
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0349AL381_3
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL381_3.T0349.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      L      12          0.735
LGA    L      13      L      13          1.570
LGA    S      14      S      14          1.606
LGA    A      15      A      15          0.755
LGA    V      16      V      16          0.325
LGA    G      17      G      17          1.143
LGA    A      18      A      18          0.840
LGA    L      19      L      19          0.549
LGA    L      20      L      20          0.908
LGA    D      21      D      21          1.037
LGA    G      22      G      22          0.511
LGA    A      23      A      23          1.660
LGA    D      24      D      24          2.289
LGA    I      25      I      25          0.827
LGA    G      26      G      26          1.802
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      L      30           -
LGA    V      29      D      31          1.967
LGA    L      30      Q      32          2.617
LGA    D      31      N      33           #
LGA    Q      32      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    N      33      V      43          4.167
LGA    M      34      I      44          1.026
LGA    S      35      P      45          0.829
LGA    R      46      R      46          1.044
LGA    R      47      R      47          0.796
LGA    V      48      V      48          1.139
LGA    L      49      L      49          1.269
LGA    V      50      V      50          1.111
LGA    H      51      H      51          1.233
LGA    E      52      E      52          1.656
LGA    D      53      D      53          1.639
LGA    D      54      D      54          1.344
LGA    L      55      L      55          0.511
LGA    A      56      A      56          0.443
LGA    G      57      G      57          0.440
LGA    A      58      A      58          0.522
LGA    R      59      R      59          0.398
LGA    R      60      R      60          0.190
LGA    L      61      L      61          0.282
LGA    L      62      L      62          0.497
LGA    T      63      T      63          0.517
LGA    D      64      D      64          0.935
LGA    A      65      A      65          2.760
LGA    -       -      G      66           -
LGA    G      66      L      67          1.621
LGA    L      67      A      68          3.064
LGA    A      68      H      69          3.369
LGA    H      69      E      70          5.993
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   75    5.0     44    1.76    79.55     54.395     2.363

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.678527 * X  +  -0.606536 * Y  +   0.414384 * Z  +   3.307559
  Y_new =   0.687785 * X  +   0.722684 * Y  +  -0.068408 * Z  + -63.254967
  Z_new =  -0.257977 * X  +   0.331424 * Y  +   0.907527 * Z  + -45.840931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.350146   -2.791446  [ DEG:    20.0619   -159.9381 ]
  Theta =   0.260928    2.880665  [ DEG:    14.9501    165.0499 ]
  Phi   =   0.792174   -2.349419  [ DEG:    45.3882   -134.6118 ]
 
# 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: T0349AL381_3                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_3.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   75   5.0   44   1.76   79.55  54.395
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_3
REMARK Aligment from pdb entry: 1yj7A
ATOM      1  N   LEU    12      -2.817  -4.325   7.285  1.00  0.00              
ATOM      2  CA  LEU    12      -1.742  -3.352   7.442  1.00  0.00              
ATOM      3  C   LEU    12      -1.965  -2.111   6.569  1.00  0.00              
