
#######################################################
#                                                     #
#                        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   32 (  159),  selected   32 , name T0354TS239_2_2
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS239_2_2.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    E       2      -       -           -
LGA    I       3      M       1           #
LGA    Q       4      E       2          2.370
LGA    E       5      I       3          2.661
LGA    I       6      Q       4          3.703
LGA    S       7      E       5          3.138
LGA    K       8      I       6          4.767
LGA    L       9      S       7          3.938
LGA    A      10      K       8          1.183
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    I      11      I      11          4.412
LGA    -       -      E      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      D      16           -
LGA    -       -      I      17           -
LGA    -       -      K      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      I      22           -
LGA    -       -      I      23           -
LGA    E      12      E      24          2.689
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    A      13      M      37           #
LGA    L      14      I      38           #
LGA    E      15      V      39           #
LGA    D      16      A      40          2.762
LGA    I      17      T      41          1.801
LGA    K      18      G      42          3.080
LGA    -       -      D      43           -
LGA    G      19      S      44          2.973
LGA    -       -      N      45           -
LGA    -       -      R      46           -
LGA    -       -      Q      47           -
LGA    K      20      V      48          2.165
LGA    D      21      K      49          2.323
LGA    -       -      A      50           -
LGA    -       -      L      51           -
LGA    -       -      A      52           -
LGA    I      22      N      53          3.493
LGA    I      23      S      54          1.529
LGA    E      24      V      55          2.269
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    L      25      K      58          1.941
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    D      26      E      61          2.518
LGA    -       -      A      62           -
LGA    -       -      G      63           -
LGA    -       -      V      64           -
LGA    -       -      D      65           -
LGA    -       -      I      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    T      27      V      80          3.094
LGA    S      28      D      81          2.042
LGA    K      29      A      82           #
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    L      30      V      87          1.952
LGA    T      31      H      88          3.791
LGA    S      32      V      89          4.824
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    -       -      Y      98           -
LGA    -       -      D      99           -
LGA    -       -      I     100           -
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    -       -      K     108           -
LGA    -       -      P     109           -
LGA    -       -      S     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    -       -      A     115           -
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    -       -      P     118           -
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    -       -      A     121           -
LGA    -       -      V     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  122    5.0     25    3.01     8.00     13.306     0.803

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.941759 * X  +   0.277795 * Y  +   0.189524 * Z  +  21.901253
