
#######################################################
#                                                     #
#                        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   55 (  220),  selected   55 , name T0349TS307_3u-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS307_3u-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          1.573
LGA    R       2      R       2          1.318
LGA    E       3      E       3          1.171
LGA    L       4      L       4          0.801
LGA    L       5      L       5          0.713
LGA    R       6      R       6          1.688
LGA    T       7      T       7          2.911
LGA    N       8      N       8          4.359
LGA    D       9      D       9          1.368
LGA    A      10      A      10          1.810
LGA    V      11      V      11          1.182
LGA    L      12      L      12          0.294
LGA    L      13      L      13          1.441
LGA    S      14      S      14          1.349
LGA    A      15      A      15          0.462
LGA    V      16      V      16          0.449
LGA    G      17      G      17          1.109
LGA    A      18      A      18          0.771
LGA    L      19      L      19          0.584
LGA    L      20      L      20          1.004
LGA    D      21      D      21          1.091
LGA    G      22      G      22          0.437
LGA    A      23      A      23          1.509
LGA    D      24      D      24          2.198
LGA    I      25      I      25          0.803
LGA    G      26      G      26          1.633
LGA    H      27      H      27          1.199
LGA    L      28      L      28          1.259
LGA    V      29      V      29          1.141
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    R      47      R      47          0.572
LGA    V      48      V      48          0.725
LGA    L      49      L      49          0.765
LGA    V      50      V      50          0.644
LGA    H      51      H      51          0.967
LGA    E      52      E      52          1.692
LGA    D      53      D      53          2.090
LGA    D      54      D      54          1.378
LGA    L      55      L      55          0.796
LGA    A      56      A      56          0.176
LGA    G      57      G      57          0.254
LGA    A      58      A      58          0.454
LGA    R      59      R      59          0.510
LGA    R      60      R      60          0.415
LGA    L      61      L      61          0.198
LGA    L      62      L      62          0.246
LGA    T      63      T      63          0.356
LGA    D      64      D      64          0.979
LGA    A      65      A      65          2.328
LGA    -       -      G      66           -
LGA    G      66      L      67          1.816
LGA    L      67      A      68          3.080
LGA    A      68      H      69          3.283
LGA    H      69      E      70          6.814
LGA    E      70      L      71           -
LGA    L      71      R      72           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   55   57    5.0     52    1.74    92.31     84.942     2.828

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.688892 * X  +  -0.616443 * Y  +   0.381346 * Z  +   5.110063
  Y_new =   0.676417 * X  +   0.735801 * Y  +  -0.032513 * Z  + -65.285370
  Z_new =  -0.260552 * X  +   0.280347 * Y  +   0.923860 * Z  + -42.619896 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.294621   -2.846972  [ DEG:    16.8805   -163.1195 ]
  Theta =   0.263594    2.877998  [ DEG:    15.1028    164.8972 ]
  Phi   =   0.776261   -2.365332  [ DEG:    44.4765   -135.5235 ]
 
# 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_3u-D1                              
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS307_3u-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   55   57   5.0   52   1.74   92.31  84.942
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS307_3u-D1
PFRMAT   TS
TARGET   T0349
MODEL    3  UNREFINED
PARENT   1yj7_A
ATOM     1   N   MET     1       1.173  11.016  -8.491  1.00                    
ATOM     1   CA  MET     1       1.019  10.124  -7.346  1.00                    
ATOM     1   C   MET     1       2.346   9.420  -7.146  1.00                    
ATOM     1   O   MET     1       3.093   9.214  -8.104  1.00                    
ATOM     1   N   ARG     2       2.645   9.025  -5.909  1.00                    