ATOM      4  O   LEU    12      -1.715  -0.999   7.030  1.00  0.00              
ATOM      5  N   LEU    13      -2.428  -2.282   5.332  1.00  0.00              
ATOM      6  CA  LEU    13      -2.746  -1.127   4.500  1.00  0.00              
ATOM      7  C   LEU    13      -3.790  -0.289   5.217  1.00  0.00              
ATOM      8  O   LEU    13      -3.704   0.926   5.204  1.00  0.00              
ATOM      9  N   SER    14      -4.791  -0.928   5.834  1.00  0.00              
ATOM     10  CA  SER    14      -5.789  -0.173   6.583  1.00  0.00              
ATOM     11  C   SER    14      -5.212   0.607   7.753  1.00  0.00              
ATOM     12  O   SER    14      -5.599   1.744   7.988  1.00  0.00              
ATOM     13  N   ALA    15      -4.289  -0.005   8.481  1.00  0.00              
ATOM     14  CA  ALA    15      -3.648   0.668   9.600  1.00  0.00              
ATOM     15  C   ALA    15      -2.855   1.887   9.107  1.00  0.00              
ATOM     16  O   ALA    15      -2.944   2.971   9.678  1.00  0.00              
ATOM     17  N   VAL    16      -2.127   1.709   8.022  1.00  0.00              
ATOM     18  CA  VAL    16      -1.315   2.786   7.445  1.00  0.00              
ATOM     19  C   VAL    16      -2.180   3.915   6.870  1.00  0.00              
ATOM     20  O   VAL    16      -1.870   5.103   7.054  1.00  0.00              
ATOM     21  N   GLY    17      -3.262   3.546   6.172  1.00  0.00              
ATOM     22  CA  GLY    17      -4.186   4.505   5.585  1.00  0.00              
ATOM     23  C   GLY    17      -4.879   5.318   6.670  1.00  0.00              
ATOM     24  O   GLY    17      -4.941   6.543   6.602  1.00  0.00              
ATOM     25  N   ALA    18      -5.351   4.653   7.720  1.00  0.00              
ATOM     26  CA  ALA    18      -5.994   5.368   8.812  1.00  0.00              
ATOM     27  C   ALA    18      -5.011   6.273   9.552  1.00  0.00              
ATOM     28  O   ALA    18      -5.359   7.388   9.916  1.00  0.00              
ATOM     29  N   LEU    19      -3.778   5.815   9.749  1.00  0.00              
ATOM     30  CA  LEU    19      -2.752   6.630  10.381  1.00  0.00              
ATOM     31  C   LEU    19      -2.478   7.925   9.597  1.00  0.00              
ATOM     32  O   LEU    19      -2.400   9.014  10.163  1.00  0.00              
ATOM     33  N   LEU    20      -2.337   7.794   8.286  1.00  0.00              
ATOM     34  CA  LEU    20      -2.077   8.956   7.430  1.00  0.00              
ATOM     35  C   LEU    20      -3.260   9.898   7.443  1.00  0.00              
ATOM     36  O   LEU    20      -3.096  11.102   7.666  1.00  0.00              
ATOM     37  N   ASP    21      -4.468   9.377   7.232  1.00  0.00              
ATOM     38  CA  ASP    21      -5.632  10.250   7.202  1.00  0.00              
ATOM     39  C   ASP    21      -5.788  10.992   8.528  1.00  0.00              
ATOM     40  O   ASP    21      -6.116  12.175   8.552  1.00  0.00              
ATOM     41  N   GLY    22      -5.527  10.309   9.636  1.00  0.00              
ATOM     42  CA  GLY    22      -5.740  10.932  10.943  1.00  0.00              
ATOM     43  C   GLY    22      -4.648  11.945  11.290  1.00  0.00              
ATOM     44  O   GLY    22      -4.823  12.768  12.196  1.00  0.00              
ATOM     45  N   ALA    23      -3.550  11.904  10.539  1.00  0.00              
ATOM     46  CA  ALA    23      -2.459  12.854  10.624  1.00  0.00              
ATOM     47  C   ALA    23      -2.455  13.829   9.424  1.00  0.00              
ATOM     48  O   ALA    23      -1.418  14.379   9.029  1.00  0.00              
