
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0318AL333_5-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318AL333_5-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      47      T       2           -
LGA    D      48      Q       3           -
LGA    G      49      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      R       7           -
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    D      50      G      14          3.678
LGA    S      51      D      15          3.644
LGA    W      52      G      16          4.231
LGA    N      53      L      17          3.213
LGA    S      54      T      18          2.251
LGA    M      55      -       -           -
LGA    G      84      S      19          4.748
LGA    N      85      L      20          2.106
LGA    T      86      -       -           -
LGA    P      87      -       -           -
LGA    T      88      -       -           -
LGA    N      89      I      21          2.145
LGA    A      90      I      22          3.702
LGA    H      91      V      23          3.344
LGA    S      92      -       -           -
LGA    I      93      -       -           -
LGA    Y      94      G      24          1.084
LGA    K      95      -       -           -
LGA    E      96      K      25          3.692
LGA    L      97      K      26           #
LGA    K      98      S      27          4.124
LGA    P      99      V      28          1.826
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    -       -      P      78           -
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    -       -      N      89           -
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    I     100      F     114          3.284
LGA    N     101      A     115          1.287
LGA    Y     102      E     116          2.368
LGA    P     103      Y     117          1.348
LGA    E     104      P     118          0.799
LGA    D     105      D     119          2.406
LGA    T     106      -       -           -
LGA    K     107      V     120          4.873
LGA    N     108      L     121          4.504
LGA    V     109      S     122          2.022
LGA    H     110      H     123          1.137
LGA    F     111      V     124          2.528
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37  154    5.0     25    3.06     8.00      9.643     0.792

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.095063 * X  +   0.775905 * Y  +  -0.623646 * Z  +  52.287086
  Y_new =   0.047775 * X  +  -0.629318 * Y  +  -0.775678 * Z  +  74.593735
  Z_new =  -0.994324 * X  +   0.043944 * Y  +  -0.096894 * Z  +  34.802139 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.715812   -0.425781  [ DEG:   155.6046    -24.3954 ]
  Theta =   1.464201    1.677391  [ DEG:    83.8926     96.1074 ]
  Phi   =   0.465695   -2.675898  [ DEG:    26.6823   -153.3177 ]
 
# 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: T0318AL333_5-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318AL333_5-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37  154   5.0   25   3.06    8.00   9.643
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL333_5-D1
REMARK Aligment from pdb entry: 1qq9_A
ATOM      1  N   THR    47      43.259  46.849  -1.227  1.00  0.00              
ATOM      2  CA  THR    47      42.529  46.662   0.082  1.00  0.00              
ATOM      3  C   THR    47      43.283  47.421   1.162  1.00  0.00              
ATOM      4  O   THR    47      44.479  47.628   1.053  1.00  0.00              
ATOM      5  N   ASP    48      42.590  47.872   2.190  1.00  0.00              
ATOM      6  CA  ASP    48      43.191  48.596   3.303  1.00  0.00              
ATOM      7  C   ASP    48      43.848  47.577   4.245  1.00  0.00              
ATOM      8  O   ASP    48      43.468  46.370   4.250  1.00  0.00              
