
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0304AL243_1-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL243_1-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      47      R      17           -
LGA    G      49      P      18           -
LGA    I      50      W      19           -
LGA    R      51      W      20           -
LGA    G      52      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    L      53      H      42           #
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    F      54      P      67          3.361
LGA    L      62      L      68          3.621
LGA    D      63      L      69          3.762
LGA    -       -      M      70           -
LGA    P      67      K      71          3.383
LGA    L      68      Q      72          2.729
LGA    L      69      L      73          2.295
LGA    M      70      E      74          2.216
LGA    K      71      L      75          0.508
LGA    Q      72      M      76          1.117
LGA    L      73      L      77          2.984
LGA    E      74      T      78          3.451
LGA    -       -      S      79           -
LGA    L      75      G      80          2.010
LGA    -       -      E      81           -
LGA    M      76      L      82          2.516
LGA    L      77      N      83          3.962
LGA    T      78      P      84           #
LGA    S      79      -       -           -
LGA    G      80      R      85          2.560
LGA    E      81      H      86          2.953
LGA    Q      87      Q      87          3.325
LGA    H      88      H      88          2.942
LGA    T      89      T      89          2.299
LGA    V      90      V      90          2.192
LGA    T      91      T      91          2.072
LGA    L      92      L      92          2.192
LGA    Y      93      Y      93          2.267
LGA    A      94      A      94          4.841
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    K      95      T      98           #
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    G      96      Y     109          1.741
LGA    L      97      V     110          2.139
LGA    T      98      Y     111          2.831
LGA    C      99      L     112          2.934
LGA    K     100      A     113          3.783
LGA    A     101      V     114          2.320
LGA    D     102      Y     115          1.933
LGA    D     108      P     116          1.842
LGA    Y     109      T     117          2.561
LGA    V     110      -       -           -
LGA    Y     111      -       -           -
LGA    L     112      -       -           -
LGA    A     113      -       -           -
LGA    V     114      -       -           -
LGA    Y     115      -       -           -
LGA    P     116      -       -           -
LGA    T     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50  101    5.0     33    2.79    33.33     20.791     1.143

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.050797 * X  +   0.787267 * Y  +   0.614516 * Z  + -63.546692
  Y_new =  -0.273461 * X  +  -0.580831 * Y  +   0.766717 * Z  + 128.377167
  Z_new =   0.960541 * X  +  -0.206993 * Y  +   0.185783 * Z  + -183.989822 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.839347    2.302246  [ DEG:   -48.0910    131.9090 ]
  Theta =  -1.288940   -1.852652  [ DEG:   -73.8508   -106.1492 ]
  Phi   =  -1.387136    1.754457  [ DEG:   -79.4770    100.5230 ]
 
# 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: T0304AL243_1-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL243_1-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50  101   5.0   33   2.79   33.33  20.791
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL243_1-D1
REMARK Aligment from pdb entry: 1fjgS
ATOM      1  N   ARG    47      50.134   6.742  41.524  1.00  0.00              
ATOM      2  CA  ARG    47      50.959   7.712  40.805  1.00  0.00              
ATOM      3  C   ARG    47      52.457   7.490  41.031  1.00  0.00              
ATOM      4  O   ARG    47      52.849   6.634  41.824  1.00  0.00              
