
#######################################################
#                                                     #
#                        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 T0372AL044_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_3-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      72      M       1           -
LGA    K      74      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    R      78      T      14          4.282
LGA    K      79      I      15          2.483
LGA    L      80      T      16           #
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    I      81      F      31          0.824
LGA    E      82      S      32          2.031
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    D      83      C      35          2.072
LGA    A      84      S      36          1.204
LGA    D      85      W      37          0.878
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    K      86      L      40          1.687
LGA    E      87      Y      41          1.136
LGA    K      88      D      42          3.447
LGA    H      89      T      43          2.508
LGA    N      90      Q      44          0.971
LGA    F      91      F      45          1.015
LGA    C      92      A      46          0.886
LGA    M      93      V      47          1.524
LGA    L      94      I      48          2.072
LGA    G      95      D      49          3.076
LGA    V      96      -       -           -
LGA    C      97      -       -           -
LGA    S      98      -       -           -
LGA    N      99      -       -           -
LGA    M     100      -       -           -
LGA    D     103      -       -           -
LGA    L     104      -       -           -
LGA    E     105      D      50          3.735
LGA    A     106      F      51          2.211
LGA    I     107      L      52          3.662
LGA    L     108      V      53          2.030
LGA    P     109      F      54          1.263
LGA    E     110      K      55          1.553
LGA    R     111      F      56          1.150
LGA    F     112      W      57          1.263
LGA    I     113      A      58          1.912
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    D     117      A      63          4.605
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37  126    5.0     27    2.32     3.70     16.837     1.116

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.658629 * X  +  -0.708585 * Y  +  -0.253208 * Z  +  58.550068
  Y_new =   0.711812 * X  +  -0.695821 * Y  +   0.095685 * Z  +  54.308834
  Z_new =  -0.243988 * X  +  -0.117215 * Y  +   0.962668 * Z  + -14.477574 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.121164    3.020428  [ DEG:    -6.9422    173.0578 ]
  Theta =   0.246476    2.895116  [ DEG:    14.1221    165.8779 ]
  Phi   =   2.317407   -0.824186  [ DEG:   132.7776    -47.2224 ]
 
# 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: T0372AL044_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37  126   5.0   27   2.32    3.70  16.837
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_3-D1
REMARK Aligment from pdb entry: 1sqe_A
ATOM      1  N   ASP    72      41.526  68.772  10.203  1.00  0.00              
ATOM      2  CA  ASP    72      40.737  67.577  10.495  1.00  0.00              
ATOM      3  C   ASP    72      41.281  66.272   9.916  1.00  0.00              
ATOM      4  O   ASP    72      41.275  65.236  10.578  1.00  0.00              
ATOM      5  N   LYS    74      41.746  66.342   8.675  1.00  0.00              
ATOM      6  CA  LYS    74      42.227  65.180   7.942  1.00  0.00              
ATOM      7  C   LYS    74      43.197  64.195   8.605  1.00  0.00              
ATOM      8  O   LYS    74      43.001  62.984   8.519  1.00  0.00              
