
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0349TS307_1u-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS307_1u-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.669
LGA    R       2      R       2          2.460
LGA    E       3      E       3          1.986
LGA    L       4      L       4          1.476
LGA    L       5      L       5          1.550
LGA    R       6      R       6          4.371
LGA    T       7      T       7          3.587
LGA    N       8      N       8           #
LGA    D       9      D       9          4.829
LGA    A      10      A      10          3.555
LGA    V      11      V      11          1.049
LGA    L      12      L      12          1.176
LGA    L      13      L      13          0.673
LGA    S      14      S      14          0.678
LGA    A      15      A      15          0.818
LGA    V      16      V      16          0.718
LGA    G      17      G      17          0.382
LGA    A      18      A      18          0.293
LGA    L      19      L      19          0.644
LGA    L      20      L      20          0.338
LGA    D      21      D      21          0.885
LGA    G      22      G      22          1.573
LGA    A      23      A      23          1.484
LGA    D      24      D      24          0.900
LGA    I      25      I      25          0.361
LGA    G      26      G      26          1.463
LGA    H      27      H      27          1.978
LGA    L      28      L      28          4.463
LGA    V      29      V      29           #
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    R      47      R      47          2.561
LGA    V      48      V      48          3.078
LGA    L      49      L      49          3.109
LGA    V      50      V      50          1.486
LGA    D      53      H      51          2.483
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    D      54      D      54          1.493
LGA    L      55      L      55          1.307
LGA    A      56      A      56          0.755
LGA    G      57      G      57          0.574
LGA    A      58      A      58          0.708
LGA    R      59      R      59          0.564
LGA    R      60      R      60          1.000
LGA    L      61      L      61          0.891
LGA    L      62      L      62          0.943
LGA    T      63      T      63          1.222
LGA    D      64      D      64          2.068
LGA    -       -      A      65           -
LGA    A      65      G      66          1.083
LGA    G      66      L      67          1.084
LGA    L      67      A      68          3.109
LGA    A      68      H      69          1.956
LGA    -       -      E      70           -
LGA    H      69      L      71          0.984
LGA    E      70      R      72          1.626
LGA    L      71      -       -           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   57    5.0     49    2.07    85.71     72.733     2.260

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.889878 * X  +  -0.426637 * Y  +   0.161549 * Z  +   7.953284
  Y_new =  -0.411776 * X  +  -0.903600 * Y  +  -0.118101 * Z  +  36.296665
  Z_new =   0.196362 * X  +   0.038573 * Y  +  -0.979772 * Z  +   8.876587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.102243   -0.039349  [ DEG:   177.7455     -2.2545 ]
  Theta =  -0.197647   -2.943946  [ DEG:   -11.3243   -168.6757 ]
  Phi   =  -0.433392    2.708201  [ DEG:   -24.8315    155.1685 ]
 
# 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: T0349TS307_1u-D1                              
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS307_1u-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   57   5.0   49   2.07   85.71  72.733
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS307_1u-D1
PFRMAT   TS
TARGET   T0349
MODEL    1  UNREFINED
PARENT   2f06_A
ATOM     1   N   MET     1       7.399  11.225 -10.026  1.00                    
ATOM     1   CA  MET     1       6.675  11.209  -8.789  1.00                    
ATOM     1   C   MET     1       7.166  10.125  -7.831  1.00                    
ATOM     1   O   MET     1       7.725   9.118  -8.214  1.00                    
ATOM     1   N   ARG     2       6.929  10.363  -6.551  1.00                    