ATOM      5  N   GLY    49      53.288   8.262  40.329  1.00  0.00              
ATOM      6  CA  GLY    49      54.736   8.132  40.454  1.00  0.00              
ATOM      7  C   GLY    49      55.528   9.417  40.236  1.00  0.00              
ATOM      8  O   GLY    49      55.111  10.303  39.494  1.00  0.00              
ATOM      9  N   ILE    50      56.690   9.486  40.878  1.00  0.00              
ATOM     10  CA  ILE    50      57.575  10.637  40.800  1.00  0.00              
ATOM     11  C   ILE    50      58.973  10.189  41.195  1.00  0.00              
ATOM     12  O   ILE    50      59.910  10.404  40.442  1.00  0.00              
ATOM     13  N   ARG    51      61.781  10.766  43.895  1.00  0.00              
ATOM     14  CA  ARG    51      62.438  11.552  44.930  1.00  0.00              
ATOM     15  C   ARG    51      62.716  12.975  44.407  1.00  0.00              
ATOM     16  O   ARG    51      63.735  13.233  43.760  1.00  0.00              
ATOM     17  N   GLY    52      61.785  13.887  44.679  1.00  0.00              
ATOM     18  CA  GLY    52      61.934  15.259  44.232  1.00  0.00              
ATOM     19  C   GLY    52      60.614  15.955  43.931  1.00  0.00              
ATOM     20  O   GLY    52      60.617  17.031  43.327  1.00  0.00              
ATOM     21  N   LEU    53      59.501  15.352  44.356  1.00  0.00              
ATOM     22  CA  LEU    53      58.142  15.886  44.134  1.00  0.00              
ATOM     23  C   LEU    53      58.074  17.288  43.523  1.00  0.00              
ATOM     24  O   LEU    53      57.742  18.260  44.194  1.00  0.00              
ATOM     25  N   PHE    54      58.354  17.349  42.225  1.00  0.00              
ATOM     26  CA  PHE    54      58.399  18.567  41.412  1.00  0.00              
ATOM     27  C   PHE    54      57.396  19.713  41.607  1.00  0.00              
ATOM     28  O   PHE    54      56.196  19.500  41.791  1.00  0.00              
ATOM     29  N   LEU    62      57.926  20.936  41.528  1.00  0.00              
ATOM     30  CA  LEU    62      57.148  22.173  41.637  1.00  0.00              
ATOM     31  C   LEU    62      57.878  23.298  40.903  1.00  0.00              
ATOM     32  O   LEU    62      59.047  23.568  41.182  1.00  0.00              
ATOM     33  N   ASP    63      57.193  23.945  39.963  1.00  0.00              
ATOM     34  CA  ASP    63      57.790  25.048  39.212  1.00  0.00              
ATOM     35  C   ASP    63      57.950  26.232  40.149  1.00  0.00              
ATOM     36  O   ASP    63      56.970  26.777  40.654  1.00  0.00              
ATOM     37  N   PRO    67      59.189  26.634  40.377  1.00  0.00              
ATOM     38  CA  PRO    67      59.452  27.745  41.271  1.00  0.00              
ATOM     39  C   PRO    67      58.866  29.070  40.816  1.00  0.00              
ATOM     40  O   PRO    67      59.139  30.098  41.425  1.00  0.00              
ATOM     41  N   LEU    68      58.065  29.058  39.750  1.00  0.00              
ATOM     42  CA  LEU    68      57.429  30.294  39.291  1.00  0.00              
ATOM     43  C   LEU    68      56.610  30.730  40.485  1.00  0.00              
ATOM     44  O   LEU    68      56.849  31.773  41.090  1.00  0.00              
ATOM     45  N   LEU    69      55.633  29.889  40.803  1.00  0.00              
ATOM     46  CA  LEU    69      54.721  30.125  41.902  1.00  0.00              
ATOM     47  C   LEU    69      55.265  29.666  43.243  1.00  0.00              
ATOM     48  O   LEU    69      54.823  30.145  44.282  1.00  0.00              
ATOM     49  N   MET    70      56.215  28.741  43.236  1.00  0.00              
ATOM     50  CA  MET    70      56.756  28.279  44.503  1.00  0.00              
ATOM     51  C   MET    70      57.398  29.460  45.209  1.00  0.00              
ATOM     52  O   MET    70      56.877  29.940  46.217  1.00  0.00              
ATOM     53  N   LYS    71      58.516  29.945  44.678  1.00  0.00              