ATOM      9  N   ARG    78      44.233  64.689   9.271  1.00  0.00              
ATOM     10  CA  ARG    78      45.208  63.784   9.871  1.00  0.00              
ATOM     11  C   ARG    78      44.656  62.694  10.784  1.00  0.00              
ATOM     12  O   ARG    78      45.287  61.653  10.953  1.00  0.00              
ATOM     13  N   LYS    79      44.805  57.331  10.839  1.00  0.00              
ATOM     14  CA  LYS    79      44.942  56.245  11.798  1.00  0.00              
ATOM     15  C   LYS    79      44.352  54.966  11.216  1.00  0.00              
ATOM     16  O   LYS    79      43.164  54.913  10.902  1.00  0.00              
ATOM     17  N   LEU    80      45.187  53.942  11.068  1.00  0.00              
ATOM     18  CA  LEU    80      44.746  52.659  10.524  1.00  0.00              
ATOM     19  C   LEU    80      43.875  51.892  11.519  1.00  0.00              
ATOM     20  O   LEU    80      42.963  51.156  11.134  1.00  0.00              
ATOM     21  N   ILE    81      44.174  52.064  12.802  1.00  0.00              
ATOM     22  CA  ILE    81      43.430  51.412  13.871  1.00  0.00              
ATOM     23  C   ILE    81      43.306  49.901  13.681  1.00  0.00              
ATOM     24  O   ILE    81      42.217  49.340  13.788  1.00  0.00              
ATOM     25  N   GLU    82      44.432  49.257  13.385  1.00  0.00              
ATOM     26  CA  GLU    82      44.463  47.813  13.215  1.00  0.00              
ATOM     27  C   GLU    82      43.836  47.217  11.966  1.00  0.00              
ATOM     28  O   GLU    82      43.603  46.007  11.908  1.00  0.00              
ATOM     29  N   ASP    83      45.183  46.724   9.181  1.00  0.00              
ATOM     30  CA  ASP    83      46.126  45.823   8.523  1.00  0.00              
ATOM     31  C   ASP    83      46.231  44.445   9.174  1.00  0.00              
ATOM     32  O   ASP    83      46.950  43.577   8.677  1.00  0.00              
ATOM     33  N   ALA    84      45.518  44.239  10.278  1.00  0.00              
ATOM     34  CA  ALA    84      45.543  42.938  10.945  1.00  0.00              
ATOM     35  C   ALA    84      44.466  42.048  10.342  1.00  0.00              
ATOM     36  O   ALA    84      44.339  40.879  10.713  1.00  0.00              
ATOM     37  N   ASP    85      43.680  42.601   9.422  1.00  0.00              
ATOM     38  CA  ASP    85      42.621  41.824   8.787  1.00  0.00              
ATOM     39  C   ASP    85      43.137  41.123   7.537  1.00  0.00              
ATOM     40  O   ASP    85      43.694  41.755   6.641  1.00  0.00              
ATOM     41  N   LYS    86      42.943  39.809   7.487  1.00  0.00              
ATOM     42  CA  LYS    86      43.366  39.001   6.349  1.00  0.00              
ATOM     43  C   LYS    86      42.631  39.515   5.119  1.00  0.00              
ATOM     44  O   LYS    86      41.409  39.658   5.141  1.00  0.00              
ATOM     45  N   GLU    87      43.366  39.798   4.050  1.00  0.00              
ATOM     46  CA  GLU    87      42.726  40.302   2.848  1.00  0.00              
ATOM     47  C   GLU    87      42.918  41.796   2.642  1.00  0.00              
ATOM     48  O   GLU    87      42.739  42.288   1.524  1.00  0.00              
ATOM     49  N   LYS    88      43.257  42.527   3.706  1.00  0.00              
ATOM     50  CA  LYS    88      43.497  43.967   3.573  1.00  0.00              
ATOM     51  C   LYS    88      44.767  44.191   2.749  1.00  0.00              
ATOM     52  O   LYS    88      45.800  43.568   3.011  1.00  0.00              
ATOM     53  N   HIS    89      44.705  45.093   1.772  1.00  0.00              
ATOM     54  CA  HIS    89      45.875  45.343   0.942  1.00  0.00              
ATOM     55  C   HIS    89      46.436  46.758   0.995  1.00  0.00              