ATOM     49  N   ASP    24      -3.634  14.013   8.845  1.00  0.00              
ATOM     50  CA  ASP    24      -3.887  15.040   7.841  1.00  0.00              
ATOM     51  C   ASP    24      -3.025  14.904   6.594  1.00  0.00              
ATOM     52  O   ASP    24      -2.542  15.882   6.010  1.00  0.00              
ATOM     53  N   ILE    25      -2.896  13.660   6.151  1.00  0.00              
ATOM     54  CA  ILE    25      -2.349  13.340   4.847  1.00  0.00              
ATOM     55  C   ILE    25      -3.346  12.495   4.066  1.00  0.00              
ATOM     56  O   ILE    25      -3.735  11.405   4.502  1.00  0.00              
ATOM     57  N   GLY    26      -3.754  12.996   2.903  1.00  0.00              
ATOM     58  CA  GLY    26      -4.618  12.255   1.996  1.00  0.00              
ATOM     59  C   GLY    26      -3.923  11.004   1.493  1.00  0.00              
ATOM     60  O   GLY    26      -2.709  10.993   1.340  1.00  0.00              
ATOM     61  N   VAL    29      -5.358   0.979  -3.759  1.00  0.00              
ATOM     62  CA  VAL    29      -5.846   0.062  -4.790  1.00  0.00              
ATOM     63  C   VAL    29      -5.408  -1.364  -4.477  1.00  0.00              
ATOM     64  O   VAL    29      -4.462  -1.570  -3.743  1.00  0.00              
ATOM     65  N   LEU    30      -6.108  -2.343  -5.050  1.00  0.00              
ATOM     66  CA  LEU    30      -5.695  -3.733  -4.958  1.00  0.00              
ATOM     67  C   LEU    30      -5.080  -4.148  -6.291  1.00  0.00              
ATOM     68  O   LEU    30      -5.674  -3.889  -7.342  1.00  0.00              
ATOM     69  N   ASP    31      -3.901  -4.770  -6.260  1.00  0.00              
ATOM     70  CA  ASP    31      -3.250  -5.223  -7.492  1.00  0.00              
ATOM     71  C   ASP    31      -3.793  -6.591  -7.920  1.00  0.00              
ATOM     72  O   ASP    31      -4.705  -7.133  -7.286  1.00  0.00              
ATOM     73  N   GLN    32      -3.241  -7.127  -9.005  1.00  0.00              
ATOM     74  CA  GLN    32      -3.750  -8.362  -9.603  1.00  0.00              
ATOM     75  C   GLN    32      -3.513  -9.604  -8.748  1.00  0.00              
ATOM     76  O   GLN    32      -4.169 -10.630  -8.965  1.00  0.00              
ATOM     77  N   ASN    33      -2.586  -9.527  -7.791  1.00  0.00              
ATOM     78  CA  ASN    33      -2.323 -10.630  -6.859  1.00  0.00              
ATOM     79  C   ASN    33      -3.131 -10.569  -5.564  1.00  0.00              
ATOM     80  O   ASN    33      -2.979 -11.437  -4.694  1.00  0.00              
ATOM     81  N   MET    34      -3.980  -9.552  -5.425  1.00  0.00              
ATOM     82  CA  MET    34      -4.806  -9.381  -4.246  1.00  0.00              
ATOM     83  C   MET    34      -4.161  -8.587  -3.112  1.00  0.00              
ATOM     84  O   MET    34      -4.729  -8.504  -2.032  1.00  0.00              
ATOM     85  N   SER    35      -2.982  -8.015  -3.351  1.00  0.00              
ATOM     86  CA  SER    35      -2.310  -7.195  -2.351  1.00  0.00              
ATOM     87  C   SER    35      -2.663  -5.716  -2.523  1.00  0.00              
ATOM     88  O   SER    35      -3.158  -5.304  -3.577  1.00  0.00              
ATOM     89  N   ARG    46      -2.388  -4.916  -1.487  1.00  0.00              
ATOM     90  CA  ARG    46      -2.813  -3.527  -1.451  1.00  0.00              
ATOM     91  C   ARG    46      -1.654  -2.579  -1.704  1.00  0.00              
ATOM     92  O   ARG    46      -0.542  -2.814  -1.243  1.00  0.00              
ATOM     93  N   ARG    47      -1.946  -1.520  -2.450  1.00  0.00              
ATOM     94  CA  ARG    47      -1.005  -0.448  -2.743  1.00  0.00              