ATOM      9  N   GLY    49      44.768  48.060   5.049  1.00  0.00              
ATOM     10  CA  GLY    49      45.402  47.308   6.144  1.00  0.00              
ATOM     11  C   GLY    49      44.373  47.428   7.300  1.00  0.00              
ATOM     12  O   GLY    49      43.968  48.525   7.661  1.00  0.00              
ATOM     13  N   ASP    50      43.937  46.309   7.878  1.00  0.00              
ATOM     14  CA  ASP    50      42.977  46.398   8.985  1.00  0.00              
ATOM     15  C   ASP    50      43.788  46.705  10.264  1.00  0.00              
ATOM     16  O   ASP    50      44.714  46.008  10.622  1.00  0.00              
ATOM     17  N   SER    51      43.376  47.734  11.018  1.00  0.00              
ATOM     18  CA  SER    51      44.174  48.055  12.215  1.00  0.00              
ATOM     19  C   SER    51      43.939  47.045  13.329  1.00  0.00              
ATOM     20  O   SER    51      42.801  46.897  13.818  1.00  0.00              
ATOM     21  N   TRP    52      45.000  46.397  13.753  1.00  0.00              
ATOM     22  CA  TRP    52      44.889  45.418  14.873  1.00  0.00              
ATOM     23  C   TRP    52      44.239  46.051  16.096  1.00  0.00              
ATOM     24  O   TRP    52      43.411  45.408  16.757  1.00  0.00              
ATOM     25  N   ASN    53      44.570  47.293  16.458  1.00  0.00              
ATOM     26  CA  ASN    53      43.971  47.883  17.637  1.00  0.00              
ATOM     27  C   ASN    53      42.449  47.942  17.552  1.00  0.00              
ATOM     28  O   ASN    53      41.785  47.834  18.575  1.00  0.00              
ATOM     29  N   SER    54      41.882  48.119  16.339  1.00  0.00              
ATOM     30  CA  SER    54      40.437  48.212  16.225  1.00  0.00              
ATOM     31  C   SER    54      39.821  46.815  16.416  1.00  0.00              
ATOM     32  O   SER    54      38.790  46.691  17.045  1.00  0.00              
ATOM     33  N   MET    55      40.502  45.781  15.926  1.00  0.00              
ATOM     34  CA  MET    55      39.971  44.435  16.106  1.00  0.00              
ATOM     35  C   MET    55      40.011  44.070  17.577  1.00  0.00              
ATOM     36  O   MET    55      39.050  43.458  18.084  1.00  0.00              
ATOM     37  N   GLY    84      41.130  44.374  18.234  1.00  0.00              
ATOM     38  CA  GLY    84      41.266  44.072  19.701  1.00  0.00              
ATOM     39  C   GLY    84      40.205  44.845  20.492  1.00  0.00              
ATOM     40  O   GLY    84      39.701  44.322  21.524  1.00  0.00              
ATOM     41  N   ASN    85      39.845  46.067  20.076  1.00  0.00              
ATOM     42  CA  ASN    85      38.806  46.816  20.811  1.00  0.00              
ATOM     43  C   ASN    85      37.455  46.059  20.773  1.00  0.00              
ATOM     44  O   ASN    85      36.724  46.033  21.755  1.00  0.00              
ATOM     45  N   THR    86      37.126  45.437  19.643  1.00  0.00              
ATOM     46  CA  THR    86      35.873  44.641  19.592  1.00  0.00              
ATOM     47  C   THR    86      35.989  43.454  20.543  1.00  0.00              
ATOM     48  O   THR    86      34.992  43.095  21.180  1.00  0.00              
ATOM     49  N   PRO    87      37.148  42.814  20.597  1.00  0.00              
ATOM     50  CA  PRO    87      37.322  41.656  21.514  1.00  0.00              
ATOM     51  C   PRO    87      37.151  42.143  22.976  1.00  0.00              
ATOM     52  O   PRO    87      36.536  41.416  23.788  1.00  0.00              
ATOM     53  N   THR    88      37.689  43.320  23.320  1.00  0.00              
ATOM     54  CA  THR    88      37.504  43.818  24.688  1.00  0.00              