ATOM     54  CA  LYS    71      59.180  31.083  45.296  1.00  0.00              
ATOM     55  C   LYS    71      58.150  32.202  45.386  1.00  0.00              
ATOM     56  O   LYS    71      58.216  33.052  46.269  1.00  0.00              
ATOM     57  N   GLN    72      57.187  32.178  44.472  1.00  0.00              
ATOM     58  CA  GLN    72      56.128  33.178  44.430  1.00  0.00              
ATOM     59  C   GLN    72      55.093  32.986  45.530  1.00  0.00              
ATOM     60  O   GLN    72      54.434  33.940  45.932  1.00  0.00              
ATOM     61  N   LEU    73      54.946  31.758  46.012  1.00  0.00              
ATOM     62  CA  LEU    73      53.959  31.474  47.045  1.00  0.00              
ATOM     63  C   LEU    73      54.517  31.666  48.446  1.00  0.00              
ATOM     64  O   LEU    73      53.811  32.127  49.341  1.00  0.00              
ATOM     65  N   GLU    74      55.785  31.314  48.633  1.00  0.00              
ATOM     66  CA  GLU    74      56.428  31.454  49.934  1.00  0.00              
ATOM     67  C   GLU    74      56.611  32.925  50.305  1.00  0.00              
ATOM     68  O   GLU    74      56.727  33.266  51.486  1.00  0.00              
ATOM     69  N   LEU    75      56.638  33.788  49.292  1.00  0.00              
ATOM     70  CA  LEU    75      56.774  35.222  49.513  1.00  0.00              
ATOM     71  C   LEU    75      55.437  35.734  50.022  1.00  0.00              
ATOM     72  O   LEU    75      55.384  36.630  50.861  1.00  0.00              
ATOM     73  N   MET    76      54.354  35.159  49.507  1.00  0.00              
ATOM     74  CA  MET    76      53.013  35.546  49.927  1.00  0.00              
ATOM     75  C   MET    76      52.792  35.155  51.381  1.00  0.00              
ATOM     76  O   MET    76      52.118  35.865  52.127  1.00  0.00              
ATOM     77  N   LEU    77      53.358  34.017  51.778  1.00  0.00              
ATOM     78  CA  LEU    77      53.224  33.545  53.151  1.00  0.00              
ATOM     79  C   LEU    77      53.872  34.554  54.090  1.00  0.00              
ATOM     80  O   LEU    77      53.282  34.940  55.099  1.00  0.00              
ATOM     81  N   THR    78      55.084  34.981  53.749  1.00  0.00              
ATOM     82  CA  THR    78      55.806  35.956  54.554  1.00  0.00              
ATOM     83  C   THR    78      54.900  37.124  54.940  1.00  0.00              
ATOM     84  O   THR    78      55.103  37.758  55.975  1.00  0.00              
ATOM     85  N   SER    79      53.903  37.402  54.103  1.00  0.00              
ATOM     86  CA  SER    79      52.956  38.485  54.356  1.00  0.00              
ATOM     87  C   SER    79      51.530  37.943  54.481  1.00  0.00              
ATOM     88  O   SER    79      51.185  37.314  55.479  1.00  0.00              
ATOM     89  N   GLY    80      50.710  38.184  53.461  1.00  0.00              
ATOM     90  CA  GLY    80      49.332  37.724  53.490  1.00  0.00              
ATOM     91  C   GLY    80      48.917  36.854  52.314  1.00  0.00              
ATOM     92  O   GLY    80      49.749  36.192  51.691  1.00  0.00              
ATOM     93  N   GLU    81      47.620  36.862  52.008  1.00  0.00              
ATOM     94  CA  GLU    81      47.070  36.060  50.915  1.00  0.00              
ATOM     95  C   GLU    81      46.609  36.914  49.735  1.00  0.00              
ATOM     96  O   GLU    81      45.644  37.673  49.843  1.00  0.00              
ATOM     97  N   GLN    87      47.296  36.787  48.605  1.00  0.00              
ATOM     98  CA  GLN    87      46.926  37.548  47.419  1.00  0.00              
ATOM     99  C   GLN    87      45.817  36.843  46.645  1.00  0.00              
ATOM    100  O   GLN    87      46.012  35.750  46.104  1.00  0.00              
ATOM    101  N   HIS    88      44.654  37.485  46.597  1.00  0.00              
ATOM    102  CA  HIS    88      43.498  36.945  45.895  1.00  0.00              
