
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0304AL243_3
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304AL243_3.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D      16           -
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    A      32      G      21          3.999
LGA    R      33      L      22          2.935
LGA    L      34      P      23          3.834
LGA    V      35      C      24           #
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    Q      36      F      30          2.224
LGA    E      37      G      31          2.802
LGA    G      38      A      32          1.390
LGA    N      39      R      33          0.763
LGA    R      40      L      34          1.282
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    L      41      H      42          4.810
LGA    H      42      Y      43          2.154
LGA    Y      43      L      44          3.979
LGA    L      44      -       -           -
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      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    A      48      L      62          4.048
LGA    G      49      D      63          1.679
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    I      50      F      66          1.544
LGA    L      53      P      67          2.524
LGA    F      54      L      68           #
LGA    S      55      L      69           -
LGA    D      56      M      70           -
LGA    A      57      K      71          4.452
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    D      58      E      74          1.725
LGA    A      59      L      75          1.423
LGA    Y      60      M      76           #
LGA    H      61      L      77           -
LGA    L      62      T      78           -
LGA    D      63      S      79           -
LGA    Q      64      G      80           -
LGA    A      65      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    F      66      T      91          3.695
LGA    P      67      L      92          0.826
LGA    L      68      Y      93          3.057
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    L      69      T      98          2.795
LGA    M      70      C      99          4.554
LGA    K      71      K     100           -
LGA    Q      72      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    L      73      Y     115          5.717
LGA    E      74      P     116           #
LGA    L      75      T     117          2.184
LGA    M      76      P     118          1.998
LGA    -       -      E     119           -
LGA    -       -      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43  107    5.0     26    3.08     0.00     14.616     0.818

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.195731 * X  +  -0.083925 * Y  +  -0.977060 * Z  +  89.094528
  Y_new =  -0.359483 * X  +  -0.920836 * Y  +   0.151109 * Z  +  60.841816
  Z_new =  -0.912393 * X  +   0.380813 * Y  +   0.150066 * Z  +  35.533070 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.195414   -1.946179  [ DEG:    68.4922   -111.5078 ]
  Theta =   1.149094    1.992499  [ DEG:    65.8382    114.1618 ]
  Phi   =  -2.069391    1.072202  [ DEG:  -118.5674     61.4326 ]
 
# 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_3                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL243_3.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43  107   5.0   26   3.08    0.00  14.616
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL243_3
REMARK Aligment from pdb entry: 2f96A
ATOM      1  N   ALA    32      43.733  27.748  42.327  1.00  0.00              
ATOM      2  CA  ALA    32      43.727  26.261  42.188  1.00  0.00              
ATOM      3  C   ALA    32      42.362  25.642  42.531  1.00  0.00              
ATOM      4  O   ALA    32      41.955  24.624  41.946  1.00  0.00              
ATOM      5  N   ARG    33      41.657  26.268  43.471  1.00  0.00              
ATOM      6  CA  ARG    33      40.274  25.912  43.748  1.00  0.00              
ATOM      7  C   ARG    33      39.438  25.986  42.468  1.00  0.00              
ATOM      8  O   ARG    33      38.716  25.073  42.148  1.00  0.00              
ATOM      9  N   LEU    34      39.524  27.099  41.760  1.00  0.00              
ATOM     10  CA  LEU    34      38.808  27.269  40.511  1.00  0.00              