ATOM     1   CA  ARG     2       3.845   8.261  -5.620  1.00                    
ATOM     1   C   ARG     2       3.514   7.090  -4.709  1.00                    
ATOM     1   O   ARG     2       2.883   7.273  -3.677  1.00                    
ATOM     1   N   GLU     3       3.937   5.899  -5.114  1.00                    
ATOM     1   CA  GLU     3       3.703   4.695  -4.321  1.00                    
ATOM     1   C   GLU     3       4.504   4.821  -3.047  1.00                    
ATOM     1   O   GLU     3       5.626   5.296  -3.076  1.00                    
ATOM     1   N   LEU     4       3.916   4.423  -1.943  1.00                    
ATOM     1   CA  LEU     4       4.671   4.273  -0.682  1.00                    
ATOM     1   C   LEU     4       5.129   2.825  -0.523  1.00                    
ATOM     1   O   LEU     4       6.321   2.528  -0.575  1.00                    
ATOM     1   N   LEU     5       4.169   1.920  -0.383  1.00                    
ATOM     1   CA  LEU     5       4.431   0.515  -0.131  1.00                    
ATOM     1   C   LEU     5       3.463  -0.386  -0.907  1.00                    
ATOM     1   O   LEU     5       2.288  -0.067  -1.040  1.00                    
ATOM     1   N   ARG     6       3.982  -1.501  -1.399  1.00                    
ATOM     1   CA  ARG     6       3.183  -2.617  -1.914  1.00                    
ATOM     1   C   ARG     6       3.341  -3.855  -1.027  1.00                    
ATOM     1   O   ARG     6       4.160  -3.880  -0.088  1.00                    
ATOM     1   N   THR     7       2.566  -4.894  -1.335  1.00                    
ATOM     1   CA  THR     7       2.683  -6.171  -0.652  1.00                    
ATOM     1   C   THR     7       2.119  -6.191   0.753  1.00                    
ATOM     1   O   THR     7       2.454  -7.072   1.552  1.00                    
ATOM     1   N   ASN     8       1.272  -5.218   1.094  1.00                    
ATOM     1   CA  ASN     8       0.753  -5.117   2.458  1.00                    
ATOM     1   C   ASN     8      -0.467  -6.025   2.661  1.00                    
ATOM     1   O   ASN     8      -1.257  -6.236   1.737  1.00                    
ATOM     1   N   ASP     9      -0.632  -6.542   3.879  1.00                    
ATOM     1   CA  ASP     9      -1.895  -7.174   4.262  1.00                    
ATOM     1   C   ASP     9      -2.987  -6.124   4.323  1.00                    
ATOM     1   O   ASP     9      -2.721  -4.925   4.441  1.00                    
ATOM     1   N   ALA    10      -4.232  -6.577   4.253  1.00                    
ATOM     1   CA  ALA    10      -5.348  -5.659   4.358  1.00                    
ATOM     1   C   ALA    10      -5.330  -4.949   5.715  1.00                    
ATOM     1   O   ALA    10      -5.508  -3.735   5.780  1.00                    
ATOM     1   N   VAL    11      -5.061  -5.684   6.794  1.00                    
ATOM     1   CA  VAL    11      -5.068  -5.112   8.144  1.00                    
ATOM     1   C   VAL    11      -4.014  -4.010   8.307  1.00                    
ATOM     1   O   VAL    11      -4.309  -2.934   8.828  1.00                    
ATOM     1   N   LEU    12      -2.789  -4.280   7.864  1.00                    
ATOM     1   CA  LEU    12      -1.718  -3.303   8.020  1.00                    
ATOM     1   C   LEU    12      -1.906  -2.097   7.091  1.00                    
ATOM     1   O   LEU    12      -1.671  -0.968   7.517  1.00                    
ATOM     1   N   LEU    13      -2.325  -2.317   5.846  1.00                    
ATOM     1   CA  LEU    13      -2.611  -1.196   4.958  1.00                    
ATOM     1   C   LEU    13      -3.678  -0.329   5.603  1.00                    
ATOM     1   O   LEU    13      -3.588   0.885   5.545  1.00                    
ATOM     1   N   SER    14      -4.701  -0.942   6.208  1.00                    
ATOM     1   CA  SER    14      -5.724  -0.157   6.890  1.00                    
ATOM     1   C   SER    14      -5.188   0.669   8.048  1.00                    
ATOM     1   O   SER    14      -5.580   1.815   8.224  1.00                    
ATOM     1   N   ALA    15      -4.293   0.085   8.833  1.00                    
ATOM     1   CA  ALA    15      -3.691   0.802   9.946  1.00                    
ATOM     1   C   ALA    15      -2.878   2.000   9.434  1.00                    