ATOM    103  C   HIS    88      43.868  36.557  44.467  1.00  0.00              
ATOM    104  O   HIS    88      44.172  37.415  43.638  1.00  0.00              
ATOM    105  N   THR    89      43.848  35.257  44.198  1.00  0.00              
ATOM    106  CA  THR    89      44.169  34.728  42.879  1.00  0.00              
ATOM    107  C   THR    89      45.641  34.902  42.542  1.00  0.00              
ATOM    108  O   THR    89      46.256  35.911  42.876  1.00  0.00              
ATOM    109  N   VAL    90      46.191  33.894  41.878  1.00  0.00              
ATOM    110  CA  VAL    90      47.585  33.880  41.463  1.00  0.00              
ATOM    111  C   VAL    90      47.631  33.097  40.163  1.00  0.00              
ATOM    112  O   VAL    90      47.884  31.894  40.166  1.00  0.00              
ATOM    113  N   THR    91      47.373  33.779  39.052  1.00  0.00              
ATOM    114  CA  THR    91      47.367  33.124  37.751  1.00  0.00              
ATOM    115  C   THR    91      48.690  32.438  37.435  1.00  0.00              
ATOM    116  O   THR    91      49.756  33.051  37.521  1.00  0.00              
ATOM    117  N   LEU    92      48.603  31.158  37.073  1.00  0.00              
ATOM    118  CA  LEU    92      49.777  30.366  36.734  1.00  0.00              
ATOM    119  C   LEU    92      49.524  29.496  35.510  1.00  0.00              
ATOM    120  O   LEU    92      48.381  29.259  35.115  1.00  0.00              
ATOM    121  N   TYR    93      50.616  29.035  34.915  1.00  0.00              
ATOM    122  CA  TYR    93      50.579  28.167  33.751  1.00  0.00              
ATOM    123  C   TYR    93      51.297  26.888  34.147  1.00  0.00              
ATOM    124  O   TYR    93      51.438  25.963  33.346  1.00  0.00              
ATOM    125  N   ALA    94      51.756  26.848  35.396  1.00  0.00              
ATOM    126  CA  ALA    94      52.462  25.684  35.903  1.00  0.00              
ATOM    127  C   ALA    94      51.466  24.624  36.328  1.00  0.00              
ATOM    128  O   ALA    94      51.363  24.253  37.497  1.00  0.00              
ATOM    129  N   LYS    95      50.722  24.154  35.342  1.00  0.00              
ATOM    130  CA  LYS    95      49.721  23.122  35.520  1.00  0.00              
ATOM    131  C   LYS    95      50.443  21.877  36.058  1.00  0.00              
ATOM    132  O   LYS    95      49.862  21.062  36.770  1.00  0.00              
ATOM    133  N   GLY    96      45.433  26.874  51.582  1.00  0.00              
ATOM    134  CA  GLY    96      44.867  28.145  51.991  1.00  0.00              
ATOM    135  C   GLY    96      44.853  29.193  50.896  1.00  0.00              
ATOM    136  O   GLY    96      43.923  29.999  50.824  1.00  0.00              
ATOM    137  N   LEU    97      45.879  29.187  50.046  1.00  0.00              
ATOM    138  CA  LEU    97      45.985  30.150  48.952  1.00  0.00              
ATOM    139  C   LEU    97      44.877  29.989  47.918  1.00  0.00              
ATOM    140  O   LEU    97      43.877  29.318  48.172  1.00  0.00              
ATOM    141  N   THR    98      45.061  30.603  46.752  1.00  0.00              
ATOM    142  CA  THR    98      44.067  30.519  45.686  1.00  0.00              
ATOM    143  C   THR    98      44.695  30.662  44.308  1.00  0.00              
ATOM    144  O   THR    98      44.484  31.666  43.631  1.00  0.00              
ATOM    145  N   CYS    99      45.458  29.654  43.894  1.00  0.00              
ATOM    146  CA  CYS    99      46.117  29.675  42.591  1.00  0.00              
ATOM    147  C   CYS    99      45.147  29.469  41.427  1.00  0.00              
ATOM    148  O   CYS    99      44.333  28.544  41.440  1.00  0.00              
ATOM    149  N   LYS   100      45.243  30.331  40.418  1.00  0.00              
ATOM    150  CA  LYS   100      44.381  30.229  39.243  1.00  0.00              
ATOM    151  C   LYS   100      45.143  29.547  38.112  1.00  0.00              