ATOM     95  C   ARG    47      -1.553   0.860  -2.188  1.00  0.00              
ATOM     96  O   ARG    47      -2.722   1.181  -2.395  1.00  0.00              
ATOM     97  N   VAL    48      -0.712   1.609  -1.476  1.00  0.00              
ATOM     98  CA  VAL    48      -1.064   2.931  -0.977  1.00  0.00              
ATOM     99  C   VAL    48      -0.228   3.959  -1.709  1.00  0.00              
ATOM    100  O   VAL    48       0.967   3.752  -1.923  1.00  0.00              
ATOM    101  N   LEU    49      -0.874   5.050  -2.110  1.00  0.00              
ATOM    102  CA  LEU    49      -0.248   6.192  -2.780  1.00  0.00              
ATOM    103  C   LEU    49      -0.664   7.497  -2.121  1.00  0.00              
ATOM    104  O   LEU    49      -1.675   7.552  -1.426  1.00  0.00              
ATOM    105  N   VAL    50       0.102   8.552  -2.364  1.00  0.00              
ATOM    106  CA  VAL    50      -0.235   9.893  -1.914  1.00  0.00              
ATOM    107  C   VAL    50      -0.026  10.881  -3.059  1.00  0.00              
ATOM    108  O   VAL    50       0.621  10.570  -4.054  1.00  0.00              
ATOM    109  N   HIS    51      -0.564  12.080  -2.903  1.00  0.00              
ATOM    110  CA  HIS    51      -0.228  13.169  -3.813  1.00  0.00              
ATOM    111  C   HIS    51       1.264  13.395  -3.687  1.00  0.00              
ATOM    112  O   HIS    51       1.823  13.306  -2.580  1.00  0.00              
ATOM    113  N   GLU    52       1.947  13.648  -4.805  1.00  0.00              
ATOM    114  CA  GLU    52       3.410  13.726  -4.766  1.00  0.00              
ATOM    115  C   GLU    52       3.958  14.736  -3.772  1.00  0.00              
ATOM    116  O   GLU    52       5.000  14.492  -3.165  1.00  0.00              
ATOM    117  N   ASP    53       3.260  15.857  -3.586  1.00  0.00              
ATOM    118  CA  ASP    53       3.712  16.919  -2.716  1.00  0.00              
ATOM    119  C   ASP    53       3.713  16.483  -1.262  1.00  0.00              
ATOM    120  O   ASP    53       4.415  17.069  -0.445  1.00  0.00              
ATOM    121  N   ASP    54       2.939  15.445  -0.961  1.00  0.00              
ATOM    122  CA  ASP    54       2.786  14.945   0.399  1.00  0.00              
ATOM    123  C   ASP    54       3.743  13.796   0.736  1.00  0.00              
ATOM    124  O   ASP    54       3.683  13.233   1.848  1.00  0.00              
ATOM    125  N   LEU    55       4.622  13.434  -0.200  1.00  0.00              
ATOM    126  CA  LEU    55       5.425  12.238  -0.028  1.00  0.00              
ATOM    127  C   LEU    55       6.311  12.293   1.233  1.00  0.00              
ATOM    128  O   LEU    55       6.339  11.339   2.016  1.00  0.00              
ATOM    129  N   ALA    56       7.005  13.393   1.440  1.00  0.00              
ATOM    130  CA  ALA    56       7.917  13.479   2.599  1.00  0.00              
ATOM    131  C   ALA    56       7.141  13.414   3.923  1.00  0.00              
ATOM    132  O   ALA    56       7.506  12.658   4.815  1.00  0.00              
ATOM    133  N   GLY    57       6.057  14.169   4.040  1.00  0.00              
ATOM    134  CA  GLY    57       5.198  14.141   5.222  1.00  0.00              
ATOM    135  C   GLY    57       4.687  12.737   5.494  1.00  0.00              
ATOM    136  O   GLY    57       4.696  12.267   6.637  1.00  0.00              
ATOM    137  N   ALA    58       4.248  12.050   4.435  1.00  0.00              
ATOM    138  CA  ALA    58       3.733  10.688   4.558  1.00  0.00              
ATOM    139  C   ALA    58       4.766   9.680   5.040  1.00  0.00              
