
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0283AL381_5-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283AL381_5-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    -       -      E       5           -
LGA    -       -      K       6           -
LGA    -       -      M       7           -
LGA    -       -      I       8           -
LGA    -       -      G       9           -
LGA    -       -      S      10           -
LGA    -       -      L      11           -
LGA    -       -      N      12           -
LGA    -       -      D      13           -
LGA    -       -      K      14           -
LGA    -       -      R      15           -
LGA    -       -      E      16           -
LGA    -       -      W      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      A      22           -
LGA    -       -      R      23           -
LGA    -       -      A      24           -
LGA    -       -      K      25           -
LGA    -       -      A      26           -
LGA    F      58      L      27          3.692
LGA    G      59      P      28          3.484
LGA    G      60      K      29          2.837
LGA    I      61      E      30          2.129
LGA    L      62      Y      31          1.702
LGA    D      63      H      32          2.100
LGA    L      64      H      33          1.635
LGA    F      65      A      34          0.688
LGA    E      66      Y      35          0.769
LGA    E      67      K      36          1.234
LGA    G      68      A      37          0.558
LGA    A      69      I      38          1.132
LGA    A      70      Q      39          1.711
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    E      71      I      57           #
LGA    G      72      F      58          3.245
LGA    K      73      G      59          5.192
LGA    K      74      G      60           -
LGA    V      75      I      61          5.326
LGA    T      76      L      62          1.859
LGA    T      79      D      63          3.909
LGA    G      80      L      64          3.186
LGA    -       -      F      65           -
LGA    E      81      E      66          1.611
LGA    D      82      E      67          1.749
LGA    V      83      G      68          1.171
LGA    A      84      A      69          2.721
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    A      85      K      73          1.472
LGA    F      86      K      74          4.897
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    C      87      D      77          1.382
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    -       -      V      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      F      86           -
LGA    -       -      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28   97    5.0     26    2.72     7.69     19.190     0.921

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.230121 * X  +   0.422916 * Y  +   0.876463 * Z  +  39.764030
  Y_new =  -0.450643 * X  +  -0.844561 * Y  +   0.289203 * Z  +  61.998646
  Z_new =   0.862534 * X  +  -0.328420 * Y  +   0.384935 * Z  + -75.939758 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.706339    2.435254  [ DEG:   -40.4702    139.5298 ]
  Theta =  -1.040257   -2.101336  [ DEG:   -59.6023   -120.3977 ]
  Phi   =  -2.042929    1.098664  [ DEG:  -117.0512     62.9488 ]
 
# 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: T0283AL381_5-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_5-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   97   5.0   26   2.72    7.69  19.190
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_5-D1
REMARK Aligment from pdb entry: 1nq4A
ATOM      1  N   PHE    58      21.290  23.806 -17.024  1.00  0.00              
ATOM      2  CA  PHE    58      20.474  24.421 -15.979  1.00  0.00              
ATOM      3  C   PHE    58      21.024  24.072 -14.603  1.00  0.00              
ATOM      4  O   PHE    58      21.100  24.917 -13.712  1.00  0.00              
ATOM      5  N   GLY    59      21.408  22.811 -14.444  1.00  0.00              
ATOM      6  CA  GLY    59      21.954  22.341 -13.172  1.00  0.00              
ATOM      7  C   GLY    59      23.215  23.118 -12.805  1.00  0.00              
ATOM      8  O   GLY    59      23.527  23.303 -11.629  1.00  0.00              
