
#######################################################
#                                                     #
#                        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   34 (  168),  selected   34 , name T0335TS239_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS239_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5           -
LGA    K       6      K       6           -
LGA    I       7      I       7           -
LGA    A       8      A       8           -
LGA    -       -      R       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    R       9      K      18           #
LGA    I      10      A      19          3.306
LGA    N      11      -       -           -
LGA    E      12      G      20          1.043
LGA    L      13      -       -           -
LGA    A      14      -       -           -
LGA    A      15      V      21          2.148
LGA    K      16      -       -           -
LGA    A      17      I      22          4.254
LGA    K      18      T      23          1.353
LGA    A      19      E      24          0.888
LGA    G      20      E      25          0.682
LGA    V      21      E      26          0.515
LGA    I      22      K      27          0.615
LGA    E      25      A      28          1.261
LGA    E      26      E      29          1.216
LGA    K      27      Q      30          0.684
LGA    A      28      Q      31          1.577
LGA    E      29      K      32          1.702
LGA    Q      30      L      33          1.070
LGA    Q      31      R      34          0.446
LGA    K      32      Q      35          0.692
LGA    L      33      E      36          0.251
LGA    R      34      Y      37          0.800
LGA    Q      35      L      38          1.177
LGA    E      36      K      39          0.690
LGA    Y      37      G      40          1.950
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   36    5.0     22    1.59     4.55     58.041     1.302

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.171844 * X  +   0.222849 * Y  +   0.959587 * Z  + -130.608795
  Y_new =  -0.967124 * X  +   0.223518 * Y  +   0.121285 * Z  +  -2.127265
  Z_new =  -0.187457 * X  +  -0.948883 * Y  +   0.253933 * Z  +  38.795197 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.309311    1.832282  [ DEG:   -75.0180    104.9820 ]
  Theta =   0.188572    2.953020  [ DEG:    10.8044    169.1956 ]
  Phi   =  -1.394946    1.746646  [ DEG:   -79.9245    100.0755 ]
 
# 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: T0335TS239_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS239_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   36   5.0   22   1.59    4.55  58.041
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS239_3-D1
PFRMAT TS
TARGET T0335
MODEL 3
PARENT 1wyt_B
ATOM     21  N   ALA     5     -21.250   6.651   4.445  1.00  9.99
ATOM     22  CA  ALA     5     -20.775   5.281   4.354  1.00  9.99
ATOM     23  C   ALA     5     -19.336   5.243   3.839  1.00  9.99
ATOM     24  O   ALA     5     -18.546   4.397   4.241  1.00  9.99
ATOM     25  CB  ALA     5     -21.723   4.463   3.474  1.00  9.99
ATOM     26  N   LYS     6     -18.991   6.172   2.959  1.00  9.99
ATOM     27  CA  LYS     6     -17.630   6.247   2.445  1.00  9.99
ATOM     28  C   LYS     6     -16.686   6.671   3.571  1.00  9.99
ATOM     29  O   LYS     6     -15.563   6.194   3.660  1.00  9.99
ATOM     30  CB  LYS     6     -17.554   7.252   1.300  1.00  9.99
ATOM     31  N   ILE     7     -17.146   7.577   4.427  1.00  9.99