ATOM    140  O   ALA    58       4.497   8.906   5.964  1.00  0.00              
ATOM    141  N   ARG    59       5.945   9.681   4.428  1.00  0.00              
ATOM    142  CA  ARG    59       7.000   8.766   4.832  1.00  0.00              
ATOM    143  C   ARG    59       7.442   9.078   6.270  1.00  0.00              
ATOM    144  O   ARG    59       7.728   8.153   7.022  1.00  0.00              
ATOM    145  N   ARG    60       7.458  10.345   6.636  1.00  0.00              
ATOM    146  CA  ARG    60       7.802  10.756   8.005  1.00  0.00              
ATOM    147  C   ARG    60       6.855  10.135   9.028  1.00  0.00              
ATOM    148  O   ARG    60       7.300   9.495   9.992  1.00  0.00              
ATOM    149  N   LEU    61       5.547  10.276   8.789  1.00  0.00              
ATOM    150  CA  LEU    61       4.526   9.715   9.643  1.00  0.00              
ATOM    151  C   LEU    61       4.640   8.188   9.719  1.00  0.00              
ATOM    152  O   LEU    61       4.545   7.604  10.802  1.00  0.00              
ATOM    153  N   LEU    62       4.822   7.540   8.571  1.00  0.00              
ATOM    154  CA  LEU    62       4.926   6.093   8.548  1.00  0.00              
ATOM    155  C   LEU    62       6.178   5.632   9.312  1.00  0.00              
ATOM    156  O   LEU    62       6.073   4.708  10.143  1.00  0.00              
ATOM    157  N   THR    63       7.317   6.262   9.034  1.00  0.00              
ATOM    158  CA  THR    63       8.592   5.944   9.698  1.00  0.00              
ATOM    159  C   THR    63       8.446   6.090  11.216  1.00  0.00              
ATOM    160  O   THR    63       8.907   5.219  11.985  1.00  0.00              
ATOM    161  N   ASP    64       7.801   7.176  11.636  1.00  0.00              
ATOM    162  CA  ASP    64       7.602   7.474  13.063  1.00  0.00              
ATOM    163  C   ASP    64       6.695   6.495  13.768  1.00  0.00              
ATOM    164  O   ASP    64       6.653   6.480  15.004  1.00  0.00              
ATOM    165  N   ALA    65       5.934   5.699  13.012  1.00  0.00              
ATOM    166  CA  ALA    65       5.063   4.688  13.572  1.00  0.00              
ATOM    167  C   ALA    65       5.490   3.263  13.247  1.00  0.00              
ATOM    168  O   ALA    65       4.759   2.314  13.511  1.00  0.00              
ATOM    169  N   GLY    66       6.685   3.116  12.677  1.00  0.00              
ATOM    170  CA  GLY    66       7.255   1.816  12.382  1.00  0.00              
ATOM    171  C   GLY    66       6.630   1.045  11.230  1.00  0.00              
ATOM    172  O   GLY    66       6.665  -0.173  11.226  1.00  0.00              
ATOM    173  N   LEU    67       6.024   1.755  10.276  1.00  0.00              
ATOM    174  CA  LEU    67       5.401   1.119   9.112  1.00  0.00              
ATOM    175  C   LEU    67       6.290   1.290   7.891  1.00  0.00              
ATOM    176  O   LEU    67       6.924   2.340   7.735  1.00  0.00              
ATOM    177  N   ALA    68       6.328   0.294   7.001  1.00  0.00              
ATOM    178  CA  ALA    68       5.643  -0.996   7.162  1.00  0.00              
ATOM    179  C   ALA    68       6.311  -1.823   8.256  1.00  0.00              
ATOM    180  O   ALA    68       7.506  -1.694   8.462  1.00  0.00              
ATOM    181  N   HIS    69       5.520  -2.646   8.923  1.00  0.00              
ATOM    182  CA  HIS    69       5.954  -3.339  10.135  1.00  0.00              
ATOM    183  C   HIS    69       6.964  -4.424   9.835  1.00  0.00              
ATOM    184  O   HIS    69       6.810  -5.216   8.901  1.00  0.00              
END