ATOM      9  N   GLY    60      23.939  23.570 -13.826  1.00  0.00              
ATOM     10  CA  GLY    60      25.164  24.324 -13.603  1.00  0.00              
ATOM     11  C   GLY    60      24.847  25.708 -13.048  1.00  0.00              
ATOM     12  O   GLY    60      25.190  26.032 -11.913  1.00  0.00              
ATOM     13  N   ILE    61      24.191  26.520 -13.875  1.00  0.00              
ATOM     14  CA  ILE    61      23.826  27.888 -13.488  1.00  0.00              
ATOM     15  C   ILE    61      23.091  27.920 -12.150  1.00  0.00              
ATOM     16  O   ILE    61      23.193  28.888 -11.397  1.00  0.00              
ATOM     17  N   LEU    62      22.340  26.863 -11.871  1.00  0.00              
ATOM     18  CA  LEU    62      21.576  26.788 -10.627  1.00  0.00              
ATOM     19  C   LEU    62      22.497  26.644  -9.417  1.00  0.00              
ATOM     20  O   LEU    62      22.413  27.418  -8.462  1.00  0.00              
ATOM     21  N   ASP    63      23.376  25.649  -9.465  1.00  0.00              
ATOM     22  CA  ASP    63      24.312  25.401  -8.382  1.00  0.00              
ATOM     23  C   ASP    63      25.174  26.631  -8.115  1.00  0.00              
ATOM     24  O   ASP    63      25.238  27.126  -6.990  1.00  0.00              
ATOM     25  N   LEU    64      25.840  27.128  -9.157  1.00  0.00              
ATOM     26  CA  LEU    64      26.692  28.314  -8.997  1.00  0.00              
ATOM     27  C   LEU    64      25.887  29.457  -8.383  1.00  0.00              
ATOM     28  O   LEU    64      26.402  30.234  -7.580  1.00  0.00              
ATOM     29  N   PHE    65      24.606  29.522  -8.739  1.00  0.00              
ATOM     30  CA  PHE    65      23.732  30.540  -8.178  1.00  0.00              
ATOM     31  C   PHE    65      23.462  30.184  -6.721  1.00  0.00              
ATOM     32  O   PHE    65      23.452  31.043  -5.839  1.00  0.00              
ATOM     33  N   GLU    66      23.266  28.887  -6.487  1.00  0.00              
ATOM     34  CA  GLU    66      23.019  28.381  -5.146  1.00  0.00              
ATOM     35  C   GLU    66      24.218  28.690  -4.243  1.00  0.00              
ATOM     36  O   GLU    66      24.059  29.137  -3.106  1.00  0.00              
ATOM     37  N   GLU    67      25.417  28.446  -4.766  1.00  0.00              
ATOM     38  CA  GLU    67      26.642  28.699  -4.005  1.00  0.00              
ATOM     39  C   GLU    67      26.731  30.176  -3.659  1.00  0.00              
ATOM     40  O   GLU    67      27.097  30.556  -2.546  1.00  0.00              
ATOM     41  N   GLY    68      26.385  30.999  -4.639  1.00  0.00              
ATOM     42  CA  GLY    68      26.414  32.452  -4.458  1.00  0.00              
ATOM     43  C   GLY    68      25.486  32.870  -3.323  1.00  0.00              
ATOM     44  O   GLY    68      25.909  33.494  -2.350  1.00  0.00              
ATOM     45  N   ALA    69      24.214  32.513  -3.462  1.00  0.00              
ATOM     46  CA  ALA    69      23.218  32.850  -2.447  1.00  0.00              
ATOM     47  C   ALA    69      23.584  32.216  -1.108  1.00  0.00              
ATOM     48  O   ALA    69      23.394  32.813  -0.049  1.00  0.00              
ATOM     49  N   ALA    70      24.114  30.997  -1.170  1.00  0.00              
ATOM     50  CA  ALA    70      24.507  30.285   0.044  1.00  0.00              
ATOM     51  C   ALA    70      23.431  29.289   0.468  1.00  0.00              
ATOM     52  O   ALA    70      23.280  28.986   1.652  1.00  0.00              
ATOM     53  N   GLU    71      22.685  28.782  -0.510  1.00  0.00              
ATOM     54  CA  GLU    71      21.628  27.820  -0.226  1.00  0.00              
ATOM     55  C   GLU    71      22.217  26.430  -0.012  1.00  0.00              
ATOM     56  O   GLU    71      23.433  26.241  -0.062  1.00  0.00              
ATOM     57  N   GLY    72      21.342  25.459   0.226  1.00  0.00              
ATOM     58  CA  GLY    72      21.785  24.085   0.447  1.00  0.00              
ATOM     59  C   GLY    72      21.183  23.156  -0.603  1.00  0.00              
ATOM     60  O   GLY    72      20.853  22.004  -0.322  1.00  0.00              
