
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0331AL044_3
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331AL044_3.T0331.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      19      M       1           -
LGA    T      20      E       2           -
LGA    L      21      L       3           -
LGA    D      22      K       4           -
LGA    E      23      D       5           -
LGA    G      25      I       6           -
LGA    -       -      M       7           -
LGA    -       -      H       8           -
LGA    -       -      I       9           -
LGA    -       -      L      10           -
LGA    -       -      E      11           -
LGA    -       -      D      12           -
LGA    -       -      M      13           -
LGA    -       -      K      14           -
LGA    -       -      V      15           -
LGA    -       -      G      16           -
LGA    -       -      V      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      T      20           -
LGA    -       -      L      21           -
LGA    A      29      D      22          4.946
LGA    R      30      E      23          5.165
LGA    -       -      Y      24           -
LGA    -       -      G      25           -
LGA    H      31      N      26          1.392
LGA    A      32      P      27          3.632
LGA    H      33      H      28           -
LGA    I      34      -       -           -
LGA    T      35      -       -           -
LGA    A      36      A      29           #
LGA    -       -      R      30           -
LGA    -       -      H      31           -
LGA    -       -      A      32           -
LGA    -       -      H      33           -
LGA    -       -      I      34           -
LGA    -       -      T      35           -
LGA    -       -      A      36           -
LGA    -       -      A      37           -
LGA    -       -      N      38           -
LGA    -       -      E      39           -
LGA    -       -      E      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      F      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      T      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      E      49           -
LGA    -       -      T      50           -
LGA    -       -      H      51           -
LGA    -       -      F      52           -
LGA    -       -      Y      53           -
LGA    -       -      D      54           -
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      M      57           -
LGA    -       -      G      58           -
LGA    -       -      D      59           -
LGA    -       -      Q      60           -
LGA    A      37      R      61          2.455
LGA    N      38      V      62          3.157
LGA    E      39      A      63          1.855
LGA    -       -      M      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      I      67           -
LGA    -       -      S      68           -
LGA    -       -      E      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      V      77           -
LGA    -       -      R      78           -
LGA    -       -      V      79           -
LGA    -       -      E      80           -
LGA    -       -      G      81           -
LGA    -       -      T      82           -
LGA    E      40      A      83          4.620
LGA    G      41      R      84          2.647
LGA    I      42      P      85          4.346
LGA    F      43      V      86          2.987
LGA    -       -      E      87           -
LGA    F      44      N      88          3.019
LGA    M      45      D      89          1.293
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    T      46      K      92          2.121
LGA    S      47      T      93          1.558
LGA    P      48      V      94          1.877
LGA    E      49      F      95          2.723
LGA    T      50      A      96          1.271
LGA    H      51      D      97           #
LGA    F      52      -       -           -
LGA    Y      53      -       -           -
LGA    D      54      N      98          3.664
LGA    Q      55      P      99          1.878
LGA    L      56      Y     100           -
LGA    M      57      Y     101           -
LGA    G      58      Q     102           -
LGA    -       -      H     103           -
LGA    -       -      I     104           -
LGA    -       -      Y     105           -
LGA    -       -      K     106           -
LGA    -       -      T     112           -
LGA    -       -      M     113           -
LGA    -       -      Q     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      Q     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      A     120           -
LGA    -       -      G     121           -
LGA    -       -      H     122           -
LGA    -       -      G     123           -
LGA    -       -      F     124           -
LGA    -       -      Y     125           -
LGA    -       -      H     126           -
LGA    -       -      S     127           -
LGA    -       -      L     128           -
LGA    -       -      T     129           -