ATOM     56  O   HIS    89      47.642  46.937   1.176  1.00  0.00              
ATOM     57  N   ASN    90      45.577  47.763   0.838  1.00  0.00              
ATOM     58  CA  ASN    90      46.041  49.150   0.839  1.00  0.00              
ATOM     59  C   ASN    90      45.006  50.123   1.385  1.00  0.00              
ATOM     60  O   ASN    90      43.816  49.832   1.419  1.00  0.00              
ATOM     61  N   PHE    91      45.479  51.298   1.783  1.00  0.00              
ATOM     62  CA  PHE    91      44.616  52.354   2.300  1.00  0.00              
ATOM     63  C   PHE    91      45.143  53.694   1.776  1.00  0.00              
ATOM     64  O   PHE    91      46.347  53.933   1.785  1.00  0.00              
ATOM     65  N   CYS    92      44.240  54.542   1.293  1.00  0.00              
ATOM     66  CA  CYS    92      44.601  55.872   0.803  1.00  0.00              
ATOM     67  C   CYS    92      43.676  56.880   1.474  1.00  0.00              
ATOM     68  O   CYS    92      42.496  56.602   1.684  1.00  0.00              
ATOM     69  N   MET    93      44.202  58.050   1.806  1.00  0.00              
ATOM     70  CA  MET    93      43.368  59.109   2.355  1.00  0.00              
ATOM     71  C   MET    93      43.646  60.294   1.435  1.00  0.00              
ATOM     72  O   MET    93      44.787  60.761   1.332  1.00  0.00              
ATOM     73  N   LEU    94      42.608  60.758   0.744  1.00  0.00              
ATOM     74  CA  LEU    94      42.766  61.846  -0.211  1.00  0.00              
ATOM     75  C   LEU    94      41.945  63.094   0.095  1.00  0.00              
ATOM     76  O   LEU    94      40.942  63.035   0.803  1.00  0.00              
ATOM     77  N   GLY    95      42.394  64.217  -0.458  1.00  0.00              
ATOM     78  CA  GLY    95      41.707  65.499  -0.329  1.00  0.00              
ATOM     79  C   GLY    95      41.482  65.968  -1.763  1.00  0.00              
ATOM     80  O   GLY    95      42.436  66.106  -2.531  1.00  0.00              
ATOM     81  N   VAL    96      40.228  66.204  -2.130  1.00  0.00              
ATOM     82  CA  VAL    96      39.917  66.635  -3.486  1.00  0.00              
ATOM     83  C   VAL    96      40.401  68.049  -3.782  1.00  0.00              
ATOM     84  O   VAL    96      40.165  68.981  -3.012  1.00  0.00              
ATOM     85  N   CYS    97      41.083  68.206  -4.910  1.00  0.00              
ATOM     86  CA  CYS    97      41.592  69.512  -5.303  1.00  0.00              
ATOM     87  C   CYS    97      40.512  70.389  -5.931  1.00  0.00              
ATOM     88  O   CYS    97      39.547  69.899  -6.522  1.00  0.00              
ATOM     89  N   SER    98      40.684  71.695  -5.765  1.00  0.00              
ATOM     90  CA  SER    98      39.797  72.704  -6.330  1.00  0.00              
ATOM     91  C   SER    98      38.303  72.649  -6.006  1.00  0.00              
ATOM     92  O   SER    98      37.473  72.970  -6.860  1.00  0.00              
ATOM     93  N   ASN    99      37.952  72.249  -4.786  1.00  0.00              
ATOM     94  CA  ASN    99      36.548  72.226  -4.380  1.00  0.00              
ATOM     95  C   ASN    99      36.241  73.606  -3.794  1.00  0.00              
ATOM     96  O   ASN    99      37.124  74.240  -3.214  1.00  0.00              
ATOM     97  N   MET   100      32.552  74.491  -2.521  1.00  0.00              
ATOM     98  CA  MET   100      31.469  74.374  -1.555  1.00  0.00              
ATOM     99  C   MET   100      31.888  73.767  -0.221  1.00  0.00              
ATOM    100  O   MET   100      31.401  74.177   0.833  1.00  0.00              
ATOM    101  N   ASP   103      32.780  72.786  -0.271  1.00  0.00              
