
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0349AL242_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL242_4-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    L       4      S      14           #
LGA    L       5      A      15          1.611
LGA    V      16      V      16          1.819
LGA    G      17      G      17          1.063
LGA    A      18      A      18          1.401
LGA    L      19      L      19          2.218
LGA    L      20      L      20          1.670
LGA    D      21      D      21          1.058
LGA    G      22      G      22          3.054
LGA    A      23      A      23          3.620
LGA    D      24      D      24          2.342
LGA    -       -      I      25           -
LGA    I      25      G      26          2.060
LGA    G      26      H      27          3.012
LGA    H      27      L      28          4.773
LGA    L      28      V      29          1.994
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    V      29      V      50          2.686
LGA    -       -      H      51           -
LGA    P      45      E      52          4.054
LGA    R      46      D      53          1.771
LGA    R      47      D      54          1.665
LGA    V      48      L      55          1.563
LGA    L      49      A      56          2.359
LGA    V      50      G      57          2.270
LGA    H      51      A      58          0.801
LGA    E      52      R      59          1.450
LGA    D      53      R      60          1.983
LGA    D      54      L      61          0.910
LGA    L      55      L      62          0.864
LGA    A      56      T      63          1.159
LGA    G      57      D      64          1.625
LGA    A      58      A      65          2.176
LGA    -       -      G      66           -
LGA    R      59      L      67          2.729
LGA    R      60      A      68          3.245
LGA    L      61      H      69          2.319
LGA    D      64      E      70          1.607
LGA    A      65      L      71           -
LGA    G      66      -       -           -
LGA    L      67      -       -           -
LGA    A      68      R      72           #
LGA    H      69      -       -           -
LGA    E      70      -       -           -
LGA    L      71      -       -           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   57    5.0     33    2.28    36.36     42.829     1.387

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.703427 * X  +  -0.582121 * Y  +   0.407829 * Z  +   4.261539
  Y_new =   0.673306 * X  +  -0.361925 * Y  +   0.644724 * Z  +   5.029470
  Z_new =  -0.227704 * X  +   0.728111 * Y  +   0.646534 * Z  +   1.989017 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.844673   -2.296920  [ DEG:    48.3962   -131.6038 ]
  Theta =   0.229719    2.911874  [ DEG:    13.1619    166.8381 ]
  Phi   =   2.378070   -0.763523  [ DEG:   136.2534    -43.7466 ]
 
# 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: T0349AL242_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_4-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   57   5.0   33   2.28   36.36  42.829
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_4-D1
REMARK Aligment from pdb entry: 1uxd
ATOM      1  N   LEU     4      -0.085   0.513  13.231  1.00  0.00              
ATOM      2  CA  LEU     4      -0.469   1.745  12.483  1.00  0.00              
ATOM      3  C   LEU     4      -0.714   1.387  11.007  1.00  0.00              
ATOM      4  O   LEU     4       0.074   1.718  10.139  1.00  0.00              
ATOM      5  N   LEU     5      -1.810   0.705  10.747  1.00  0.00              
ATOM      6  CA  LEU     5      -2.199   0.268   9.363  1.00  0.00              
ATOM      7  C   LEU     5      -2.181   1.411   8.334  1.00  0.00              
ATOM      8  O   LEU     5      -2.101   2.579   8.671  1.00  0.00              
ATOM      9  N   VAL    16      -2.263   1.056   7.072  1.00  0.00              
ATOM     10  CA  VAL    16      -2.263   2.051   5.950  1.00  0.00              
ATOM     11  C   VAL    16      -3.361   3.104   6.165  1.00  0.00              
ATOM     12  O   VAL    16      -3.119   4.282   5.975  1.00  0.00              
ATOM     13  N   GLY    17      -4.534   2.655   6.558  1.00  0.00              