ATOM     32  CA  ILE     7     -16.331   8.052   5.540  1.00  9.99
ATOM     33  C   ILE     7     -16.024   6.872   6.459  1.00  9.99
ATOM     34  O   ILE     7     -14.887   6.696   6.920  1.00  9.99
ATOM     35  CB  ILE     7     -17.068   9.143   6.326  1.00  9.99
ATOM     36  N   ALA     8     -17.049   6.062   6.713  1.00  9.99
ATOM     37  CA  ALA     8     -16.900   4.889   7.558  1.00  9.99
ATOM     38  C   ALA     8     -15.767   4.024   7.018  1.00  9.99
ATOM     39  O   ALA     8     -14.874   3.622   7.771  1.00  9.99
ATOM     40  CB  ALA     8     -18.199   4.049   7.595  1.00  9.99
ATOM     41  N   ARG     9     -15.792   3.754   5.712  1.00  9.99
ATOM     42  CA  ARG     9     -14.767   2.924   5.089  1.00  9.99
ATOM     43  C   ARG     9     -13.368   3.529   5.269  1.00  9.99
ATOM     44  O   ARG     9     -12.439   2.841   5.692  1.00  9.99
ATOM     45  CB  ARG     9     -15.060   2.724   3.598  1.00  9.99
ATOM     46  N   ILE    10     -13.224   4.810   4.950  1.00  9.99
ATOM     47  CA  ILE    10     -11.945   5.488   5.082  1.00  9.99
ATOM     48  C   ILE    10     -11.452   5.359   6.518  1.00  9.99
ATOM     49  O   ILE    10     -10.271   5.118   6.766  1.00  9.99
ATOM     50  CB  ILE    10     -12.092   6.971   4.705  1.00  9.99
ATOM     51  N   ASN    11     -12.371   5.524   7.460  1.00  9.99
ATOM     52  CA  ASN    11     -12.050   5.421   8.873  1.00  9.99
ATOM     53  C   ASN    11     -11.491   4.033   9.186  1.00  9.99
ATOM     54  O   ASN    11     -10.425   3.902   9.786  1.00  9.99
ATOM     55  CB  ASN    11     -13.309   5.669   9.687  1.00  9.99
ATOM     56  N   GLU    12     -12.215   2.999   8.780  1.00  9.99
ATOM     57  CA  GLU    12     -11.770   1.632   9.019  1.00  9.99
ATOM     58  C   GLU    12     -10.359   1.403   8.476  1.00  9.99
ATOM     59  O   GLU    12      -9.515   0.812   9.146  1.00  9.99
ATOM     60  CB  GLU    12     -12.743   0.640   8.378  1.00  9.99
ATOM     61  N   LEU    13     -10.112   1.891   7.266  1.00  9.99
ATOM     62  CA  LEU    13      -8.816   1.750   6.604  1.00  9.99
ATOM     63  C   LEU    13      -7.677   2.342   7.438  1.00  9.99
ATOM     64  O   LEU    13      -6.681   1.677   7.711  1.00  9.99
ATOM     65  CB  LEU    13      -8.874   2.444   5.247  1.00  9.99
ATOM     66  N   ALA    14      -7.842   3.597   7.835  1.00  9.99
ATOM     67  CA  ALA    14      -6.851   4.304   8.627  1.00  9.99
ATOM     68  C   ALA    14      -6.645   3.664   9.990  1.00  9.99
ATOM     69  O   ALA    14      -5.510   3.560  10.453  1.00  9.99
ATOM     70  CB  ALA    14      -7.253   5.777   8.799  1.00  9.99
ATOM     71  N   ALA    15      -7.730   3.237  10.636  1.00  9.99
ATOM     72  CA  ALA    15      -7.617   2.580  11.940  1.00  9.99
ATOM     73  C   ALA    15      -6.969   1.199  11.791  1.00  9.99
ATOM     74  O   ALA    15      -6.480   0.622  12.769  1.00  9.99
ATOM     75  CB  ALA    15      -8.988   2.439  12.608  1.00  9.99
ATOM     76  N   LYS    16      -6.967   0.664  10.571  1.00  9.99
ATOM     77  CA  LYS    16      -6.345  -0.634  10.330  1.00  9.99
ATOM     78  C   LYS    16      -4.822  -0.504  10.166  1.00  9.99
ATOM     79  O   LYS    16      -4.053  -1.156  10.879  1.00  9.99
ATOM     80  CB  LYS    16      -6.916  -1.321   9.070  1.00  9.99
ATOM     81  N   ALA    17      -4.393   0.348   9.240  1.00  9.99
ATOM     82  CA  ALA    17      -2.965   0.543   8.977  1.00  9.99
ATOM     83  C   ALA    17      -2.194   1.435   9.944  1.00  9.99