ATOM     1   CA  ARG     2       7.243   9.412  -5.514  1.00                    
ATOM     1   C   ARG     2       5.998   8.560  -5.268  1.00                    
ATOM     1   O   ARG     2       4.898   9.074  -4.987  1.00                    
ATOM     1   N   GLU     3       6.171   7.253  -5.439  1.00                    
ATOM     1   CA  GLU     3       5.168   6.312  -5.043  1.00                    
ATOM     1   C   GLU     3       5.583   5.623  -3.747  1.00                    
ATOM     1   O   GLU     3       6.717   5.175  -3.594  1.00                    
ATOM     1   N   LEU     4       4.683   5.523  -2.798  1.00                    
ATOM     1   CA  LEU     4       4.976   4.710  -1.618  1.00                    
ATOM     1   C   LEU     4       4.655   3.242  -1.895  1.00                    
ATOM     1   O   LEU     4       3.600   2.888  -2.442  1.00                    
ATOM     1   N   LEU     5       4.252   0.040   0.530  1.00                    
ATOM     1   CA  LEU     5       4.103  -0.281   1.899  1.00                    
ATOM     1   C   LEU     5       3.811  -1.788   2.119  1.00                    
ATOM     1   O   LEU     5       2.805  -2.333   1.576  1.00                    
ATOM     1   N   ARG     6       4.673  -2.423   2.927  1.00                    
ATOM     1   CA  ARG     6       4.595  -3.865   3.224  1.00                    
ATOM     1   C   ARG     6       3.499  -4.092   4.273  1.00                    
ATOM     1   O   ARG     6       3.567  -3.553   5.358  1.00                    
ATOM     1   N   THR     7       2.434  -4.797   3.883  1.00                    
ATOM     1   CA  THR     7       1.267  -5.010   4.756  1.00                    
ATOM     1   C   THR     7       1.446  -6.454   5.183  1.00                    
ATOM     1   O   THR     7       1.277  -7.397   4.360  1.00                    
ATOM     1   N   ASN     8       1.816  -6.648   6.429  1.00                    
ATOM     1   CA  ASN     8       1.946  -7.983   6.976  1.00                    
ATOM     1   C   ASN     8       0.572  -8.604   7.332  1.00                    
ATOM     1   O   ASN     8      -0.447  -7.995   7.071  1.00                    
ATOM     1   N   ASP     9       0.504  -9.821   7.861  1.00                    
ATOM     1   CA  ASP     9      -0.816 -10.279   8.426  1.00                    
ATOM     1   C   ASP     9      -1.872 -10.423   7.246  1.00                    
ATOM     1   O   ASP     9      -1.586 -11.172   6.311  1.00                    
ATOM     1   N   ALA    10      -5.438  -8.311   7.616  1.00                    
ATOM     1   CA  ALA    10      -6.674  -8.508   8.437  1.00                    
ATOM     1   C   ALA    10      -7.375  -7.458   9.378  1.00                    
ATOM     1   O   ALA    10      -8.281  -7.891  10.105  1.00                    
ATOM     1   N   VAL    11      -6.937  -6.208   9.566  1.00                    
ATOM     1   CA  VAL    11      -5.585  -5.897   9.901  1.00                    
ATOM     1   C   VAL    11      -4.978  -4.553   9.589  1.00                    
ATOM     1   O   VAL    11      -5.494  -3.470   9.919  1.00                    
ATOM     1   N   LEU    12      -3.832  -4.701   8.968  1.00                    
ATOM     1   CA  LEU    12      -2.822  -3.701   8.835  1.00                    
ATOM     1   C   LEU    12      -3.157  -2.697   7.790  1.00                    
ATOM     1   O   LEU    12      -2.699  -1.573   7.890  1.00                    
ATOM     1   N   LEU    13      -3.948  -3.088   6.787  1.00                    
ATOM     1   CA  LEU    13      -4.312  -2.113   5.750  1.00                    
ATOM     1   C   LEU    13      -5.182  -0.962   6.361  1.00                    
ATOM     1   O   LEU    13      -5.029   0.228   6.001  1.00                    
ATOM     1   N   SER    14      -6.065  -1.333   7.277  1.00                    
ATOM     1   CA  SER    14      -6.894  -0.333   7.926  1.00                    
ATOM     1   C   SER    14      -6.054   0.637   8.772  1.00                    
ATOM     1   O   SER    14      -6.162   1.868   8.607  1.00                    
ATOM     1   N   ALA    15      -5.188   0.088   9.608  1.00                    