ATOM     11  C   LEU    34      39.256  26.252  39.466  1.00  0.00              
ATOM     12  O   LEU    34      38.454  25.523  38.890  1.00  0.00              
ATOM     13  N   VAL    35      40.551  26.229  39.207  1.00  0.00              
ATOM     14  CA  VAL    35      41.089  25.508  38.067  1.00  0.00              
ATOM     15  C   VAL    35      41.025  24.015  38.272  1.00  0.00              
ATOM     16  O   VAL    35      40.668  23.280  37.341  1.00  0.00              
ATOM     17  N   GLN    36      41.368  23.566  39.485  1.00  0.00              
ATOM     18  CA  GLN    36      41.524  22.127  39.741  1.00  0.00              
ATOM     19  C   GLN    36      40.658  21.598  40.861  1.00  0.00              
ATOM     20  O   GLN    36      40.668  20.402  41.124  1.00  0.00              
ATOM     21  N   GLU    37      39.888  22.459  41.511  1.00  0.00              
ATOM     22  CA  GLU    37      39.140  22.047  42.686  1.00  0.00              
ATOM     23  C   GLU    37      39.988  21.616  43.877  1.00  0.00              
ATOM     24  O   GLU    37      39.505  20.834  44.716  1.00  0.00              
ATOM     25  N   GLY    38      41.228  22.115  43.955  1.00  0.00              
ATOM     26  CA  GLY    38      42.186  21.772  45.016  1.00  0.00              
ATOM     27  C   GLY    38      42.689  23.023  45.686  1.00  0.00              
ATOM     28  O   GLY    38      43.001  23.974  45.008  1.00  0.00              
ATOM     29  N   ASN    39      42.815  23.024  47.003  1.00  0.00              
ATOM     30  CA  ASN    39      43.403  24.179  47.720  1.00  0.00              
ATOM     31  C   ASN    39      44.789  23.943  48.330  1.00  0.00              
ATOM     32  O   ASN    39      45.416  24.891  48.789  1.00  0.00              
ATOM     33  N   ARG    40      45.230  22.692  48.389  1.00  0.00              
ATOM     34  CA  ARG    40      46.542  22.346  48.901  1.00  0.00              
ATOM     35  C   ARG    40      47.557  22.397  47.779  1.00  0.00              
ATOM     36  O   ARG    40      47.324  21.815  46.726  1.00  0.00              
ATOM     37  N   LEU    41      48.699  23.034  48.046  1.00  0.00              
ATOM     38  CA  LEU    41      49.683  23.390  47.003  1.00  0.00              
ATOM     39  C   LEU    41      50.181  22.205  46.230  1.00  0.00              
ATOM     40  O   LEU    41      50.212  22.241  45.006  1.00  0.00              
ATOM     41  N   HIS    42      50.598  21.168  46.951  1.00  0.00              
ATOM     42  CA  HIS    42      51.112  19.928  46.325  1.00  0.00              
ATOM     43  C   HIS    42      50.068  19.238  45.460  1.00  0.00              
ATOM     44  O   HIS    42      50.349  18.786  44.350  1.00  0.00              
ATOM     45  N   TYR    43      48.850  19.171  45.970  1.00  0.00              
ATOM     46  CA  TYR    43      47.740  18.576  45.245  1.00  0.00              
ATOM     47  C   TYR    43      47.300  19.396  44.042  1.00  0.00              
ATOM     48  O   TYR    43      46.854  18.851  43.028  1.00  0.00              
ATOM     49  N   LEU    44      47.426  20.707  44.145  1.00  0.00              
ATOM     50  CA  LEU    44      47.141  21.593  43.018  1.00  0.00              
ATOM     51  C   LEU    44      48.161  21.383  41.900  1.00  0.00              
ATOM     52  O   LEU    44      47.790  21.203  40.721  1.00  0.00              
ATOM     53  N   ALA    45      49.448  21.414  42.258  1.00  0.00              
ATOM     54  CA  ALA    45      50.533  21.141  41.288  1.00  0.00              
ATOM     55  C   ALA    45      50.441  19.751  40.644  1.00  0.00              
ATOM     56  O   ALA    45      50.742  19.575  39.462  1.00  0.00              
ATOM     57  N   ASP    46      50.022  18.766  41.424  1.00  0.00              
ATOM     58  CA  ASP    46      49.848  17.418  40.908  1.00  0.00              
ATOM     59  C   ASP    46      48.702  17.430  39.880  1.00  0.00              
ATOM     60  O   ASP    46      48.849  16.934  38.756  1.00  0.00              
ATOM     61  N   ARG    47      47.584  18.053  40.252  1.00  0.00              
ATOM     62  CA  ARG    47      46.444  18.230  39.340  1.00  0.00              
ATOM     63  C   ARG    47      46.845  18.962  38.053  1.00  0.00              
ATOM     64  O   ARG    47      46.357  18.635  36.978  1.00  0.00              