ATOM    102  CA  ASP   103      33.268  72.124   0.930  1.00  0.00              
ATOM    103  C   ASP   103      34.605  71.474   0.649  1.00  0.00              
ATOM    104  O   ASP   103      35.106  71.518  -0.470  1.00  0.00              
ATOM    105  N   LEU   104      35.190  70.887   1.680  1.00  0.00              
ATOM    106  CA  LEU   104      36.447  70.179   1.536  1.00  0.00              
ATOM    107  C   LEU   104      35.998  68.732   1.424  1.00  0.00              
ATOM    108  O   LEU   104      35.071  68.326   2.113  1.00  0.00              
ATOM    109  N   GLU   105      36.624  67.954   0.551  1.00  0.00              
ATOM    110  CA  GLU   105      36.221  66.565   0.398  1.00  0.00              
ATOM    111  C   GLU   105      37.367  65.625   0.708  1.00  0.00              
ATOM    112  O   GLU   105      38.438  65.708   0.103  1.00  0.00              
ATOM    113  N   ALA   106      37.127  64.735   1.661  1.00  0.00              
ATOM    114  CA  ALA   106      38.113  63.759   2.091  1.00  0.00              
ATOM    115  C   ALA   106      37.579  62.372   1.797  1.00  0.00              
ATOM    116  O   ALA   106      36.401  62.093   2.016  1.00  0.00              
ATOM    117  N   ILE   107      38.444  61.506   1.289  1.00  0.00              
ATOM    118  CA  ILE   107      38.043  60.148   0.995  1.00  0.00              
ATOM    119  C   ILE   107      39.038  59.187   1.617  1.00  0.00              
ATOM    120  O   ILE   107      40.245  59.420   1.599  1.00  0.00              
ATOM    121  N   LEU   108      38.508  58.113   2.184  1.00  0.00              
ATOM    122  CA  LEU   108      39.323  57.074   2.776  1.00  0.00              
ATOM    123  C   LEU   108      39.019  55.857   1.915  1.00  0.00              
ATOM    124  O   LEU   108      37.904  55.339   1.933  1.00  0.00              
ATOM    125  N   PRO   109      39.942  51.968   0.875  1.00  0.00              
ATOM    126  CA  PRO   109      40.601  50.765   1.343  1.00  0.00              
ATOM    127  C   PRO   109      40.464  49.679   0.280  1.00  0.00              
ATOM    128  O   PRO   109      39.373  49.434  -0.237  1.00  0.00              
ATOM    129  N   GLU   110      41.601  49.069  -0.063  1.00  0.00              
ATOM    130  CA  GLU   110      41.695  48.024  -1.088  1.00  0.00              
ATOM    131  C   GLU   110      41.791  46.642  -0.434  1.00  0.00              
ATOM    132  O   GLU   110      42.639  46.420   0.433  1.00  0.00              
ATOM    133  N   ARG   111      40.940  45.717  -0.880  1.00  0.00              
ATOM    134  CA  ARG   111      40.877  44.370  -0.324  1.00  0.00              
ATOM    135  C   ARG   111      40.927  43.296  -1.390  1.00  0.00              
ATOM    136  O   ARG   111      40.602  43.549  -2.550  1.00  0.00              
ATOM    137  N   PHE   112      41.321  42.088  -1.001  1.00  0.00              
ATOM    138  CA  PHE   112      41.369  41.010  -1.978  1.00  0.00              
ATOM    139  C   PHE   112      39.948  40.564  -2.302  1.00  0.00              
ATOM    140  O   PHE   112      39.708  39.926  -3.326  1.00  0.00              
ATOM    141  N   ILE   113      39.009  40.914  -1.428  1.00  0.00              
ATOM    142  CA  ILE   113      37.608  40.557  -1.622  1.00  0.00              
ATOM    143  C   ILE   113      36.707  41.350  -0.689  1.00  0.00              
ATOM    144  O   ILE   113      37.157  41.884   0.328  1.00  0.00              
ATOM    145  N   ASP   117      35.429  41.422  -1.040  1.00  0.00              
ATOM    146  CA  ASP   117      34.462  42.128  -0.223  1.00  0.00              
ATOM    147  C   ASP   117      34.249  41.405   1.109  1.00  0.00              
ATOM    148  O   ASP   117      33.848  42.019   2.095  1.00  0.00              
END