ATOM     1   CA  ALA    15      -4.211   0.909  10.321  1.00                    
ATOM     1   C   ALA    15      -3.389   1.815   9.425  1.00                    
ATOM     1   O   ALA    15      -3.157   2.924   9.823  1.00                    
ATOM     1   N   VAL    16      -2.944   1.369   8.233  1.00                    
ATOM     1   CA  VAL    16      -2.150   2.232   7.340  1.00                    
ATOM     1   C   VAL    16      -2.998   3.386   6.868  1.00                    
ATOM     1   O   VAL    16      -2.551   4.553   6.745  1.00                    
ATOM     1   N   GLY    17      -4.225   3.088   6.522  1.00                    
ATOM     1   CA  GLY    17      -5.078   4.190   6.029  1.00                    
ATOM     1   C   GLY    17      -5.448   5.132   7.171  1.00                    
ATOM     1   O   GLY    17      -5.665   6.334   6.930  1.00                    
ATOM     1   N   ALA    18      -5.519   4.583   8.367  1.00                    
ATOM     1   CA  ALA    18      -5.663   5.397   9.603  1.00                    
ATOM     1   C   ALA    18      -4.470   6.326   9.944  1.00                    
ATOM     1   O   ALA    18      -4.677   7.486  10.265  1.00                    
ATOM     1   N   LEU    19      -3.248   5.817   9.968  1.00                    
ATOM     1   CA  LEU    19      -2.021   6.666   9.926  1.00                    
ATOM     1   C   LEU    19      -2.071   7.829   8.934  1.00                    
ATOM     1   O   LEU    19      -1.824   8.974   9.310  1.00                    
ATOM     1   N   LEU    20      -2.391   7.552   7.685  1.00                    
ATOM     1   CA  LEU    20      -2.474   8.594   6.683  1.00                    
ATOM     1   C   LEU    20      -3.612   9.582   6.903  1.00                    
ATOM     1   O   LEU    20      -3.385  10.777   6.729  1.00                    
ATOM     1   N   ASP    21      -4.811   9.102   7.289  1.00                    
ATOM     1   CA  ASP    21      -5.940   9.966   7.639  1.00                    
ATOM     1   C   ASP    21      -5.600  10.944   8.757  1.00                    
ATOM     1   O   ASP    21      -6.055  12.110   8.751  1.00                    
ATOM     1   N   GLY    22      -4.881  10.452   9.765  1.00                    
ATOM     1   CA  GLY    22      -4.579  11.265  10.948  1.00                    
ATOM     1   C   GLY    22      -3.674  12.470  10.569  1.00                    
ATOM     1   O   GLY    22      -3.707  13.530  11.238  1.00                    
ATOM     1   N   ALA    23      -2.879  12.303   9.501  1.00                    
ATOM     1   CA  ALA    23      -2.008  13.360   9.058  1.00                    
ATOM     1   C   ALA    23      -2.674  14.319   8.040  1.00                    
ATOM     1   O   ALA    23      -2.008  15.285   7.557  1.00                    
ATOM     1   N   ASP    24      -3.959  14.070   7.735  1.00                    
ATOM     1   CA  ASP    24      -4.727  14.749   6.672  1.00                    
ATOM     1   C   ASP    24      -3.986  14.578   5.347  1.00                    
ATOM     1   O   ASP    24      -3.829  15.531   4.579  1.00                    
ATOM     1   N   ILE    25      -3.511  13.343   5.109  1.00                    
ATOM     1   CA  ILE    25      -2.867  12.979   3.876  1.00                    
ATOM     1   C   ILE    25      -3.911  12.296   3.051  1.00                    
ATOM     1   O   ILE    25      -4.521  11.305   3.472  1.00                    
ATOM     1   N   GLY    26      -4.161  12.876   1.877  1.00                    
ATOM     1   CA  GLY    26      -5.083  12.298   0.888  1.00                    
ATOM     1   C   GLY    26      -4.396  11.249   0.002  1.00                    
ATOM     1   O   GLY    26      -3.265  11.439  -0.523  1.00                    
ATOM     1   N   HIS    27      -5.135  10.182  -0.249  1.00                    
ATOM     1   CA  HIS    27      -4.742   9.165  -1.207  1.00                    
ATOM     1   C   HIS    27      -5.281   9.541  -2.592  1.00                    
ATOM     1   O   HIS    27      -6.450   9.776  -2.742  1.00                    
ATOM     1   N   LEU    28      -4.431   9.583  -3.605  1.00                    