  Y_new =  -0.011627 * X  +   0.590138 * Y  +  -0.807219 * Z  +  30.471462
  Z_new =  -0.336086 * X  +   0.758002 * Y  +   0.558998 * Z  +   9.024275 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.935368   -2.206225  [ DEG:    53.5926   -126.4074 ]
  Theta =   0.342759    2.798834  [ DEG:    19.6386    160.3614 ]
  Phi   =  -0.012346    3.129247  [ DEG:    -0.7074    179.2926 ]
 
# 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: T0354TS239_2_2                                
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS239_2_2.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  122   5.0   25   3.01    8.00  13.306
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS239_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0354
PARENT 1dus_A
ATOM      1  N   MET     1      53.828  27.386   9.798  1.00  9.99
ATOM      2  CA  MET     1      53.289  26.334   8.946  1.00  9.99
ATOM      3  C   MET     1      52.539  25.149   9.537  1.00  9.99
ATOM      4  O   MET     1      52.088  24.281   8.788  1.00  9.99
ATOM      5  CB  MET     1      54.470  25.804   8.115  1.00  9.99
ATOM      6  N   GLU     2      52.411  25.072  10.860  1.00  9.99
ATOM      7  CA  GLU     2      51.662  23.972  11.460  1.00  9.99
ATOM      8  C   GLU     2      51.464  24.248  12.923  1.00  9.99
ATOM      9  O   GLU     2      52.229  25.001  13.521  1.00  9.99
ATOM     10  CB  GLU     2      52.405  22.643  11.315  1.00  9.99
ATOM     11  N   ILE     3      50.418  23.669  13.500  1.00  9.99
ATOM     12  CA  ILE     3      50.214  23.851  14.924  1.00  9.99
ATOM     13  C   ILE     3      51.121  22.829  15.602  1.00  9.99
ATOM     14  O   ILE     3      51.080  21.628  15.304  1.00  9.99
ATOM     15  CB  ILE     3      48.743  23.628  15.345  1.00  9.99
ATOM     16  N   GLN     4      51.956  23.337  16.497  1.00  9.99
ATOM     17  CA  GLN     4      52.920  22.565  17.244  1.00  9.99
ATOM     18  C   GLN     4      52.275  21.397  18.000  1.00  9.99
ATOM     19  O   GLN     4      51.248  21.573  18.626  1.00  9.99
ATOM     20  CB  GLN     4      53.632  23.516  18.209  1.00  9.99
ATOM     21  N   GLU     5      52.878  20.210  17.935  1.00  9.99
ATOM     22  CA  GLU     5      52.312  19.047  18.632  1.00  9.99
ATOM     23  C   GLU     5      52.173  19.279  20.131  1.00  9.99
ATOM     24  O   GLU     5      51.161  18.929  20.711  1.00  9.99
ATOM     25  CB  GLU     5      53.155  17.791  18.370  1.00  9.99
ATOM     26  N   ILE     6      53.194  19.876  20.744  1.00  9.99
ATOM     27  CA  ILE     6      53.131  20.157  22.168  1.00  9.99
ATOM     28  C   ILE     6      51.993  21.108  22.476  1.00  9.99
ATOM     29  O   ILE     6      51.209  20.914  23.428  1.00  9.99
ATOM     30  CB  ILE     6      54.479  20.731  22.636  1.00  9.99
ATOM     31  N   SER     7      51.885  22.157  21.673  1.00  9.99
ATOM     32  CA  SER     7      50.813  23.107  21.901  1.00  9.99
ATOM     33  C   SER     7      49.452  22.407  21.776  1.00  9.99
ATOM     34  O   SER     7      48.565  22.634  22.584  1.00  9.99
ATOM     35  CB  SER     7      50.917  24.276  20.908  1.00  9.99
ATOM     36  N   LYS     8      49.284  21.559  20.767  1.00  9.99
ATOM     37  CA  LYS     8      48.023  20.853  20.586  1.00  9.99
ATOM     38  C   LYS     8      47.654  19.975  21.771  1.00  9.99
ATOM     39  O   LYS     8      46.498  19.933  22.171  1.00  9.99
ATOM     40  CB  LYS     8      48.072  20.001  19.316  1.00  9.99
ATOM     41  N   LEU     9      48.636  19.265  22.322  1.00  9.99
ATOM     42  CA  LEU     9      48.400  18.395  23.462  1.00  9.99
ATOM     43  C   LEU     9      47.984  19.259  24.664  1.00  9.99
ATOM     44  O   LEU     9      47.004  18.962  25.359  1.00  9.99
ATOM     45  CB  LEU     9      49.682  17.571  23.751  1.00  9.99