ATOM    152  O   LYS   100      46.182  30.034  37.664  1.00  0.00              
ATOM    153  N   ALA   101      44.619  28.415  37.658  1.00  0.00              
ATOM    154  CA  ALA   101      45.256  27.655  36.592  1.00  0.00              
ATOM    155  C   ALA   101      44.557  27.796  35.243  1.00  0.00              
ATOM    156  O   ALA   101      43.348  28.026  35.163  1.00  0.00              
ATOM    157  N   ASP   102      43.201  26.604  31.498  1.00  0.00              
ATOM    158  CA  ASP   102      42.555  25.442  30.890  1.00  0.00              
ATOM    159  C   ASP   102      43.298  25.242  29.594  1.00  0.00              
ATOM    160  O   ASP   102      43.378  24.139  29.049  1.00  0.00              
ATOM    161  N   ASP   108      43.844  26.353  29.121  1.00  0.00              
ATOM    162  CA  ASP   108      44.554  26.392  27.860  1.00  0.00              
ATOM    163  C   ASP   108      43.760  27.469  27.157  1.00  0.00              
ATOM    164  O   ASP   108      44.035  27.851  26.018  1.00  0.00              
ATOM    165  N   TYR   109      42.759  27.960  27.887  1.00  0.00              
ATOM    166  CA  TYR   109      41.867  28.998  27.398  1.00  0.00              
ATOM    167  C   TYR   109      41.552  30.052  28.451  1.00  0.00              
ATOM    168  O   TYR   109      41.514  31.243  28.144  1.00  0.00              
ATOM    169  N   VAL   110      41.317  29.614  29.686  1.00  0.00              
ATOM    170  CA  VAL   110      40.983  30.534  30.775  1.00  0.00              
ATOM    171  C   VAL   110      41.765  30.212  32.044  1.00  0.00              
ATOM    172  O   VAL   110      42.355  29.144  32.173  1.00  0.00              
ATOM    173  N   TYR   111      41.762  31.147  32.985  1.00  0.00              
ATOM    174  CA  TYR   111      42.422  30.945  34.269  1.00  0.00              
ATOM    175  C   TYR   111      41.280  30.694  35.245  1.00  0.00              
ATOM    176  O   TYR   111      40.342  31.490  35.323  1.00  0.00              
ATOM    177  N   LEU   112      41.334  29.584  35.972  1.00  0.00              
ATOM    178  CA  LEU   112      40.270  29.284  36.921  1.00  0.00              
ATOM    179  C   LEU   112      40.716  29.338  38.369  1.00  0.00              
ATOM    180  O   LEU   112      41.793  28.859  38.724  1.00  0.00              
ATOM    181  N   ALA   113      39.879  29.932  39.228  1.00  0.00              
ATOM    182  CA  ALA   113      40.146  30.073  40.659  1.00  0.00              
ATOM    183  C   ALA   113      40.131  28.713  41.350  1.00  0.00              
ATOM    184  O   ALA   113      39.118  28.015  41.333  1.00  0.00              
ATOM    185  N   VAL   114      41.249  28.337  41.961  1.00  0.00              
ATOM    186  CA  VAL   114      41.321  27.051  42.637  1.00  0.00              
ATOM    187  C   VAL   114      41.782  27.159  44.092  1.00  0.00              
ATOM    188  O   VAL   114      42.979  27.249  44.372  1.00  0.00              
ATOM    189  N   TYR   115      40.820  27.149  45.012  1.00  0.00              
ATOM    190  CA  TYR   115      41.112  27.230  46.441  1.00  0.00              
ATOM    191  C   TYR   115      41.802  25.934  46.845  1.00  0.00              
ATOM    192  O   TYR   115      41.172  24.881  46.936  1.00  0.00              
ATOM    193  N   PRO   116      43.103  26.023  47.082  1.00  0.00              
ATOM    194  CA  PRO   116      43.898  24.864  47.456  1.00  0.00              
ATOM    195  C   PRO   116      43.754  24.489  48.945  1.00  0.00              
ATOM    196  O   PRO   116      44.071  25.279  49.833  1.00  0.00              
ATOM    197  N   THR   117      43.266  23.271  49.193  1.00  0.00              
ATOM    198  CA  THR   117      43.041  22.749  50.544  1.00  0.00              
ATOM    199  C   THR   117      44.103  21.750  51.005  1.00  0.00              
ATOM    200  O   THR   117      44.841  21.185  50.196  1.00  0.00              
END
