
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0349AL243_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL243_3-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    -       -      S      14           -
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    A      10      L      20          3.899
LGA    V      11      D      21          2.199
LGA    L      12      G      22          2.650
LGA    L      13      -       -           -
LGA    S      14      -       -           -
LGA    A      15      A      23          3.630
LGA    V      16      D      24           -
LGA    G      17      I      25           -
LGA    A      18      G      26           -
LGA    L      19      H      27           -
LGA    L      20      L      28           -
LGA    D      21      V      29           -
LGA    G      22      P      45           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      R      46          0.766
LGA    R      46      R      47          0.510
LGA    R      47      V      48          1.383
LGA    V      48      L      49          1.912
LGA    L      49      V      50          1.083
LGA    V      50      H      51          1.931
LGA    A      56      E      52          0.446
LGA    G      57      D      53          2.559
LGA    A      58      D      54          1.460
LGA    R      59      L      55          1.310
LGA    R      60      A      56          1.227
LGA    L      61      G      57          1.309
LGA    L      62      A      58          2.431
LGA    T      63      R      59          3.102
LGA    D      64      R      60          1.703
LGA    A      65      L      61          1.927
LGA    G      66      L      62          4.112
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    L      67      A      68          4.540
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)   38   57    5.0     22    2.38     9.09     31.297     0.886

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.937198 * X  +   0.213002 * Y  +  -0.276207 * Z  +  42.133308
  Y_new =  -0.273951 * X  +  -0.939662 * Y  +   0.204907 * Z  +  34.567970
  Z_new =  -0.215896 * X  +   0.267706 * Y  +   0.939001 * Z  + -19.968193 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.277728   -2.863864  [ DEG:    15.9127   -164.0873 ]
  Theta =   0.217609    2.923983  [ DEG:    12.4681    167.5319 ]
  Phi   =  -2.857207    0.284386  [ DEG:  -163.7059     16.2941 ]
 
# 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: T0349AL243_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL243_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   57   5.0   22   2.38    9.09  31.297
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL243_3-D1
REMARK Aligment from pdb entry: 1rp0A
ATOM      1  N   ALA    10      -7.649   7.066   7.297  1.00  0.00              
ATOM      2  CA  ALA    10      -6.386   7.760   7.078  1.00  0.00              
ATOM      3  C   ALA    10      -6.428   9.228   7.502  1.00  0.00              
ATOM      4  O   ALA    10      -5.446   9.764   8.019  1.00  0.00              
ATOM      5  N   VAL    11      -7.537   9.909   7.260  1.00  0.00              
ATOM      6  CA  VAL    11      -7.604  11.311   7.625  1.00  0.00              
ATOM      7  C   VAL    11      -7.645  11.511   9.153  1.00  0.00              
ATOM      8  O   VAL    11      -6.920  12.328   9.692  1.00  0.00              
ATOM      9  N   LEU    12      -8.507  10.771   9.836  1.00  0.00              
ATOM     10  CA  LEU    12      -8.586  10.875  11.279  1.00  0.00              
ATOM     11  C   LEU    12      -7.332  10.462  12.003  1.00  0.00              
ATOM     12  O   LEU    12      -6.956  11.089  12.967  1.00  0.00              
ATOM     13  N   LEU    13      -6.684   9.385  11.557  1.00  0.00              
