7.131  1.00 48.49           N  
ATOM    245  CA  GLU    36       1.448  -3.158   7.252  1.00 50.08           C  
ATOM    246  C   GLU    36       1.275  -4.438   6.446  1.00 48.26           C  
ATOM    247  O   GLU    36       0.715  -5.413   6.946  1.00 51.10           O  
ATOM    253  N   TYR    37       1.753  -4.435   5.206  1.00 51.65           N  
ATOM    254  CA  TYR    37       1.686  -5.621   4.353  1.00 49.13           C  
ATOM    255  C   TYR    37       2.417  -6.806   4.999  1.00 50.61           C  
ATOM    256  O   TYR    37       1.935  -7.941   4.964  1.00 50.62           O  
ATOM    261  N   LEU    38       3.573  -6.522   5.591  1.00 51.37           N  
ATOM    262  CA  LEU    38       4.394  -7.534   6.259  1.00 51.21           C  
ATOM    263  C   LEU    38       3.688  -8.027   7.533  1.00 52.28           C  
ATOM    264  O   LEU    38       3.667  -9.222   7.814  1.00 48.55           O  
ATOM    269  N   LYS    39       3.116  -7.092   8.291  1.00 50.29           N  
ATOM    270  CA  LYS    39       2.371  -7.403   9.511  1.00 50.84           C  
ATOM    271  C   LYS    39       1.138  -8.259   9.214  1.00 50.37           C  
ATOM    272  O   LYS    39       0.952  -9.316   9.821  1.00 48.57           O  
ATOM    278  N   GLY    40       0.315  -7.808   8.270  1.00 48.06           N  
ATOM    279  CA  GLY    40      -0.973  -8.444   7.988  1.00 48.79           C  
ATOM    280  C   GLY    40      -0.854  -9.767   7.246  1.00 48.76           C  
ATOM    281  O   GLY    40      -1.634 -10.682   7.503  1.00 45.36           O  
TER
END