LGA    -       -      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    -       -      Y     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      S     137           -
LGA    -       -      I     138           -
LGA    -       -      G     139           -
LGA    -       -      E     145           -
LGA    -       -      V     146           -
LGA    -       -      R     147           -
LGA    -       -      A     148           -
LGA    -       -      L     149           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36  139    5.0     20    3.07     0.00      9.011     0.630

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.640348 * X  +   0.498418 * Y  +   0.584410 * Z  +  12.729314
  Y_new =  -0.759794 * X  +   0.522535 * Y  +   0.386872 * Z  +  62.443829
  Z_new =  -0.112551 * X  +  -0.691763 * Y  +   0.713299 * Z  +  70.723625 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.770072    2.371521  [ DEG:   -44.1219    135.8781 ]
  Theta =   0.112790    3.028803  [ DEG:     6.4624    173.5376 ]
  Phi   =  -0.870502    2.271090  [ DEG:   -49.8761    130.1239 ]
 
# 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: T0331AL044_3                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331AL044_3.T0331.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36  139   5.0   20   3.07    0.00   9.011
REMARK  ---------------------------------------------------------- 
MOLECULE T0331AL044_3
REMARK Aligment from pdb entry: 1kf6_B
ATOM      1  N   ALA    19      34.011  34.180  45.150  1.00  0.00              
ATOM      2  CA  ALA    19      35.108  35.138  45.047  1.00  0.00              
ATOM      3  C   ALA    19      34.905  36.409  45.889  1.00  0.00              
ATOM      4  O   ALA    19      33.793  36.967  45.927  1.00  0.00              
ATOM      5  N   THR    20      35.956  36.883  46.554  1.00  0.00              
ATOM      6  CA  THR    20      35.887  38.068  47.385  1.00  0.00              
ATOM      7  C   THR    20      36.795  39.152  46.816  1.00  0.00              
ATOM      8  O   THR    20      37.763  38.860  46.090  1.00  0.00              
ATOM      9  N   LEU    21      36.479  40.406  47.144  1.00  0.00              
ATOM     10  CA  LEU    21      37.199  41.557  46.607  1.00  0.00              
ATOM     11  C   LEU    21      38.707  41.475  46.604  1.00  0.00              
ATOM     12  O   LEU    21      39.352  41.846  45.618  1.00  0.00              
ATOM     13  N   ASP    22      39.280  41.003  47.693  1.00  0.00              
ATOM     14  CA  ASP    22      40.740  40.878  47.830  1.00  0.00              
ATOM     15  C   ASP    22      41.400  39.951  46.813  1.00  0.00              
ATOM     16  O   ASP    22      42.585  40.090  46.518  1.00  0.00              
ATOM     17  N   GLU    23      40.645  39.001  46.247  1.00  0.00              
ATOM     18  CA  GLU    23      41.224  38.096  45.260  1.00  0.00              
ATOM     19  C   GLU    23      41.219  38.702  43.866  1.00  0.00              
ATOM     20  O   GLU    23      41.718  38.078  42.928  1.00  0.00              
ATOM     21  N   GLY    25      40.683  39.918  43.729  1.00  0.00              
ATOM     22  CA  GLY    25      40.655  40.547  42.416  1.00  0.00              
ATOM     23  C   GLY    25      39.336  40.238  41.727  1.00  0.00              
ATOM     24  O   GLY    25      38.501  39.498  42.286  1.00  0.00              
ATOM     25  N   ALA    29      39.132  40.759  40.525  1.00  0.00              
ATOM     26  CA  ALA    29      37.860  40.510  39.861  1.00  0.00              
ATOM     27  C   ALA    29      37.855  39.181  39.138  1.00  0.00              
ATOM     28  O   ALA    29      38.871  38.489  39.010  1.00  0.00              
ATOM     29  N   ARG    30      36.677  38.803  38.665  1.00  0.00              
ATOM     30  CA  ARG    30      36.537  37.577  37.886  1.00  0.00              
ATOM     31  C   ARG    30      37.226  37.856  36.546  1.00  0.00              
ATOM     32  O   ARG    30      37.458  38.988  36.183  1.00  0.00              
ATOM     33  N   HIS    31      37.557  36.802  35.815  1.00  0.00              
ATOM     34  CA  HIS    31      38.138  36.917  34.491  1.00  0.00              
ATOM     35  C   HIS    31      36.987  36.604  33.574  1.00  0.00              
ATOM     36  O   HIS    31      36.283  35.658  33.840  1.00  0.00              
ATOM     37  N   ALA    32      36.754  37.453  32.573  1.00  0.00              
ATOM     38  CA  ALA    32      35.646  37.264  31.655  1.00  0.00              
ATOM     39  C   ALA    32      36.115  37.918  30.356  1.00  0.00              
ATOM     40  O   ALA    32      36.599  39.037  30.336  1.00  0.00              
ATOM     41  N   HIS    33      35.972  37.236  29.260  1.00  0.00              
ATOM     42  CA  HIS    33      36.507  37.712  28.018  1.00  0.00              
ATOM     43  C   HIS    33      35.469  38.376  27.158  1.00  0.00              
ATOM     44  O   HIS    33      34.243  38.244  27.358  1.00  0.00              
ATOM     45  N   ILE    34      35.942  39.096  26.169  1.00  0.00              
ATOM     46  CA  ILE    34      34.907  39.700  25.329  1.00  0.00              