ATOM     14  CA  LEU    13      -5.415   8.997  12.152  1.00  0.00              
ATOM     15  C   LEU    13      -4.366  10.082  11.965  1.00  0.00              
ATOM     16  O   LEU    13      -3.603  10.371  12.874  1.00  0.00              
ATOM     17  N   SER    14      -4.311  10.645  10.768  1.00  0.00              
ATOM     18  CA  SER    14      -3.359  11.708  10.462  1.00  0.00              
ATOM     19  C   SER    14      -3.616  12.948  11.329  1.00  0.00              
ATOM     20  O   SER    14      -2.689  13.600  11.789  1.00  0.00              
ATOM     21  N   ALA    15      -4.879  13.298  11.543  1.00  0.00              
ATOM     22  CA  ALA    15      -5.224  14.430  12.394  1.00  0.00              
ATOM     23  C   ALA    15      -4.843  14.163  13.841  1.00  0.00              
ATOM     24  O   ALA    15      -4.211  14.995  14.503  1.00  0.00              
ATOM     25  N   VAL    16      -5.194  12.989  14.355  1.00  0.00              
ATOM     26  CA  VAL    16      -4.821  12.651  15.727  1.00  0.00              
ATOM     27  C   VAL    16      -3.310  12.618  15.960  1.00  0.00              
ATOM     28  O   VAL    16      -2.827  13.064  17.008  1.00  0.00              
ATOM     29  N   GLY    17      -2.576  12.069  14.992  1.00  0.00              
ATOM     30  CA  GLY    17      -1.124  12.013  15.001  1.00  0.00              
ATOM     31  C   GLY    17      -0.539  13.426  15.055  1.00  0.00              
ATOM     32  O   GLY    17       0.364  13.708  15.832  1.00  0.00              
ATOM     33  N   ALA    18      -1.069  14.326  14.231  1.00  0.00              
ATOM     34  CA  ALA    18      -0.578  15.699  14.208  1.00  0.00              
ATOM     35  C   ALA    18      -0.857  16.443  15.515  1.00  0.00              
ATOM     36  O   ALA    18       0.045  17.087  16.044  1.00  0.00              
ATOM     37  N   LEU    19      -2.078  16.335  16.039  1.00  0.00              
ATOM     38  CA  LEU    19      -2.461  17.052  17.250  1.00  0.00              
ATOM     39  C   LEU    19      -1.623  16.564  18.438  1.00  0.00              
ATOM     40  O   LEU    19      -1.166  17.368  19.248  1.00  0.00              
ATOM     41  N   LEU    20      -1.448  15.252  18.531  1.00  0.00              
ATOM     42  CA  LEU    20      -0.918  14.664  19.758  1.00  0.00              
ATOM     43  C   LEU    20       0.594  14.799  19.820  1.00  0.00              
ATOM     44  O   LEU    20       1.200  14.421  20.816  1.00  0.00              
ATOM     45  N   ASP    21       1.201  15.347  18.775  1.00  0.00              
ATOM     46  CA  ASP    21       2.584  15.793  18.871  1.00  0.00              
ATOM     47  C   ASP    21       2.755  16.855  19.954  1.00  0.00              
ATOM     48  O   ASP    21       3.838  17.040  20.475  1.00  0.00              
ATOM     49  N   GLY    22       1.682  17.570  20.291  1.00  0.00              
ATOM     50  CA  GLY    22       1.634  18.407  21.482  1.00  0.00              
ATOM     51  C   GLY    22       1.213  17.538  22.664  1.00  0.00              
ATOM     52  O   GLY    22       0.076  17.059  22.702  1.00  0.00              
ATOM     53  N   ALA    23       2.116  17.269  23.596  1.00  0.00              
ATOM     54  CA  ALA    23       1.854  16.308  24.684  1.00  0.00              
ATOM     55  C   ALA    23       0.829  16.790  25.700  1.00  0.00              
ATOM     56  O   ALA    23       0.340  15.959  26.465  1.00  0.00              
ATOM     57  N   ASP    24       0.489  18.072  25.644  1.00  0.00              
ATOM     58  CA  ASP    24      -0.394  18.736  26.590  1.00  0.00              
ATOM     59  C   ASP    24      -1.850  18.654  26.136  1.00  0.00              