ATOM     1   CA  LEU    28      -4.828   9.896  -4.994  1.00                    
ATOM     1   C   LEU    28      -5.120   8.682  -5.827  1.00                    
ATOM     1   O   LEU    28      -5.974   8.697  -6.696  1.00                    
ATOM     1   N   VAL    29      -4.330   7.662  -5.572  1.00                    
ATOM     1   CA  VAL    29      -4.272   6.454  -6.398  1.00                    
ATOM     1   C   VAL    29      -3.575   5.397  -5.577  1.00                    
ATOM     1   O   VAL    29      -2.513   5.645  -4.959  1.00                    
ATOM     1   N   ARG    47       0.825  -0.127  -3.025  1.00                    
ATOM     1   CA  ARG    47       1.413   0.912  -3.832  1.00                    
ATOM     1   C   ARG    47       0.493   2.119  -3.847  1.00                    
ATOM     1   O   ARG    47      -0.713   1.981  -4.077  1.00                    
ATOM     1   N   VAL    48       1.051   3.296  -3.627  1.00                    
ATOM     1   CA  VAL    48       0.245   4.401  -3.198  1.00                    
ATOM     1   C   VAL    48       0.783   5.707  -3.745  1.00                    
ATOM     1   O   VAL    48       1.961   6.006  -3.602  1.00                    
ATOM     1   N   LEU    49      -0.106   6.465  -4.370  1.00                    
ATOM     1   CA  LEU    49       0.118   7.898  -4.649  1.00                    
ATOM     1   C   LEU    49      -0.620   8.743  -3.602  1.00                    
ATOM     1   O   LEU    49      -1.839   8.649  -3.489  1.00                    
ATOM     1   N   VAL    50       0.119   9.526  -2.803  1.00                    
ATOM     1   CA  VAL    50      -0.498  10.340  -1.758  1.00                    
ATOM     1   C   VAL    50      -0.249  11.868  -1.982  1.00                    
ATOM     1   O   VAL    50       0.571  12.235  -2.844  1.00                    
ATOM     1   N   ASP    53      -0.916  12.716  -1.187  1.00                    
ATOM     1   CA  ASP    53      -0.817  14.198  -1.346  1.00                    
ATOM     1   C   ASP    53       0.512  14.826  -0.873  1.00                    
ATOM     1   O   ASP    53       0.914  15.899  -1.360  1.00                    
ATOM     1   N   ASP    54       1.180  14.153   0.065  1.00                    
ATOM     1   CA  ASP    54       2.467  14.580   0.600  1.00                    
ATOM     1   C   ASP    54       3.332  13.330   0.890  1.00                    
ATOM     1   O   ASP    54       3.296  12.792   2.007  1.00                    
ATOM     1   N   LEU    55       4.075  12.832  -0.127  1.00                    
ATOM     1   CA  LEU    55       4.802  11.560   0.104  1.00                    
ATOM     1   C   LEU    55       5.866  11.566   1.226  1.00                    
ATOM     1   O   LEU    55       5.991  10.572   1.932  1.00                    
ATOM     1   N   ALA    56       6.552  12.683   1.438  1.00                    
ATOM     1   CA  ALA    56       7.597  12.774   2.468  1.00                    
ATOM     1   C   ALA    56       7.010  12.744   3.892  1.00                    
ATOM     1   O   ALA    56       7.537  12.048   4.768  1.00                    
ATOM     1   N   GLY    57       5.927  13.489   4.092  1.00                    
ATOM     1   CA  GLY    57       5.218  13.493   5.383  1.00                    
ATOM     1   C   GLY    57       4.629  12.093   5.636  1.00                    
ATOM     1   O   GLY    57       4.719  11.578   6.756  1.00                    
ATOM     1   N   ALA    58       4.026  11.499   4.599  1.00                    
ATOM     1   CA  ALA    58       3.471  10.152   4.675  1.00                    
ATOM     1   C   ALA    58       4.502   9.104   5.006  1.00                    
ATOM     1   O   ALA    58       4.280   8.290   5.942  1.00                    
ATOM     1   N   ARG    59       5.611   9.124   4.279  1.00                    
ATOM     1   CA  ARG    59       6.731   8.239   4.598  1.00                    
ATOM     1   C   ARG    59       7.214   8.321   6.060  1.00                    
ATOM     1   O   ARG    59       7.444   7.305   6.717  1.00                    