ATOM     46  N   ALA    10      48.704  20.353  24.876  1.00  9.99
ATOM     47  CA  ALA    10      48.386  21.247  25.982  1.00  9.99
ATOM     48  C   ALA    10      46.969  21.779  25.859  1.00  9.99
ATOM     49  O   ALA    10      46.195  21.711  26.810  1.00  9.99
ATOM     50  CB  ALA    10      49.359  22.432  26.021  1.00  9.99
ATOM     51  N   ILE    11      46.633  22.316  24.690  1.00  9.99
ATOM     52  CA  ILE    11      45.295  22.878  24.463  1.00  9.99
ATOM     53  C   ILE    11      44.161  21.854  24.622  1.00  9.99
ATOM     54  O   ILE    11      43.080  22.178  25.114  1.00  9.99
ATOM     55  CB  ILE    11      45.209  23.515  23.053  1.00  9.99
ATOM     56  N   GLU    12      44.406  20.614  24.212  1.00  9.99
ATOM     57  CA  GLU    12      43.368  19.604  24.334  1.00  9.99
ATOM     58  C   GLU    12      43.156  19.174  25.778  1.00  9.99
ATOM     59  O   GLU    12      42.047  18.806  26.164  1.00  9.99
ATOM     60  CB  GLU    12      43.720  18.365  23.506  1.00  9.99
ATOM     61  N   ALA    13      44.210  19.243  26.579  1.00  9.99
ATOM     62  CA  ALA    13      44.136  18.782  27.959  1.00  9.99
ATOM     63  C   ALA    13      43.901  19.788  29.063  1.00  9.99
ATOM     64  O   ALA    13      43.534  19.412  30.181  1.00  9.99
ATOM     65  CB  ALA    13      45.378  17.930  28.257  1.00  9.99
ATOM     66  N   LEU    14      44.065  21.069  28.766  1.00  9.99
ATOM     67  CA  LEU    14      43.847  22.065  29.798  1.00  9.99
ATOM     68  C   LEU    14      42.356  22.130  30.180  1.00  9.99
ATOM     69  O   LEU    14      41.458  21.963  29.351  1.00  9.99
ATOM     70  CB  LEU    14      44.393  23.460  29.351  1.00  9.99
ATOM     71  N   GLU    15      42.106  22.312  31.465  1.00  9.99
ATOM     72  CA  GLU    15      40.747  22.377  31.980  1.00  9.99
ATOM     73  C   GLU    15      40.522  23.813  32.407  1.00  9.99
ATOM     74  O   GLU    15      41.312  24.360  33.182  1.00  9.99
ATOM     75  CB  GLU    15      40.571  21.426  33.210  1.00  9.99
ATOM     76  N   ASP    16      39.478  24.440  31.869  1.00  9.99
ATOM     77  CA  ASP    16      39.176  25.817  32.228  1.00  9.99
ATOM     78  C   ASP    16      37.728  25.984  32.659  1.00  9.99
ATOM     79  O   ASP    16      36.855  25.181  32.308  1.00  9.99
ATOM     80  CB  ASP    16      39.474  26.814  31.065  1.00  9.99
ATOM     81  N   ILE    17      37.496  27.040  33.430  1.00  9.99
ATOM     82  CA  ILE    17      36.170  27.368  33.964  1.00  9.99
ATOM     83  C   ILE    17      35.638  28.620  33.271  1.00  9.99
ATOM     84  O   ILE    17      36.412  29.480  32.899  1.00  9.99
ATOM     85  CB  ILE    17      36.293  27.610  35.472  1.00  9.99
ATOM     86  N   LYS    18      34.322  28.736  33.121  1.00  9.99
ATOM     87  CA  LYS    18      33.741  29.900  32.455  1.00  9.99
ATOM     88  C   LYS    18      34.075  31.253  33.093  1.00  9.99
ATOM     89  O   LYS    18      33.968  32.284  32.436  1.00  9.99
ATOM     90  CB  LYS    18      32.220  29.777  32.390  1.00  9.99
ATOM     91  N   GLY    19      34.451  31.260  34.371  1.00  9.99
ATOM     92  CA  GLY    19      34.787  32.510  35.042  1.00  9.99
ATOM     93  C   GLY    19      36.294  32.768  35.118  1.00  9.99
ATOM     94  O   GLY    19      36.728  33.699  35.786  1.00  9.99
ATOM     95  N   LYS    20      37.094  31.974  34.420  1.00  9.99
ATOM     96  CA  LYS    20      38.534  32.173  34.489  1.00  9.99
ATOM     97  C   LYS    20      39.067  33.341  33.696  1.00  9.99
ATOM     98  O   LYS    20      38.619  33.597  32.579  1.00  9.99
ATOM     99  CB  LYS    20      39.288  30.951  33.968  1.00  9.99
ATOM    100  N   ASP    21      40.054  34.021  34.273  1.00  9.99
ATOM    101  CA  ASP    21      40.774  35.093  33.581  1.00  9.99
ATOM    102  C   ASP    21      42.066  34.333  33.285  1.00  9.99