ATOM     60  O   ASP    24      -2.762  19.087  26.843  1.00  0.00              
ATOM     61  N   ILE    25      -2.062  18.133  24.935  1.00  0.00              
ATOM     62  CA  ILE    25      -3.403  18.086  24.352  1.00  0.00              
ATOM     63  C   ILE    25      -3.991  16.693  24.446  1.00  0.00              
ATOM     64  O   ILE    25      -3.414  15.708  24.001  1.00  0.00              
ATOM     65  N   GLY    26      -5.163  16.597  25.060  1.00  0.00              
ATOM     66  CA  GLY    26      -5.869  15.330  25.157  1.00  0.00              
ATOM     67  C   GLY    26      -6.681  15.018  23.916  1.00  0.00              
ATOM     68  O   GLY    26      -7.460  15.874  23.458  1.00  0.00              
ATOM     69  N   HIS    27      -6.446  13.831  23.373  1.00  0.00              
ATOM     70  CA  HIS    27      -7.084  13.388  22.153  1.00  0.00              
ATOM     71  C   HIS    27      -7.848  12.090  22.312  1.00  0.00              
ATOM     72  O   HIS    27      -7.246  11.024  22.478  1.00  0.00              
ATOM     73  N   LEU    28      -9.174  12.161  22.178  1.00  0.00              
ATOM     74  CA  LEU    28      -9.986  10.954  22.118  1.00  0.00              
ATOM     75  C   LEU    28     -10.288  10.630  20.656  1.00  0.00              
ATOM     76  O   LEU    28     -10.622  11.541  19.917  1.00  0.00              
ATOM     77  N   VAL    29     -10.167   9.378  20.272  1.00  0.00              
ATOM     78  CA  VAL    29     -10.544   8.931  18.932  1.00  0.00              
ATOM     79  C   VAL    29     -11.732   8.009  19.118  1.00  0.00              
ATOM     80  O   VAL    29     -11.664   7.003  19.817  1.00  0.00              
ATOM    137  N   PRO    45      -3.197  -3.912  -3.159  1.00  0.00              
ATOM    138  CA  PRO    45      -2.503  -3.552  -1.908  1.00  0.00              
ATOM    139  C   PRO    45      -1.840  -2.172  -1.933  1.00  0.00              
ATOM    140  O   PRO    45      -1.751  -1.489  -0.909  1.00  0.00              
ATOM    141  N   ARG    46      -1.343  -1.738  -3.089  1.00  0.00              
ATOM    142  CA  ARG    46      -0.397  -0.622  -3.129  1.00  0.00              
ATOM    143  C   ARG    46      -1.115   0.695  -2.906  1.00  0.00              
ATOM    144  O   ARG    46      -2.239   0.912  -3.364  1.00  0.00              
ATOM    145  N   ARG    47      -0.436   1.543  -2.159  1.00  0.00              
ATOM    146  CA  ARG    47      -0.929   2.828  -1.719  1.00  0.00              
ATOM    147  C   ARG    47      -0.136   3.905  -2.420  1.00  0.00              
ATOM    148  O   ARG    47       1.083   4.125  -2.181  1.00  0.00              
ATOM    149  N   VAL    48      -0.813   4.624  -3.307  1.00  0.00              
ATOM    150  CA  VAL    48      -0.183   5.719  -4.038  1.00  0.00              
ATOM    151  C   VAL    48      -0.390   7.019  -3.268  1.00  0.00              
ATOM    152  O   VAL    48      -1.512   7.366  -2.894  1.00  0.00              
ATOM    153  N   LEU    49       0.713   7.708  -3.015  1.00  0.00              
ATOM    154  CA  LEU    49       0.728   8.997  -2.339  1.00  0.00              
ATOM    155  C   LEU    49       1.457  10.015  -3.219  1.00  0.00              
ATOM    156  O   LEU    49       2.656   9.869  -3.550  1.00  0.00              
ATOM    157  N   VAL    50       0.746  11.056  -3.654  1.00  0.00              
ATOM    158  CA  VAL    50       1.357  12.067  -4.491  1.00  0.00              
ATOM    159  C   VAL    50       2.299  12.977  -3.701  1.00  0.00              
ATOM    160  O   VAL    50       2.039  13.339  -2.544  1.00  0.00              
ATOM    161  N   ALA    56       3.395  13.360  -4.338  1.00  0.00              
ATOM    162  CA  ALA    56       4.260  14.368  -3.764  1.00  0.00              