ATOM     84  O   ALA    17      -1.020   1.196  10.194  1.00  9.99
ATOM     85  CB  ALA    17      -2.759   1.110   7.571  1.00  9.99
ATOM     86  N   LYS    18      -2.836   2.470  10.472  1.00  9.99
ATOM     87  CA  LYS    18      -2.119   3.381  11.347  1.00  9.99
ATOM     88  C   LYS    18      -1.120   4.169  10.510  1.00  9.99
ATOM     89  O   LYS    18      -1.064   4.015   9.285  1.00  9.99
ATOM     90  CB  LYS    18      -1.430   2.593  12.474  1.00  9.99
ATOM     91  N   ALA    19      -0.319   5.014  11.150  1.00  9.99
ATOM     92  CA  ALA    19       0.670   5.803  10.420  1.00  9.99
ATOM     93  C   ALA    19       1.674   4.924   9.673  1.00  9.99
ATOM     94  O   ALA    19       1.983   5.179   8.508  1.00  9.99
ATOM     95  CB  ALA    19       1.430   6.735  11.367  1.00  9.99
ATOM     96  N   GLY    20       2.175   3.888  10.336  1.00  9.99
ATOM     97  CA  GLY    20       3.161   3.020   9.706  1.00  9.99
ATOM     98  C   GLY    20       2.612   2.248   8.502  1.00  9.99
ATOM     99  O   GLY    20       3.347   1.968   7.561  1.00  9.99
ATOM    100  N   VAL    21       1.325   1.910   8.532  1.00  9.99
ATOM    101  CA  VAL    21       0.729   1.187   7.421  1.00  9.99
ATOM    102  C   VAL    21       0.491   2.085   6.213  1.00  9.99
ATOM    103  O   VAL    21       0.658   1.666   5.067  1.00  9.99
ATOM    104  CB  VAL    21      -0.583   0.540   7.895  1.00  9.99
ATOM    105  N   ILE    22       0.091   3.326   6.471  1.00  9.99
ATOM    106  CA  ILE    22      -0.144   4.279   5.398  1.00  9.99
ATOM    107  C   ILE    22       1.208   4.701   4.815  1.00  9.99
ATOM    108  O   ILE    22       1.368   4.828   3.597  1.00  9.99
ATOM    109  CB  ILE    22      -0.896   5.497   5.939  1.00  9.99
ATOM    110  N   GLU    25       2.189   4.893   5.689  1.00  9.99
ATOM    111  CA  GLU    25       3.517   5.296   5.246  1.00  9.99
ATOM    112  C   GLU    25       4.125   4.220   4.343  1.00  9.99
ATOM    113  O   GLU    25       4.700   4.524   3.294  1.00  9.99
ATOM    114  CB  GLU    25       4.419   5.545   6.457  1.00  9.99
ATOM    115  N   GLU    26       3.986   2.963   4.751  1.00  9.99
ATOM    116  CA  GLU    26       4.505   1.849   3.978  1.00  9.99
ATOM    117  C   GLU    26       3.744   1.698   2.660  1.00  9.99
ATOM    118  O   GLU    26       4.327   1.334   1.637  1.00  9.99
ATOM    119  CB  GLU    26       4.398   0.553   4.782  1.00  9.99
ATOM    120  N   LYS    27       2.443   1.972   2.684  1.00  9.99
ATOM    121  CA  LYS    27       1.639   1.862   1.475  1.00  9.99
ATOM    122  C   LYS    27       2.188   2.831   0.428  1.00  9.99
ATOM    123  O   LYS    27       2.402   2.466  -0.727  1.00  9.99
ATOM    124  CB  LYS    27       0.171   2.180   1.783  1.00  9.99
ATOM    125  N   ALA    28       2.418   4.069   0.846  1.00  9.99
ATOM    126  CA  ALA    28       2.956   5.093  -0.036  1.00  9.99
ATOM    127  C   ALA    28       4.293   4.643  -0.612  1.00  9.99
ATOM    128  O   ALA    28       4.515   4.719  -1.817  1.00  9.99
ATOM    129  CB  ALA    28       3.137   6.400   0.730  1.00  9.99
ATOM    130  N   GLU    29       5.180   4.167   0.253  1.00  9.99
ATOM    131  CA  GLU    29       6.495   3.725  -0.188  1.00  9.99
ATOM    132  C   GLU    29       6.396   2.649  -1.250  1.00  9.99
ATOM    133  O   GLU    29       7.038   2.734  -2.288  1.00  9.99
ATOM    134  CB  GLU    29       7.303   3.213   1.001  1.00  9.99
ATOM    135  N   GLN    30       5.580   1.636  -0.989  1.00  9.99
ATOM    136  CA  GLN    30       5.418   0.537  -1.925  1.00  9.99