ATOM     55  C   THR    88      36.019  44.008  24.986  1.00  0.00              
ATOM     56  O   THR    88      35.560  43.642  26.094  1.00  0.00              
ATOM     57  N   ASN    89      35.252  44.578  24.055  1.00  0.00              
ATOM     58  CA  ASN    89      33.802  44.722  24.273  1.00  0.00              
ATOM     59  C   ASN    89      33.137  43.349  24.424  1.00  0.00              
ATOM     60  O   ASN    89      32.293  43.170  25.297  1.00  0.00              
ATOM     61  N   ALA    90      33.478  42.349  23.589  1.00  0.00              
ATOM     62  CA  ALA    90      32.840  41.059  23.761  1.00  0.00              
ATOM     63  C   ALA    90      33.206  40.426  25.133  1.00  0.00              
ATOM     64  O   ALA    90      32.355  39.723  25.738  1.00  0.00              
ATOM     65  N   HIS    91      34.450  40.626  25.606  1.00  0.00              
ATOM     66  CA  HIS    91      34.889  40.120  26.923  1.00  0.00              
ATOM     67  C   HIS    91      34.020  40.769  28.049  1.00  0.00              
ATOM     68  O   HIS    91      33.583  40.039  28.953  1.00  0.00              
ATOM     69  N   SER    92      33.812  42.084  27.976  1.00  0.00              
ATOM     70  CA  SER    92      32.991  42.788  28.989  1.00  0.00              
ATOM     71  C   SER    92      31.555  42.308  28.913  1.00  0.00              
ATOM     72  O   SER    92      30.907  42.073  29.981  1.00  0.00              
ATOM     73  N   ILE    93      31.045  42.108  27.691  1.00  0.00              
ATOM     74  CA  ILE    93      29.681  41.569  27.586  1.00  0.00              
ATOM     75  C   ILE    93      29.567  40.205  28.258  1.00  0.00              
ATOM     76  O   ILE    93      28.573  39.912  28.985  1.00  0.00              
ATOM     77  N   TYR    94      30.533  39.298  28.069  1.00  0.00              
ATOM     78  CA  TYR    94      30.479  37.995  28.728  1.00  0.00              
ATOM     79  C   TYR    94      30.534  38.162  30.244  1.00  0.00              
ATOM     80  O   TYR    94      29.726  37.532  30.949  1.00  0.00              
ATOM     81  N   LYS    95      31.438  39.030  30.727  1.00  0.00              
ATOM     82  CA  LYS    95      31.557  39.212  32.174  1.00  0.00              
ATOM     83  C   LYS    95      30.275  39.783  32.785  1.00  0.00              
ATOM     84  O   LYS    95      29.933  39.419  33.947  1.00  0.00              
ATOM     85  N   GLU    96      29.552  40.645  32.061  1.00  0.00              
ATOM     86  CA  GLU    96      28.318  41.277  32.590  1.00  0.00              
ATOM     87  C   GLU    96      27.107  40.340  32.480  1.00  0.00              
ATOM     88  O   GLU    96      26.020  40.658  32.988  1.00  0.00              
ATOM     89  N   LEU    97      27.272  39.193  31.791  1.00  0.00              
ATOM     90  CA  LEU    97      26.174  38.289  31.542  1.00  0.00              
ATOM     91  C   LEU    97      26.478  36.859  31.941  1.00  0.00              
ATOM     92  O   LEU    97      26.252  35.888  31.168  1.00  0.00              
ATOM     93  N   LYS    98      27.036  36.648  33.111  1.00  0.00              
ATOM     94  CA  LYS    98      27.183  35.258  33.504  1.00  0.00              
ATOM     95  C   LYS    98      28.429  34.543  33.091  1.00  0.00              
ATOM     96  O   LYS    98      28.612  33.381  33.394  1.00  0.00              
ATOM     97  N   PRO    99      29.262  35.222  32.298  1.00  0.00              
ATOM     98  CA  PRO    99      30.536  34.654  31.937  1.00  0.00              
ATOM     99  C   PRO    99      30.582  34.017  30.561  1.00  0.00              
ATOM    100  O   PRO    99      31.598  33.400  30.242  1.00  0.00              
ATOM    101  N   ILE   100      29.515  34.111  29.784  1.00  0.00              