ATOM     1   O   ALA    15      -2.985   3.105   9.958  1.00                    
ATOM     1   N   VAL    16      -2.112   1.778   8.384  1.00                    
ATOM     1   CA  VAL    16      -1.277   2.830   7.794  1.00                    
ATOM     1   C   VAL    16      -2.119   3.937   7.144  1.00                    
ATOM     1   O   VAL    16      -1.812   5.130   7.292  1.00                    
ATOM     1   N   GLY    17      -3.176   3.541   6.423  1.00                    
ATOM     1   CA  GLY    17      -4.076   4.476   5.765  1.00                    
ATOM     1   C   GLY    17      -4.805   5.332   6.791  1.00                    
ATOM     1   O   GLY    17      -4.862   6.554   6.673  1.00                    
ATOM     1   N   ALA    18      -5.317   4.710   7.850  1.00                    
ATOM     1   CA  ALA    18      -5.997   5.469   8.888  1.00                    
ATOM     1   C   ALA    18      -5.039   6.402   9.626  1.00                    
ATOM     1   O   ALA    18      -5.397   7.531   9.933  1.00                    
ATOM     1   N   LEU    19      -3.815   5.951   9.885  1.00                    
ATOM     1   CA  LEU    19      -2.810   6.789  10.521  1.00                    
ATOM     1   C   LEU    19      -2.505   8.052   9.697  1.00                    
ATOM     1   O   LEU    19      -2.446   9.163  10.221  1.00                    
ATOM     1   N   LEU    20      -2.318   7.869   8.398  1.00                    
ATOM     1   CA  LEU    20      -2.024   8.996   7.506  1.00                    
ATOM     1   C   LEU    20      -3.206   9.939   7.440  1.00                    
ATOM     1   O   LEU    20      -3.047  11.150   7.620  1.00                    
ATOM     1   N   ASP    21      -4.406   9.411   7.206  1.00                    
ATOM     1   CA  ASP    21      -5.566  10.283   7.099  1.00                    
ATOM     1   C   ASP    21      -5.768  11.076   8.388  1.00                    
ATOM     1   O   ASP    21      -6.094  12.260   8.353  1.00                    
ATOM     1   N   GLY    22      -5.548  10.438   9.531  1.00                    
ATOM     1   CA  GLY    22      -5.808  11.113  10.804  1.00                    
ATOM     1   C   GLY    22      -4.726  12.138  11.149  1.00                    
ATOM     1   O   GLY    22      -4.931  12.997  12.014  1.00                    
ATOM     1   N   ALA    23      -3.601  12.067  10.440  1.00                    
ATOM     1   CA  ALA    23      -2.512  13.018  10.527  1.00                    
ATOM     1   C   ALA    23      -2.464  13.945   9.290  1.00                    
ATOM     1   O   ALA    23      -1.411  14.477   8.911  1.00                    
ATOM     1   N   ASP    24      -3.620  14.106   8.662  1.00                    
ATOM     1   CA  ASP    24      -3.834  15.093   7.610  1.00                    
ATOM     1   C   ASP    24      -2.928  14.906   6.400  1.00                    
ATOM     1   O   ASP    24      -2.423  15.860   5.796  1.00                    
ATOM     1   N   ILE    25      -2.786  13.645   6.013  1.00                    
ATOM     1   CA  ILE    25      -2.193  13.274   4.743  1.00                    
ATOM     1   C   ILE    25      -3.164  12.398   3.961  1.00                    
ATOM     1   O   ILE    25      -3.571  11.327   4.426  1.00                    
ATOM     1   N   GLY    26      -3.529  12.853   2.765  1.00                    
ATOM     1   CA  GLY    26      -4.361  12.077   1.858  1.00                    
ATOM     1   C   GLY    26      -3.651  10.807   1.430  1.00                    
ATOM     1   O   GLY    26      -2.433  10.788   1.322  1.00                    
ATOM     1   N   HIS    27      -4.410   9.747   1.195  1.00                    
ATOM     1   CA  HIS    27      -3.822   8.502   0.727  1.00                    
ATOM     1   C   HIS    27      -4.815   7.745  -0.153  1.00                    
ATOM     1   O   HIS    27      -6.043   7.836   0.028  1.00                    
ATOM     1   N   LEU    28      -4.274   7.043  -1.148  1.00                    
ATOM     1   CA  LEU    28      -5.053   6.193  -2.011  1.00                    
ATOM     1   C   LEU    28      -4.561   4.757  -1.882  1.00                    
ATOM     1   O   LEU    28      -3.403   4.509  -1.571  1.00                    
ATOM     1   N   VAL    29      -5.462   3.812  -2.112  1.00                    