ATOM    137  C   GLN    30       4.633   0.919  -3.169  1.00  9.99
ATOM    138  O   GLN    30       4.731   0.245  -4.192  1.00  9.99
ATOM    139  CB  GLN    30       4.755  -0.650  -1.230  1.00  9.99
ATOM    140  N   GLN    31       3.843   1.985  -3.086  1.00  9.99
ATOM    141  CA  GLN    31       3.086   2.427  -4.253  1.00  9.99
ATOM    142  C   GLN    31       4.112   3.047  -5.185  1.00  9.99
ATOM    143  O   GLN    31       4.043   2.886  -6.404  1.00  9.99
ATOM    144  CB  GLN    31       2.046   3.453  -3.866  1.00  9.99
ATOM    145  N   LYS    32       5.076   3.745  -4.591  1.00  9.99
ATOM    146  CA  LYS    32       6.137   4.390  -5.348  1.00  9.99
ATOM    147  C   LYS    32       7.115   3.338  -5.888  1.00  9.99
ATOM    148  O   LYS    32       7.559   3.427  -7.033  1.00  9.99
ATOM    149  CB  LYS    32       6.887   5.416  -4.467  1.00  9.99
ATOM    150  N   LEU    33       7.437   2.334  -5.078  1.00  9.99
ATOM    151  CA  LEU    33       8.355   1.295  -5.532  1.00  9.99
ATOM    152  C   LEU    33       7.774   0.533  -6.725  1.00  9.99
ATOM    153  O   LEU    33       8.474   0.258  -7.701  1.00  9.99
ATOM    154  CB  LEU    33       8.678   0.328  -4.394  1.00  9.99
ATOM    155  N   ARG    34       6.489   0.204  -6.651  1.00  9.99
ATOM    156  CA  ARG    34       5.820  -0.506  -7.738  1.00  9.99
ATOM    157  C   ARG    34       5.853   0.286  -9.039  1.00  9.99
ATOM    158  O   ARG    34       6.094  -0.276 -10.108  1.00  9.99
ATOM    159  CB  ARG    34       4.368  -0.818  -7.356  1.00  9.99
ATOM    160  N   GLN    35       5.622   1.593  -8.948  1.00  9.99
ATOM    161  CA  GLN    35       5.627   2.443 -10.133  1.00  9.99
ATOM    162  C   GLN    35       7.041   2.598 -10.699  1.00  9.99
ATOM    163  O   GLN    35       7.257   2.471 -11.909  1.00  9.99
ATOM    164  CB  GLN    35       5.040   3.811  -9.798  1.00  9.99
ATOM    165  N   GLU    36       8.004   2.859  -9.819  1.00  9.99
ATOM    166  CA  GLU    36       9.385   3.034 -10.241  1.00  9.99
ATOM    167  C   GLU    36       9.925   1.743 -10.856  1.00  9.99
ATOM    168  O   GLU    36      10.681   1.782 -11.830  1.00  9.99
ATOM    169  CB  GLU    36      10.252   3.477  -9.056  1.00  9.99
ATOM    170  N   TYR    37       9.513   0.606 -10.299  1.00  9.99
ATOM    171  CA  TYR    37       9.938  -0.697 -10.794  1.00  9.99
ATOM    172  C   TYR    37       9.271  -1.016 -12.131  1.00  9.99
ATOM    173  O   TYR    37       9.928  -1.473 -13.063  1.00  9.99
ATOM    174  CB  TYR    37       9.590  -1.795  -9.779  1.00  9.99
ATOM    175  N   LEU    38       7.963  -0.788 -12.222  1.00  9.99
ATOM    176  CA  LEU    38       7.240  -1.056 -13.462  1.00  9.99
ATOM    177  C   LEU    38       7.742  -0.143 -14.583  1.00  9.99
ATOM    178  O   LEU    38       7.781  -0.549 -15.744  1.00  9.99
ATOM    179  CB  LEU    38       5.728  -0.878 -13.259  1.00  9.99
ATOM    180  N   LYS    39       8.138   1.082 -14.234  1.00  9.99
ATOM    181  CA  LYS    39       8.659   2.015 -15.234  1.00  9.99
ATOM    182  C   LYS    39       9.917   1.432 -15.866  1.00  9.99
ATOM    183  O   LYS    39      10.113   1.522 -17.082  1.00  9.99
ATOM    184  CB  LYS    39       9.017   3.374 -14.614  1.00  9.99
ATOM    185  N   GLY    40      10.780   0.858 -15.029  1.00  9.99
ATOM    186  CA  GLY    40      12.009   0.252 -15.514  1.00  9.99
ATOM    187  C   GLY    40      11.667  -0.912 -16.425  1.00  9.99
ATOM    188  O   GLY    40      12.303  -1.102 -17.457  1.00  9.99
TER
END