ATOM     14  CA  GLY    17      -5.721   3.532   6.819  1.00  0.00              
ATOM     15  C   GLY    17      -5.359   4.695   7.754  1.00  0.00              
ATOM     16  O   GLY    17      -5.447   5.840   7.347  1.00  0.00              
ATOM     17  N   ALA    18      -4.963   4.415   8.976  1.00  0.00              
ATOM     18  CA  ALA    18      -4.588   5.471   9.960  1.00  0.00              
ATOM     19  C   ALA    18      -3.443   6.357   9.456  1.00  0.00              
ATOM     20  O   ALA    18      -3.495   7.564   9.607  1.00  0.00              
ATOM     21  N   LEU    19      -2.433   5.771   8.855  1.00  0.00              
ATOM     22  CA  LEU    19      -1.265   6.540   8.309  1.00  0.00              
ATOM     23  C   LEU    19      -1.745   7.507   7.208  1.00  0.00              
ATOM     24  O   LEU    19      -1.121   8.531   6.983  1.00  0.00              
ATOM     25  N   LEU    20      -2.839   7.194   6.543  1.00  0.00              
ATOM     26  CA  LEU    20      -3.388   8.072   5.466  1.00  0.00              
ATOM     27  C   LEU    20      -4.155   9.226   6.128  1.00  0.00              
ATOM     28  O   LEU    20      -3.948  10.371   5.772  1.00  0.00              
ATOM     29  N   ASP    21      -5.019   8.917   7.073  1.00  0.00              
ATOM     30  CA  ASP    21      -5.826   9.956   7.794  1.00  0.00              
ATOM     31  C   ASP    21      -4.928  10.832   8.686  1.00  0.00              
ATOM     32  O   ASP    21      -5.136  12.030   8.769  1.00  0.00              
ATOM     33  N   GLY    22      -3.948  10.243   9.340  1.00  0.00              
ATOM     34  CA  GLY    22      -3.006  10.979  10.233  1.00  0.00              
ATOM     35  C   GLY    22      -2.077  11.860   9.391  1.00  0.00              
ATOM     36  O   GLY    22      -1.785  12.976   9.781  1.00  0.00              
ATOM     37  N   ALA    23      -1.625  11.368   8.256  1.00  0.00              
ATOM     38  CA  ALA    23      -0.720  12.158   7.368  1.00  0.00              
ATOM     39  C   ALA    23      -1.547  13.194   6.597  1.00  0.00              
ATOM     40  O   ALA    23      -1.176  14.353   6.532  1.00  0.00              
ATOM     41  N   ASP    24      -2.653  12.766   6.028  1.00  0.00              
ATOM     42  CA  ASP    24      -3.557  13.662   5.249  1.00  0.00              
ATOM     43  C   ASP    24      -3.699  13.242   3.782  1.00  0.00              
ATOM     44  O   ASP    24      -3.715  14.099   2.914  1.00  0.00              
ATOM     45  N   ILE    25      -3.809  11.963   3.505  1.00  0.00              
ATOM     46  CA  ILE    25      -3.964  11.457   2.097  1.00  0.00              
ATOM     47  C   ILE    25      -4.984  10.304   2.054  1.00  0.00              
ATOM     48  O   ILE    25      -5.868  10.242   2.894  1.00  0.00              
ATOM     49  N   GLY    26      -4.880   9.400   1.103  1.00  0.00              
ATOM     50  CA  GLY    26      -5.824   8.246   0.987  1.00  0.00              
ATOM     51  C   GLY    26      -5.081   6.933   1.267  1.00  0.00              
ATOM     52  O   GLY    26      -3.861   6.895   1.347  1.00  0.00              
ATOM     53  N   HIS    27      -5.835   5.863   1.407  1.00  0.00              
ATOM     54  CA  HIS    27      -5.270   4.502   1.677  1.00  0.00              
ATOM     55  C   HIS    27      -4.186   4.140   0.648  1.00  0.00              
ATOM     56  O   HIS    27      -3.300   3.380   0.980  1.00  0.00              
ATOM     57  N   LEU    28      -4.245   4.654  -0.565  1.00  0.00              
ATOM     58  CA  LEU    28      -3.222   4.345  -1.612  1.00  0.00              
ATOM     59  C   LEU    28      -2.138   5.427  -1.650  1.00  0.00              
ATOM     60  O   LEU    28      -0.972   5.108  -1.759  1.00  0.00              
ATOM     61  N   VAL    29      -2.511   6.683  -1.565  1.00  0.00              
ATOM     62  CA  VAL    29      -1.517   7.803  -1.596  1.00  0.00              
ATOM     63  C   VAL    29      -0.542   7.620  -0.438  1.00  0.00              
ATOM     64  O   VAL    29       0.648   7.817  -0.591  1.00  0.00              