ATOM    102  CA  ILE   100      29.572  33.426  28.467  1.00  0.00              
ATOM    103  C   ILE   100      28.725  34.190  27.458  1.00  0.00              
ATOM    104  O   ILE   100      28.033  35.161  27.813  1.00  0.00              
ATOM    105  N   ASN   101      28.819  33.772  26.188  1.00  0.00              
ATOM    106  CA  ASN   101      27.992  34.391  25.129  1.00  0.00              
ATOM    107  C   ASN   101      27.311  33.259  24.391  1.00  0.00              
ATOM    108  O   ASN   101      27.239  33.252  23.154  1.00  0.00              
ATOM    109  N   TYR   102      26.674  32.350  25.140  1.00  0.00              
ATOM    110  CA  TYR   102      26.098  31.136  24.524  1.00  0.00              
ATOM    111  C   TYR   102      24.670  31.271  24.064  1.00  0.00              
ATOM    112  O   TYR   102      23.907  32.101  24.572  1.00  0.00              
ATOM    113  N   PRO   103      24.317  30.442  23.075  1.00  0.00              
ATOM    114  CA  PRO   103      22.928  30.410  22.611  1.00  0.00              
ATOM    115  C   PRO   103      21.916  30.267  23.770  1.00  0.00              
ATOM    116  O   PRO   103      22.106  29.446  24.692  1.00  0.00              
ATOM    117  N   GLU   104      20.911  31.110  23.672  1.00  0.00              
ATOM    118  CA  GLU   104      19.822  31.103  24.641  1.00  0.00              
ATOM    119  C   GLU   104      20.137  31.827  25.931  1.00  0.00              
ATOM    120  O   GLU   104      19.260  31.860  26.828  1.00  0.00              
ATOM    121  N   ASP   105      21.327  32.404  26.070  1.00  0.00              
ATOM    122  CA  ASP   105      21.713  33.121  27.298  1.00  0.00              
ATOM    123  C   ASP   105      21.847  34.600  26.939  1.00  0.00              
ATOM    124  O   ASP   105      22.104  34.954  25.771  1.00  0.00              
ATOM    125  N   THR   106      21.711  35.521  27.905  1.00  0.00              
ATOM    126  CA  THR   106      21.777  36.960  27.609  1.00  0.00              
ATOM    127  C   THR   106      23.026  37.497  26.913  1.00  0.00              
ATOM    128  O   THR   106      22.964  38.494  26.189  1.00  0.00              
ATOM    129  N   LYS   107      24.153  36.827  27.192  1.00  0.00              
ATOM    130  CA  LYS   107      25.401  37.244  26.586  1.00  0.00              
ATOM    131  C   LYS   107      25.376  37.131  25.076  1.00  0.00              
ATOM    132  O   LYS   107      26.150  37.879  24.422  1.00  0.00              
ATOM    133  N   ASN   108      24.571  36.229  24.523  1.00  0.00              
ATOM    134  CA  ASN   108      24.553  36.130  23.054  1.00  0.00              
ATOM    135  C   ASN   108      23.794  37.309  22.456  1.00  0.00              
ATOM    136  O   ASN   108      24.328  37.997  21.595  1.00  0.00              
ATOM    137  N   VAL   109      22.571  37.601  22.910  1.00  0.00              
ATOM    138  CA  VAL   109      21.844  38.737  22.321  1.00  0.00              
ATOM    139  C   VAL   109      22.622  40.036  22.563  1.00  0.00              
ATOM    140  O   VAL   109      22.594  40.941  21.705  1.00  0.00              
ATOM    141  N   HIS   110      23.284  40.191  23.702  1.00  0.00              
ATOM    142  CA  HIS   110      24.040  41.426  23.947  1.00  0.00              
ATOM    143  C   HIS   110      25.197  41.554  22.910  1.00  0.00              
ATOM    144  O   HIS   110      25.541  42.657  22.506  1.00  0.00              
ATOM    145  N   PHE   111      25.771  40.408  22.504  1.00  0.00              
ATOM    146  CA  PHE   111      26.831  40.430  21.459  1.00  0.00              
ATOM    147  C   PHE   111      26.235  40.886  20.119  1.00  0.00              
ATOM    148  O   PHE   111      26.835  41.719  19.428  1.00  0.00              
END