ATOM     65  N   ALA    48      47.737  19.944  38.174  1.00  0.00              
ATOM     66  CA  ALA    48      48.182  20.737  37.017  1.00  0.00              
ATOM     67  C   ALA    48      49.190  20.006  36.113  1.00  0.00              
ATOM     68  O   ALA    48      49.645  20.564  35.105  1.00  0.00              
ATOM     69  N   GLY    49      49.554  18.779  36.495  1.00  0.00              
ATOM     70  CA  GLY    49      50.546  17.981  35.769  1.00  0.00              
ATOM     71  C   GLY    49      51.994  18.283  36.138  1.00  0.00              
ATOM     72  O   GLY    49      52.898  17.733  35.525  1.00  0.00              
ATOM     73  N   ILE    50      52.221  19.166  37.113  1.00  0.00              
ATOM     74  CA  ILE    50      53.582  19.501  37.567  1.00  0.00              
ATOM     75  C   ILE    50      54.105  18.411  38.516  1.00  0.00              
ATOM     76  O   ILE    50      53.309  17.678  39.128  1.00  0.00              
ATOM     77  N   LEU    53      55.431  18.321  38.652  1.00  0.00              
ATOM     78  CA  LEU    53      56.054  17.525  39.722  1.00  0.00              
ATOM     79  C   LEU    53      55.996  18.318  41.041  1.00  0.00              
ATOM     80  O   LEU    53      56.177  19.546  41.053  1.00  0.00              
ATOM     81  N   PHE    54      55.716  17.636  42.145  1.00  0.00              
ATOM     82  CA  PHE    54      55.858  18.256  43.465  1.00  0.00              
ATOM     83  C   PHE    54      56.148  17.173  44.503  1.00  0.00              
ATOM     84  O   PHE    54      55.473  16.141  44.515  1.00  0.00              
ATOM     85  N   SER    55      57.144  17.421  45.362  1.00  0.00              
ATOM     86  CA  SER    55      57.620  16.428  46.341  1.00  0.00              
ATOM     87  C   SER    55      56.879  16.527  47.685  1.00  0.00              
ATOM     88  O   SER    55      56.782  17.609  48.277  1.00  0.00              
ATOM     89  N   ASP    56      62.465  28.938  48.243  1.00  0.00              
ATOM     90  CA  ASP    56      62.788  28.969  46.819  1.00  0.00              
ATOM     91  C   ASP    56      62.006  27.933  45.981  1.00  0.00              
ATOM     92  O   ASP    56      61.496  28.224  44.888  1.00  0.00              
ATOM     93  N   ALA    57      61.933  26.720  46.507  1.00  0.00              
ATOM     94  CA  ALA    57      61.196  25.643  45.856  1.00  0.00              
ATOM     95  C   ALA    57      59.725  26.016  45.760  1.00  0.00              
ATOM     96  O   ALA    57      59.110  25.830  44.721  1.00  0.00              
ATOM     97  N   ASP    58      59.181  26.548  46.845  1.00  0.00              
ATOM     98  CA  ASP    58      57.758  26.817  46.942  1.00  0.00              
ATOM     99  C   ASP    58      57.355  27.958  46.016  1.00  0.00              
ATOM    100  O   ASP    58      56.280  27.952  45.444  1.00  0.00              
ATOM    101  N   ALA    59      58.242  28.931  45.886  1.00  0.00              
ATOM    102  CA  ALA    59      57.998  30.118  45.086  1.00  0.00              
ATOM    103  C   ALA    59      58.061  29.787  43.577  1.00  0.00              
ATOM    104  O   ALA    59      57.252  30.242  42.788  1.00  0.00              
ATOM    105  N   TYR    60      59.032  28.977  43.203  1.00  0.00              
ATOM    106  CA  TYR    60      59.119  28.515  41.839  1.00  0.00              
ATOM    107  C   TYR    60      57.955  27.625  41.405  1.00  0.00              
ATOM    108  O   TYR    60      57.400  27.820  40.344  1.00  0.00              
ATOM    109  N   HIS    61      57.551  26.694  42.261  1.00  0.00              
ATOM    110  CA  HIS    61      56.348  25.875  41.986  1.00  0.00              
ATOM    111  C   HIS    61      55.052  26.693  41.924  1.00  0.00              
ATOM    112  O   HIS    61      54.194  26.461  41.063  1.00  0.00              
ATOM    113  N   LEU    62      54.920  27.654  42.834  1.00  0.00              
ATOM    114  CA  LEU    62      53.772  28.551  42.877  1.00  0.00              
ATOM    115  C   LEU    62      53.717  29.472  41.655  1.00  0.00              
ATOM    116  O   LEU    62      52.638  29.717  41.110  1.00  0.00              
ATOM    117  N   ASP    63      54.869  29.973  41.228  1.00  0.00              
ATOM    118  CA  ASP    63      54.928  30.770  40.008  1.00  0.00              