ATOM    125  N   PRO    45       7.256  14.895  -3.471  1.00  0.00              
ATOM    126  CA  PRO    45       7.736  15.585  -2.226  1.00  0.00              
ATOM    127  C   PRO    45       6.575  16.103  -1.371  1.00  0.00              
ATOM    128  O   PRO    45       6.599  15.953  -0.164  1.00  0.00              
ATOM    129  N   ARG    46       5.592  16.695  -2.012  1.00  0.00              
ATOM    130  CA  ARG    46       4.363  17.269  -1.373  1.00  0.00              
ATOM    131  C   ARG    46       3.866  16.387  -0.219  1.00  0.00              
ATOM    132  O   ARG    46       3.712  16.856   0.896  1.00  0.00              
ATOM    133  N   ARG    47       3.624  15.127  -0.507  1.00  0.00              
ATOM    134  CA  ARG    47       3.140  14.158   0.517  1.00  0.00              
ATOM    135  C   ARG    47       4.318  13.405   1.146  1.00  0.00              
ATOM    136  O   ARG    47       4.119  12.830   2.194  1.00  0.00              
ATOM    137  N   VAL    48       5.497  13.393   0.555  1.00  0.00              
ATOM    138  CA  VAL    48       6.663  12.671   1.146  1.00  0.00              
ATOM    139  C   VAL    48       6.818  13.197   2.574  1.00  0.00              
ATOM    140  O   VAL    48       6.475  12.501   3.501  1.00  0.00              
ATOM    141  N   LEU    49       7.301  14.395   2.760  1.00  0.00              
ATOM    142  CA  LEU    49       7.455  14.946   4.148  1.00  0.00              
ATOM    143  C   LEU    49       6.122  14.890   4.931  1.00  0.00              
ATOM    144  O   LEU    49       6.133  14.668   6.128  1.00  0.00              
ATOM    145  N   VAL    50       5.003  15.083   4.262  1.00  0.00              
ATOM    146  CA  VAL    50       3.636  15.058   4.884  1.00  0.00              
ATOM    147  C   VAL    50       3.266  13.673   5.451  1.00  0.00              
ATOM    148  O   VAL    50       2.959  13.529   6.622  1.00  0.00              
ATOM    149  N   HIS    51       3.288  12.684   4.594  1.00  0.00              
ATOM    150  CA  HIS    51       2.948  11.268   4.926  1.00  0.00              
ATOM    151  C   HIS    51       4.165  10.492   5.444  1.00  0.00              
ATOM    152  O   HIS    51       3.987   9.663   6.319  1.00  0.00              
ATOM    153  N   GLU    52       5.360  10.734   4.943  1.00  0.00              
ATOM    154  CA  GLU    52       6.574   9.995   5.430  1.00  0.00              
ATOM    155  C   GLU    52       6.793  10.338   6.903  1.00  0.00              
ATOM    156  O   GLU    52       7.156   9.474   7.680  1.00  0.00              
ATOM    157  N   ASP    53       6.560  11.581   7.267  1.00  0.00              
ATOM    158  CA  ASP    53       6.721  12.039   8.681  1.00  0.00              
ATOM    159  C   ASP    53       5.846  11.160   9.590  1.00  0.00              
ATOM    160  O   ASP    53       6.224  10.922  10.717  1.00  0.00              
ATOM    161  N   ASP    54       4.714  10.691   9.098  1.00  0.00              
ATOM    162  CA  ASP    54       3.770   9.822   9.859  1.00  0.00              
ATOM    163  C   ASP    54       4.227   8.359   9.698  1.00  0.00              
ATOM    164  O   ASP    54       4.297   7.642  10.679  1.00  0.00              
ATOM    165  N   LEU    55       4.547   7.913   8.501  1.00  0.00              
ATOM    166  CA  LEU    55       5.011   6.501   8.282  1.00  0.00              
ATOM    167  C   LEU    55       6.237   6.230   9.169  1.00  0.00              
ATOM    168  O   LEU    55       6.327   5.176   9.774  1.00  0.00              
ATOM    169  N   ALA    56       7.157   7.166   9.246  1.00  0.00              
ATOM    170  CA  ALA    56       8.380   7.015  10.073  1.00  0.00              
ATOM    171  C   ALA    56       8.117   7.380  11.545  1.00  0.00              
ATOM    172  O   ALA    56       8.866   6.953  12.404  1.00  0.00              
ATOM    173  N   GLY    57       7.079   8.134  11.832  1.00  0.00              
ATOM    174  CA  GLY    57       6.728   8.529  13.233  1.00  0.00              
ATOM    175  C   GLY    57       6.216   7.254  13.909  1.00  0.00              
ATOM    176  O   GLY    57       6.590   6.929  15.021  1.00  0.00              