ATOM    163  C   ALA    56       3.537  15.705  -3.635  1.00  0.00              
ATOM    164  O   ALA    56       2.703  16.037  -4.482  1.00  0.00              
ATOM    165  N   GLY    57       3.856  16.514  -2.636  1.00  0.00              
ATOM    166  CA  GLY    57       4.893  16.251  -1.634  1.00  0.00              
ATOM    167  C   GLY    57       4.492  15.569  -0.325  1.00  0.00              
ATOM    168  O   GLY    57       5.189  15.720   0.675  1.00  0.00              
ATOM    169  N   ALA    58       3.414  14.795  -0.318  1.00  0.00              
ATOM    170  CA  ALA    58       2.971  14.157   0.916  1.00  0.00              
ATOM    171  C   ALA    58       3.886  13.022   1.334  1.00  0.00              
ATOM    172  O   ALA    58       3.753  12.482   2.419  1.00  0.00              
ATOM    173  N   ARG    59       4.832  12.664   0.476  1.00  0.00              
ATOM    174  CA  ARG    59       5.780  11.629   0.847  1.00  0.00              
ATOM    175  C   ARG    59       6.658  12.137   2.008  1.00  0.00              
ATOM    176  O   ARG    59       7.191  11.319   2.765  1.00  0.00              
ATOM    177  N   ARG    60       6.753  13.452   2.169  1.00  0.00              
ATOM    178  CA  ARG    60       7.471  14.005   3.335  1.00  0.00              
ATOM    179  C   ARG    60       6.773  13.606   4.631  1.00  0.00              
ATOM    180  O   ARG    60       7.421  13.466   5.665  1.00  0.00              
ATOM    181  N   LEU    61       5.454  13.427   4.597  1.00  0.00              
ATOM    182  CA  LEU    61       4.705  13.030   5.776  1.00  0.00              
ATOM    183  C   LEU    61       5.045  11.587   6.088  1.00  0.00              
ATOM    184  O   LEU    61       5.260  11.224   7.257  1.00  0.00              
ATOM    185  N   LEU    62       5.101  10.759   5.044  1.00  0.00              
ATOM    186  CA  LEU    62       5.542   9.371   5.226  1.00  0.00              
ATOM    187  C   LEU    62       6.938   9.262   5.840  1.00  0.00              
ATOM    188  O   LEU    62       7.187   8.377   6.686  1.00  0.00              
ATOM    189  N   THR    63       7.838  10.136   5.396  1.00  0.00              
ATOM    190  CA  THR    63       9.192  10.201   5.930  1.00  0.00              
ATOM    191  C   THR    63       9.139  10.422   7.442  1.00  0.00              
ATOM    192  O   THR    63       9.842   9.746   8.210  1.00  0.00              
ATOM    193  N   ASP    64       8.327  11.392   7.854  1.00  0.00              
ATOM    194  CA  ASP    64       8.248  11.701   9.275  1.00  0.00              
ATOM    195  C   ASP    64       7.750  10.542  10.139  1.00  0.00              
ATOM    196  O   ASP    64       8.249  10.347  11.256  1.00  0.00              
ATOM    197  N   ALA    65       6.742   9.815   9.652  1.00  0.00              
ATOM    198  CA  ALA    65       6.158   8.709  10.377  1.00  0.00              
ATOM    199  C   ALA    65       7.004   7.448  10.289  1.00  0.00              
ATOM    200  O   ALA    65       6.862   6.535  11.092  1.00  0.00              
ATOM    201  N   GLY    66       7.892   7.396   9.303  1.00  0.00              
ATOM    202  CA  GLY    66       8.795   6.269   9.112  1.00  0.00              
ATOM    203  C   GLY    66       8.225   5.134   8.272  1.00  0.00              
ATOM    204  O   GLY    66       8.389   3.949   8.583  1.00  0.00              
ATOM    205  N   LEU    67       7.573   5.507   7.184  1.00  0.00              
ATOM    206  CA  LEU    67       6.992   4.542   6.277  1.00  0.00              
ATOM    207  C   LEU    67       7.783   4.591   4.980  1.00  0.00              
ATOM    208  O   LEU    67       7.817   5.646   4.347  1.00  0.00              
END