ATOM    103  O   ASP    21      42.714  33.835  34.210  1.00  9.99
ATOM    104  CB  ASP    21      41.078  36.258  34.510  1.00  9.99
ATOM    105  N   ILE    22      42.436  34.205  32.018  1.00  9.99
ATOM    106  CA  ILE    22      43.630  33.438  31.718  1.00  9.99
ATOM    107  C   ILE    22      44.707  34.210  31.001  1.00  9.99
ATOM    108  O   ILE    22      44.445  35.195  30.335  1.00  9.99
ATOM    109  CB  ILE    22      43.304  32.195  30.865  1.00  9.99
ATOM    110  N   ILE    23      45.929  33.721  31.141  1.00  9.99
ATOM    111  CA  ILE    23      47.092  34.321  30.500  1.00  9.99
ATOM    112  C   ILE    23      47.799  33.242  29.687  1.00  9.99
ATOM    113  O   ILE    23      48.163  32.206  30.228  1.00  9.99
ATOM    114  CB  ILE    23      48.045  34.869  31.577  1.00  9.99
ATOM    115  N   GLU    24      47.968  33.503  28.393  1.00  9.99
ATOM    116  CA  GLU    24      48.672  32.634  27.448  1.00  9.99
ATOM    117  C   GLU    24      50.026  33.329  27.325  1.00  9.99
ATOM    118  O   GLU    24      50.177  34.360  26.645  1.00  9.99
ATOM    119  CB  GLU    24      47.911  32.625  26.108  1.00  9.99
ATOM    120  N   LEU    25      51.017  32.757  27.992  1.00  9.99
ATOM    121  CA  LEU    25      52.348  33.345  28.025  1.00  9.99
ATOM    122  C   LEU    25      53.226  32.836  26.888  1.00  9.99
ATOM    123  O   LEU    25      53.398  31.633  26.733  1.00  9.99
ATOM    124  CB  LEU    25      52.975  33.032  29.380  1.00  9.99
ATOM    125  N   ASP    26      53.795  33.755  26.109  1.00  9.99
ATOM    126  CA  ASP    26      54.619  33.367  24.976  1.00  9.99
ATOM    127  C   ASP    26      53.625  32.826  23.971  1.00  9.99
ATOM    128  O   ASP    26      53.715  31.684  23.516  1.00  9.99
ATOM    129  CB  ASP    26      55.680  32.330  25.385  1.00  9.99
ATOM    130  N   THR    27      45.419  30.974  23.352  1.00  9.99
ATOM    131  CA  THR    27      44.402  31.939  23.708  1.00  9.99
ATOM    132  C   THR    27      43.157  31.845  22.832  1.00  9.99
ATOM    133  O   THR    27      42.030  31.902  23.314  1.00  9.99
ATOM    134  CB  THR    27      45.019  33.346  23.637  1.00  9.99
ATOM    135  N   SER    28      43.370  31.691  21.535  1.00  9.99
ATOM    136  CA  SER    28      42.259  31.614  20.595  1.00  9.99
ATOM    137  C   SER    28      41.420  30.354  20.792  1.00  9.99
ATOM    138  O   SER    28      40.192  30.418  20.772  1.00  9.99
ATOM    139  CB  SER    28      42.817  31.728  19.168  1.00  9.99
ATOM    140  N   LYS    29      42.088  29.231  21.027  1.00  9.99
ATOM    141  CA  LYS    29      41.409  27.948  21.238  1.00  9.99
ATOM    142  C   LYS    29      40.595  27.906  22.529  1.00  9.99
ATOM    143  O   LYS    29      39.644  27.116  22.663  1.00  9.99
ATOM    144  CB  LYS    29      42.454  26.808  21.242  1.00  9.99
ATOM    145  N   LEU    30      40.945  28.762  23.489  1.00  9.99
ATOM    146  CA  LEU    30      40.233  28.765  24.758  1.00  9.99
ATOM    147  C   LEU    30      39.341  29.975  25.019  1.00  9.99
ATOM    148  O   LEU    30      38.518  29.947  25.935  1.00  9.99
ATOM    149  CB  LEU    30      41.233  28.694  25.917  1.00  9.99
ATOM    150  N   THR    31      39.485  31.021  24.213  1.00  9.99
ATOM    151  CA  THR    31      38.782  32.293  24.455  1.00  9.99
ATOM    152  C   THR    31      37.277  32.274  24.706  1.00  9.99
ATOM    153  O   THR    31      36.773  33.025  25.554  1.00  9.99
ATOM    154  CB  THR    31      39.097  33.268  23.336  1.00  9.99
ATOM    155  N   SER    32      36.557  31.437  23.974  1.00  9.99
ATOM    156  CA  SER    32      35.106  31.373  24.137  1.00  9.99
ATOM    157  C   SER    32      34.677  30.563  25.344  1.00  9.99
ATOM    158  O   SER    32      33.488  30.500  25.649  1.00  9.99
ATOM    159  CB  SER    32      34.477  30.738  22.912  1.00  9.99
TER
END