ATOM     61  N   LYS    73      21.050  23.675  -1.817  1.00  0.00              
ATOM     62  CA  LYS    73      20.491  22.900  -2.916  1.00  0.00              
ATOM     63  C   LYS    73      20.488  23.732  -4.197  1.00  0.00              
ATOM     64  O   LYS    73      19.829  24.768  -4.276  1.00  0.00              
ATOM     65  N   LYS    74      21.233  23.257  -5.204  1.00  0.00              
ATOM     66  CA  LYS    74      21.331  23.947  -6.503  1.00  0.00              
ATOM     67  C   LYS    74      19.970  24.463  -6.971  1.00  0.00              
ATOM     68  O   LYS    74      19.855  25.566  -7.505  1.00  0.00              
ATOM     69  N   VAL    75      18.943  23.649  -6.758  1.00  0.00              
ATOM     70  CA  VAL    75      17.592  24.021  -7.156  1.00  0.00              
ATOM     71  C   VAL    75      16.667  23.959  -5.943  1.00  0.00              
ATOM     72  O   VAL    75      15.897  23.014  -5.771  1.00  0.00              
ATOM     73  N   THR    76      16.758  24.987  -5.114  1.00  0.00              
ATOM     74  CA  THR    76      15.933  25.067  -3.912  1.00  0.00              
ATOM     75  C   THR    76      14.508  25.478  -4.274  1.00  0.00              
ATOM     76  O   THR    76      13.545  25.073  -3.624  1.00  0.00              
ATOM     77  N   THR    79      14.387  26.292  -5.323  1.00  0.00              
ATOM     78  CA  THR    79      13.075  26.761  -5.773  1.00  0.00              
ATOM     79  C   THR    79      12.154  25.583  -6.084  1.00  0.00              
ATOM     80  O   THR    79      10.935  25.676  -5.941  1.00  0.00              
ATOM     81  N   GLY    80      12.750  24.473  -6.511  1.00  0.00              
ATOM     82  CA  GLY    80      11.971  23.282  -6.837  1.00  0.00              
ATOM     83  C   GLY    80      12.340  22.755  -8.218  1.00  0.00              
ATOM     84  O   GLY    80      12.766  21.609  -8.368  1.00  0.00              
ATOM     85  N   GLU    81      12.172  23.605  -9.227  1.00  0.00              
ATOM     86  CA  GLU    81      12.489  23.214 -10.596  1.00  0.00              
ATOM     87  C   GLU    81      11.775  24.111 -11.603  1.00  0.00              
ATOM     88  O   GLU    81      12.260  24.328 -12.714  1.00  0.00              
ATOM     89  N   ASP    82      10.614  24.627 -11.207  1.00  0.00              
ATOM     90  CA  ASP    82       9.838  25.494 -12.083  1.00  0.00              
ATOM     91  C   ASP    82      10.345  26.934 -11.996  1.00  0.00              
ATOM     92  O   ASP    82       9.607  27.855 -11.639  1.00  0.00              
ATOM     93  N   VAL    83      11.619  27.118 -12.329  1.00  0.00              
ATOM     94  CA  VAL    83      12.223  28.446 -12.289  1.00  0.00              
ATOM     95  C   VAL    83      13.243  28.603 -13.421  1.00  0.00              
ATOM     96  O   VAL    83      14.211  29.357 -13.315  1.00  0.00              
ATOM     97  N   ALA    84      13.010  27.884 -14.516  1.00  0.00              
ATOM     98  CA  ALA    84      13.899  27.954 -15.664  1.00  0.00              
ATOM     99  C   ALA    84      13.496  29.106 -16.589  1.00  0.00              
ATOM    100  O   ALA    84      14.322  29.657 -17.316  1.00  0.00              
ATOM    101  N   ALA    85      12.212  29.459 -16.548  1.00  0.00              
ATOM    102  CA  ALA    85      11.699  30.541 -17.379  1.00  0.00              
ATOM    103  C   ALA    85      11.090  31.642 -16.511  1.00  0.00              
ATOM    104  O   ALA    85      10.215  32.388 -16.953  1.00  0.00              
ATOM    105  N   PHE    86      11.579  31.748 -15.276  1.00  0.00              
ATOM    106  CA  PHE    86      11.098  32.772 -14.357  1.00  0.00              
ATOM    107  C   PHE    86      12.208  33.787 -14.108  1.00  0.00              
ATOM    108  O   PHE    86      13.358  33.419 -13.863  1.00  0.00              
ATOM    109  N   CYS    87      11.862  35.070 -14.188  1.00  0.00              
ATOM    110  CA  CYS    87      12.851  36.134 -13.988  1.00  0.00              
ATOM    111  C   CYS    87      13.578  35.975 -12.654  1.00  0.00              
ATOM    112  O   CYS    87      13.020  35.481 -11.674  1.00  0.00              
END