ATOM    177  N   ALA    58       5.366   6.548  13.204  1.00  0.00              
ATOM    178  CA  ALA    58       4.758   5.278  13.678  1.00  0.00              
ATOM    179  C   ALA    58       5.672   4.077  13.372  1.00  0.00              
ATOM    180  O   ALA    58       5.462   3.012  13.923  1.00  0.00              
ATOM    181  N   ARG    59       6.660   4.253  12.514  1.00  0.00              
ATOM    182  CA  ARG    59       7.638   3.189  12.110  1.00  0.00              
ATOM    183  C   ARG    59       6.942   2.069  11.324  1.00  0.00              
ATOM    184  O   ARG    59       7.301   0.901  11.400  1.00  0.00              
ATOM    185  N   ARG    60       5.949   2.441  10.564  1.00  0.00              
ATOM    186  CA  ARG    60       5.181   1.466   9.737  1.00  0.00              
ATOM    187  C   ARG    60       5.980   1.121   8.477  1.00  0.00              
ATOM    188  O   ARG    60       6.384   1.998   7.735  1.00  0.00              
ATOM    189  N   LEU    61       6.203  -0.154   8.258  1.00  0.00              
ATOM    190  CA  LEU    61       6.975  -0.649   7.074  1.00  0.00              
ATOM    191  C   LEU    61       6.341  -1.930   6.500  1.00  0.00              
ATOM    192  O   LEU    61       5.635  -2.628   7.211  1.00  0.00              
ATOM    193  N   ASP    64       6.604  -2.209   5.240  1.00  0.00              
ATOM    194  CA  ASP    64       6.064  -3.415   4.543  1.00  0.00              
ATOM    195  C   ASP    64       6.687  -4.724   5.061  1.00  0.00              
ATOM    196  O   ASP    64       7.735  -4.723   5.687  1.00  0.00              
ATOM    197  N   ALA    65       6.026  -5.829   4.791  1.00  0.00              
ATOM    198  CA  ALA    65       6.499  -7.184   5.228  1.00  0.00              
ATOM    199  C   ALA    65       7.657  -7.702   4.355  1.00  0.00              
ATOM    200  O   ALA    65       7.925  -7.179   3.285  1.00  0.00              
ATOM    201  N   GLY    66       8.332  -8.729   4.829  1.00  0.00              
ATOM    202  CA  GLY    66       9.483  -9.365   4.127  1.00  0.00              
ATOM    203  C   GLY    66       9.080  -9.934   2.757  1.00  0.00              
ATOM    204  O   GLY    66       7.911 -10.110   2.456  1.00  0.00              
ATOM    205  N   LEU    67      10.081 -10.212   1.954  1.00  0.00              
ATOM    206  CA  LEU    67       9.942 -10.775   0.572  1.00  0.00              
ATOM    207  C   LEU    67       9.208  -9.766  -0.330  1.00  0.00              
ATOM    208  O   LEU    67       7.990  -9.705  -0.369  1.00  0.00              
ATOM    209  N   ALA    68       9.975  -8.980  -1.044  1.00  0.00              
ATOM    210  CA  ALA    68       9.428  -7.939  -1.971  1.00  0.00              
ATOM    211  C   ALA    68      10.125  -8.008  -3.337  1.00  0.00              
ATOM    212  O   ALA    68      11.320  -8.248  -3.417  1.00  0.00              
ATOM    213  N   HIS    69       9.372  -7.800  -4.397  1.00  0.00              
ATOM    214  CA  HIS    69       9.910  -7.838  -5.792  1.00  0.00              
ATOM    215  C   HIS    69      11.050  -6.822  -5.979  1.00  0.00              
ATOM    216  O   HIS    69      10.839  -5.626  -5.872  1.00  0.00              
ATOM    217  N   GLU    70      12.244  -7.305  -6.254  1.00  0.00              
ATOM    218  CA  GLU    70      13.437  -6.418  -6.459  1.00  0.00              
ATOM    219  C   GLU    70      14.740  -7.200  -6.240  1.00  0.00              
ATOM    220  O   GLU    70      15.527  -6.850  -5.380  1.00  0.00              
ATOM    221  N   LEU    71      14.949  -8.242  -7.015  1.00  0.00              
ATOM    222  CA  LEU    71      16.173  -9.099  -6.911  1.00  0.00              
ATOM    223  C   LEU    71      17.386  -8.413  -7.559  1.00  0.00              
ATOM    224  O   LEU    71      18.480  -8.479  -7.028  1.00  0.00              
ATOM    225  N   ARG    72      17.180  -7.774  -8.681  1.00  0.00              
ATOM    226  CA  ARG    72      18.277  -7.067  -9.412  1.00  0.00              
ATOM    227  C   ARG    72      18.561  -5.702  -8.770  1.00  0.00              
ATOM    228  O   ARG    72      19.702  -5.421  -8.456  1.00  0.00              
END