ATOM    119  C   ASP    63      54.512  29.967  38.773  1.00  0.00              
ATOM    120  O   ASP    63      53.784  30.472  37.948  1.00  0.00              
ATOM    121  N   GLN    64      54.948  28.712  38.676  1.00  0.00              
ATOM    122  CA  GLN    64      54.533  27.815  37.610  1.00  0.00              
ATOM    123  C   GLN    64      53.027  27.526  37.659  1.00  0.00              
ATOM    124  O   GLN    64      52.331  27.571  36.645  1.00  0.00              
ATOM    125  N   ALA    65      52.507  27.221  38.846  1.00  0.00              
ATOM    126  CA  ALA    65      51.053  27.072  39.040  1.00  0.00              
ATOM    127  C   ALA    65      50.275  28.354  38.614  1.00  0.00              
ATOM    128  O   ALA    65      49.285  28.297  37.915  1.00  0.00              
ATOM    129  N   PHE    66      50.704  29.509  39.095  1.00  0.00              
ATOM    130  CA  PHE    66      50.069  30.784  38.736  1.00  0.00              
ATOM    131  C   PHE    66      50.027  31.008  37.225  1.00  0.00              
ATOM    132  O   PHE    66      48.951  31.165  36.660  1.00  0.00              
ATOM    133  N   PRO    67      51.188  30.978  36.569  1.00  0.00              
ATOM    134  CA  PRO    67      51.292  31.239  35.099  1.00  0.00              
ATOM    135  C   PRO    67      50.513  30.222  34.267  1.00  0.00              
ATOM    136  O   PRO    67      49.904  30.578  33.262  1.00  0.00              
ATOM    137  N   LEU    68      50.549  28.961  34.693  1.00  0.00              
ATOM    138  CA  LEU    68      49.772  27.883  34.030  1.00  0.00              
ATOM    139  C   LEU    68      48.279  28.140  34.079  1.00  0.00              
ATOM    140  O   LEU    68      47.595  27.899  33.099  1.00  0.00              
ATOM    141  N   LEU    69      47.750  28.616  35.216  1.00  0.00              
ATOM    142  CA  LEU    69      46.309  28.865  35.330  1.00  0.00              
ATOM    143  C   LEU    69      45.911  30.068  34.450  1.00  0.00              
ATOM    144  O   LEU    69      44.996  29.978  33.624  1.00  0.00              
ATOM    145  N   MET    70      46.609  31.186  34.609  1.00  0.00              
ATOM    146  CA  MET    70      46.407  32.360  33.751  1.00  0.00              
ATOM    147  C   MET    70      46.557  31.995  32.260  1.00  0.00              
ATOM    148  O   MET    70      45.785  32.439  31.385  1.00  0.00              
ATOM    149  N   LYS    71      47.562  31.204  31.943  1.00  0.00              
ATOM    150  CA  LYS    71      47.740  30.789  30.542  1.00  0.00              
ATOM    151  C   LYS    71      46.636  29.861  29.985  1.00  0.00              
ATOM    152  O   LYS    71      46.244  29.955  28.762  1.00  0.00              
ATOM    153  N   GLN    72      46.131  28.971  30.844  1.00  0.00              
ATOM    154  CA  GLN    72      44.979  28.156  30.482  1.00  0.00              
ATOM    155  C   GLN    72      43.742  29.010  30.229  1.00  0.00              
ATOM    156  O   GLN    72      42.973  28.758  29.288  1.00  0.00              
ATOM    157  N   LEU    73      43.520  29.979  31.101  1.00  0.00              
ATOM    158  CA  LEU    73      42.413  30.928  30.949  1.00  0.00              
ATOM    159  C   LEU    73      42.477  31.595  29.551  1.00  0.00              
ATOM    160  O   LEU    73      41.474  31.643  28.835  1.00  0.00              
ATOM    161  N   GLU    74      43.667  32.067  29.161  1.00  0.00              
ATOM    162  CA  GLU    74      43.888  32.610  27.829  1.00  0.00              
ATOM    163  C   GLU    74      43.656  31.593  26.708  1.00  0.00              
ATOM    164  O   GLU    74      43.023  31.894  25.696  1.00  0.00              
ATOM    165  N   LEU    75      44.214  30.395  26.873  1.00  0.00              
ATOM    166  CA  LEU    75      44.062  29.334  25.886  1.00  0.00              
ATOM    167  C   LEU    75      42.605  28.959  25.709  1.00  0.00              
ATOM    168  O   LEU    75      42.220  28.630  24.628  1.00  0.00              
ATOM    169  N   MET    76      41.813  29.010  26.780  1.00  0.00              
ATOM    170  CA  MET    76      40.374  28.704  26.739  1.00  0.00              
ATOM    171  C   MET    76      39.491  29.861  26.241  1.00  0.00              
ATOM    172  O   MET    76      38.270  29.734  26.238  1.00  0.00              
END