ATOM     1   CA  VAL    29      -5.188   2.408  -1.912  1.00                    
ATOM     1   C   VAL    29      -5.675   1.605  -3.104  1.00                    
ATOM     1   O   VAL    29      -6.718   1.923  -3.679  1.00                    
ATOM     1   N   ARG    47      -1.562  -1.866  -1.938  1.00                    
ATOM     1   CA  ARG    47      -0.609  -0.807  -2.239  1.00                    
ATOM     1   C   ARG    47      -1.173   0.522  -1.757  1.00                    
ATOM     1   O   ARG    47      -2.333   0.836  -2.018  1.00                    
ATOM     1   N   VAL    48      -0.357   1.299  -1.046  1.00                    
ATOM     1   CA  VAL    48      -0.724   2.639  -0.612  1.00                    
ATOM     1   C   VAL    48       0.141   3.637  -1.354  1.00                    
ATOM     1   O   VAL    48       1.342   3.420  -1.516  1.00                    
ATOM     1   N   LEU    49      -0.488   4.712  -1.821  1.00                    
ATOM     1   CA  LEU    49       0.164   5.825  -2.513  1.00                    
ATOM     1   C   LEU    49      -0.272   7.156  -1.922  1.00                    
ATOM     1   O   LEU    49      -1.308   7.239  -1.267  1.00                    
ATOM     1   N   VAL    50       0.505   8.200  -2.179  1.00                    
ATOM     1   CA  VAL    50       0.154   9.558  -1.795  1.00                    
ATOM     1   C   VAL    50       0.406  10.500  -2.970  1.00                    
ATOM     1   O   VAL    50       1.088  10.149  -3.928  1.00                    
ATOM     1   N   HIS    51      -0.134  11.704  -2.881  1.00                    
ATOM     1   CA  HIS    51       0.236  12.756  -3.822  1.00                    
ATOM     1   C   HIS    51       1.724  12.985  -3.651  1.00                    
ATOM     1   O   HIS    51       2.242  12.941  -2.522  1.00                    
ATOM     1   N   GLU    52       2.447  13.193  -4.753  1.00                    
ATOM     1   CA  GLU    52       3.907  13.271  -4.664  1.00                    
ATOM     1   C   GLU    52       4.422  14.319  -3.692  1.00                    
ATOM     1   O   GLU    52       5.441  14.099  -3.039  1.00                    
ATOM     1   N   ASP    53       3.720  15.448  -3.576  1.00                    
ATOM     1   CA  ASP    53       4.143  16.544  -2.734  1.00                    
ATOM     1   C   ASP    53       4.091  16.165  -1.264  1.00                    
ATOM     1   O   ASP    53       4.764  16.784  -0.446  1.00                    
ATOM     1   N   ASP    54       3.304  15.141  -0.951  1.00                    
ATOM     1   CA  ASP    54       3.102  14.696   0.423  1.00                    
ATOM     1   C   ASP    54       4.043  13.560   0.839  1.00                    
ATOM     1   O   ASP    54       3.942  13.042   1.969  1.00                    
ATOM     1   N   LEU    55       4.954  13.160  -0.050  1.00                    
ATOM     1   CA  LEU    55       5.748  11.972   0.198  1.00                    
ATOM     1   C   LEU    55       6.588  12.076   1.487  1.00                    
ATOM     1   O   LEU    55       6.586  11.154   2.308  1.00                    
ATOM     1   N   ALA    56       7.277  13.184   1.676  1.00                    
ATOM     1   CA  ALA    56       8.147  13.315   2.862  1.00                    
ATOM     1   C   ALA    56       7.324  13.303   4.159  1.00                    
ATOM     1   O   ALA    56       7.654  12.582   5.093  1.00                    
ATOM     1   N   GLY    57       6.237  14.062   4.206  1.00                    
ATOM     1   CA  GLY    57       5.336  14.083   5.357  1.00                    
ATOM     1   C   GLY    57       4.813  12.691   5.666  1.00                    
ATOM     1   O   GLY    57       4.780  12.267   6.826  1.00                    
ATOM     1   N   ALA    58       4.411  11.963   4.620  1.00                    
ATOM     1   CA  ALA    58       3.889  10.607   4.778  1.00                    
ATOM     1   C   ALA    58       4.901   9.619   5.338  1.00                    
ATOM     1   O   ALA    58       4.598   8.882   6.281  1.00                    
ATOM     1   N   ARG    59       6.102   9.594   4.768  1.00                    
ATOM     1   CA  ARG    59       7.139   8.695   5.246  1.00                    