ATOM     1   N   ARG    60       7.399   9.519   6.579  1.00                    
ATOM     1   CA  ARG    60       7.932   9.608   7.947  1.00                    
ATOM     1   C   ARG    60       6.900   9.148   9.009  1.00                    
ATOM     1   O   ARG    60       7.283   8.519  10.008  1.00                    
ATOM     1   N   LEU    61       5.616   9.459   8.788  1.00                    
ATOM     1   CA  LEU    61       4.520   8.980   9.632  1.00                    
ATOM     1   C   LEU    61       4.446   7.422   9.687  1.00                    
ATOM     1   O   LEU    61       4.369   6.782  10.776  1.00                    
ATOM     1   N   LEU    62       4.513   6.816   8.515  1.00                    
ATOM     1   CA  LEU    62       4.563   5.380   8.409  1.00                    
ATOM     1   C   LEU    62       5.770   4.745   9.102  1.00                    
ATOM     1   O   LEU    62       5.566   3.803   9.855  1.00                    
ATOM     1   N   THR    63       6.998   5.232   8.860  1.00                    
ATOM     1   CA  THR    63       8.206   4.758   9.602  1.00                    
ATOM     1   C   THR    63       8.070   4.903  11.122  1.00                    
ATOM     1   O   THR    63       8.518   4.038  11.889  1.00                    
ATOM     1   N   ASP    64       7.500   6.035  11.546  1.00                    
ATOM     1   CA  ASP    64       7.225   6.336  12.949  1.00                    
ATOM     1   C   ASP    64       6.269   5.312  13.565  1.00                    
ATOM     1   O   ASP    64       6.371   5.021  14.763  1.00                    
ATOM     1   N   ALA    65       5.292   4.858  12.776  1.00                    
ATOM     1   CA  ALA    65       4.350   3.824  13.187  1.00                    
ATOM     1   C   ALA    65       4.813   2.397  12.873  1.00                    
ATOM     1   O   ALA    65       4.010   1.458  12.947  1.00                    
ATOM     1   N   GLY    66       6.094   2.261  12.495  1.00                    
ATOM     1   CA  GLY    66       6.811   0.981  12.378  1.00                    
ATOM     1   C   GLY    66       6.388   0.190  11.152  1.00                    
ATOM     1   O   GLY    66       6.558  -1.046  11.132  1.00                    
ATOM     1   N   LEU    67       5.901   0.891  10.113  1.00                    
ATOM     1   CA  LEU    67       5.673   0.262   8.816  1.00                    
ATOM     1   C   LEU    67       6.957   0.196   8.022  1.00                    
ATOM     1   O   LEU    67       7.820   1.055   8.183  1.00                    
ATOM     1   N   ALA    68       7.093  -0.852   7.193  1.00                    
ATOM     1   CA  ALA    68       8.140  -0.917   6.211  1.00                    
ATOM     1   C   ALA    68       7.631  -0.236   4.913  1.00                    
ATOM     1   O   ALA    68       6.687  -0.696   4.308  1.00                    
ATOM     1   N   HIS    69       8.256   0.868   4.502  1.00                    
ATOM     1   CA  HIS    69       7.858   1.666   3.328  1.00                    
ATOM     1   C   HIS    69       9.065   1.992   2.506  1.00                    
ATOM     1   O   HIS    69      10.111   2.364   3.027  1.00                    
ATOM     1   N   GLU    70       8.898   1.972   1.205  1.00                    
ATOM     1   CA  GLU    70       9.974   2.316   0.279  1.00                    
ATOM     1   C   GLU    70       9.356   3.307  -0.667  1.00                    
ATOM     1   O   GLU    70       8.142   3.281  -0.837  1.00                    
ATOM     1   N   LEU    71      10.163   4.181  -1.272  1.00                    
ATOM     1   CA  LEU    71       9.674   5.110  -2.309  1.00                    
ATOM     1   C   LEU    71      10.215   4.633  -3.648  1.00                    
ATOM     1   O   LEU    71      11.329   4.133  -3.710  1.00                    
ATOM     1   N   ARG    72       9.367   4.668  -4.675  1.00                    
ATOM     1   CA  ARG    72       9.734   4.308  -6.064  1.00                    
ATOM     1   C   ARG    72       9.375   5.489  -6.948  1.00                    
ATOM     1   O   ARG    72       8.397   6.169  -6.660  1.00                    
TER
END