ATOM     1   C   ARG    59       7.530   9.064   6.686  1.00                    
ATOM     1   O   ARG    59       7.787   8.169   7.484  1.00                    
ATOM     1   N   ARG    60       7.536  10.344   7.001  1.00                    
ATOM     1   CA  ARG    60       7.831  10.809   8.364  1.00                    
ATOM     1   C   ARG    60       6.847  10.231   9.377  1.00                    
ATOM     1   O   ARG    60       7.256   9.629  10.381  1.00                    
ATOM     1   N   LEU    61       5.549  10.363   9.085  1.00                    
ATOM     1   CA  LEU    61       4.496   9.837   9.923  1.00                    
ATOM     1   C   LEU    61       4.604   8.314  10.064  1.00                    
ATOM     1   O   LEU    61       4.469   7.774  11.165  1.00                    
ATOM     1   N   LEU    62       4.826   7.620   8.951  1.00                    
ATOM     1   CA  LEU    62       4.927   6.174   8.989  1.00                    
ATOM     1   C   LEU    62       6.150   5.742   9.815  1.00                    
ATOM     1   O   LEU    62       6.013   4.853  10.678  1.00                    
ATOM     1   N   THR    63       7.300   6.361   9.553  1.00                    
ATOM     1   CA  THR    63       8.549   6.068  10.275  1.00                    
ATOM     1   C   THR    63       8.349   6.275  11.779  1.00                    
ATOM     1   O   THR    63       8.780   5.435  12.599  1.00                    
ATOM     1   N   ASP    64       7.692   7.377  12.133  1.00                    
ATOM     1   CA  ASP    64       7.442   7.731  13.539  1.00                    
ATOM     1   C   ASP    64       6.509   6.782  14.249  1.00                    
ATOM     1   O   ASP    64       6.422   6.817  15.482  1.00                    
ATOM     1   N   ALA    65       5.773   5.957  13.498  1.00                    
ATOM     1   CA  ALA    65       4.881   4.970  14.067  1.00                    
ATOM     1   C   ALA    65       5.316   3.533  13.814  1.00                    
ATOM     1   O   ALA    65       4.574   2.596  14.089  1.00                    
ATOM     1   N   GLY    66       6.531   3.363  13.294  1.00                    
ATOM     1   CA  GLY    66       7.107   2.051  13.071  1.00                    
ATOM     1   C   GLY    66       6.523   1.235  11.930  1.00                    
ATOM     1   O   GLY    66       6.555   0.018  11.975  1.00                    
ATOM     1   N   LEU    67       5.952   1.908  10.927  1.00                    
ATOM     1   CA  LEU    67       5.370   1.226   9.767  1.00                    
ATOM     1   C   LEU    67       6.303   1.348   8.573  1.00                    
ATOM     1   O   LEU    67       6.945   2.390   8.398  1.00                    
ATOM     1   N   ALA    68       6.371   0.316   7.726  1.00                    
ATOM     1   CA  ALA    68       5.677  -0.965   7.913  1.00                    
ATOM     1   C   ALA    68       6.304  -1.749   9.063  1.00                    
ATOM     1   O   ALA    68       7.492  -1.612   9.306  1.00                    
ATOM     1   N   HIS    69       5.488  -2.544   9.732  1.00                    
ATOM     1   CA  HIS    69       5.876  -3.188  10.986  1.00                    
ATOM     1   C   HIS    69       6.894  -4.285  10.766  1.00                    
ATOM     1   O   HIS    69       6.773  -5.114   9.859  1.00                    
ATOM     1   N   GLU    70       7.888  -4.284  11.638  1.00                    
ATOM     1   CA  GLU    70       8.893  -5.308  11.682  1.00                    
ATOM     1   C   GLU    70       8.251  -6.630  12.036  1.00                    
ATOM     1   O   GLU    70       7.274  -6.668  12.777  1.00                    
ATOM     1   N   LEU    71       8.833  -7.700  11.512  1.00                    
ATOM     1   CA  LEU    71       8.420  -9.059  11.797  1.00                    
ATOM     1   C   LEU    71       9.354  -9.660  12.843  1.00                    
ATOM     1   O   LEU    71      10.499  -9.207  13.006  1.00                    
ATOM     1   N   ARG    72       8.861 -10.674  13.547  1.00                    
ATOM     1   CA  ARG    72       9.648 -11.372  14.548  1.00                    
ATOM     1   C   ARG    72       9.707 -12.863  14.229  1.00                    
ATOM     1   O   ARG    72       8.915 -13.383  13.439  1.00                    
TER
END