ATOM     47  C   ILE    34      33.926  38.607  24.890  1.00  0.00              
ATOM     48  O   ILE    34      32.711  38.759  24.954  1.00  0.00              
ATOM     49  N   THR    35      34.455  37.463  24.474  1.00  0.00              
ATOM     50  CA  THR    35      33.617  36.363  23.975  1.00  0.00              
ATOM     51  C   THR    35      32.610  35.940  25.021  1.00  0.00              
ATOM     52  O   THR    35      31.464  35.708  24.685  1.00  0.00              
ATOM     53  N   ALA    36      33.019  35.842  26.282  1.00  0.00              
ATOM     54  CA  ALA    36      32.038  35.473  27.310  1.00  0.00              
ATOM     55  C   ALA    36      30.947  36.563  27.536  1.00  0.00              
ATOM     56  O   ALA    36      29.787  36.265  27.763  1.00  0.00              
ATOM     57  N   ALA    37      31.335  37.821  27.490  1.00  0.00              
ATOM     58  CA  ALA    37      30.431  38.933  27.719  1.00  0.00              
ATOM     59  C   ALA    37      29.419  39.071  26.595  1.00  0.00              
ATOM     60  O   ALA    37      28.286  39.450  26.824  1.00  0.00              
ATOM     61  N   ASN    38      29.840  38.752  25.379  1.00  0.00              
ATOM     62  CA  ASN    38      28.990  38.876  24.200  1.00  0.00              
ATOM     63  C   ASN    38      27.734  38.012  24.328  1.00  0.00              
ATOM     64  O   ASN    38      26.677  38.275  23.717  1.00  0.00              
ATOM     65  N   GLU    39      27.872  36.974  25.127  1.00  0.00              
ATOM     66  CA  GLU    39      26.789  36.042  25.369  1.00  0.00              
ATOM     67  C   GLU    39      25.563  36.745  25.960  1.00  0.00              
ATOM     68  O   GLU    39      24.449  36.419  25.565  1.00  0.00              
ATOM     69  N   GLU    40      25.776  37.743  26.842  1.00  0.00              
ATOM     70  CA  GLU    40      24.671  38.437  27.472  1.00  0.00              
ATOM     71  C   GLU    40      24.649  39.943  27.312  1.00  0.00              
ATOM     72  O   GLU    40      23.671  40.606  27.620  1.00  0.00              
ATOM     73  N   GLY    41      21.247  45.928  28.287  1.00  0.00              
ATOM     74  CA  GLY    41      20.952  47.276  27.989  1.00  0.00              
ATOM     75  C   GLY    41      19.554  47.736  28.342  1.00  0.00              
ATOM     76  O   GLY    41      19.153  48.822  27.937  1.00  0.00              
ATOM     77  N   ILE    42      18.810  46.939  29.097  1.00  0.00              
ATOM     78  CA  ILE    42      17.462  47.266  29.422  1.00  0.00              
ATOM     79  C   ILE    42      17.316  48.387  30.450  1.00  0.00              
ATOM     80  O   ILE    42      17.815  48.301  31.564  1.00  0.00              
ATOM     81  N   PHE    43      16.546  49.406  30.120  1.00  0.00              
ATOM     82  CA  PHE    43      16.354  50.522  30.983  1.00  0.00              
ATOM     83  C   PHE    43      15.040  50.465  31.741  1.00  0.00              
ATOM     84  O   PHE    43      14.576  51.453  32.308  1.00  0.00              
ATOM     85  N   PHE    44      14.449  49.293  31.774  1.00  0.00              
ATOM     86  CA  PHE    44      13.190  49.085  32.516  1.00  0.00              
ATOM     87  C   PHE    44      12.129  50.109  32.200  1.00  0.00              
ATOM     88  O   PHE    44      11.388  50.462  33.057  1.00  0.00              
ATOM     89  N   MET    45      12.022  50.536  30.953  1.00  0.00              
ATOM     90  CA  MET    45      11.075  51.553  30.559  1.00  0.00              
ATOM     91  C   MET    45       9.663  50.988  30.402  1.00  0.00              
ATOM     92  O   MET    45       8.696  51.730  30.373  1.00  0.00              
ATOM     93  N   THR    46       9.533  49.678  30.242  1.00  0.00              
ATOM     94  CA  THR    46       8.226  49.077  30.093  1.00  0.00              
ATOM     95  C   THR    46       7.548  49.173  28.736  1.00  0.00              
ATOM     96  O   THR    46       6.369  48.803  28.642  1.00  0.00              
ATOM     97  N   SER    47       8.211  49.647  27.673  1.00  0.00              
ATOM     98  CA  SER    47       7.494  49.742  26.413  1.00  0.00              
ATOM     99  C   SER    47       7.186  48.338  25.869  1.00  0.00              
ATOM    100  O   SER    47       6.193  48.134  25.153  1.00  0.00              
ATOM    101  N   PRO    48       8.006  47.347  26.208  1.00  0.00              
ATOM    102  CA  PRO    48       7.740  46.014  25.743  1.00  0.00              
ATOM    103  C   PRO    48       6.476  45.419  26.396  1.00  0.00              
ATOM    104  O   PRO    48       5.796  44.580  25.775  1.00  0.00              
ATOM    105  N   GLU    49       6.130  45.855  27.613  1.00  0.00              
ATOM    106  CA  GLU    49       4.923  45.345  28.243  1.00  0.00              
ATOM    107  C   GLU    49       3.710  45.963  27.564  1.00  0.00              
ATOM    108  O   GLU    49       2.628  45.374  27.506  1.00  0.00              
ATOM    109  N   THR    50       3.877  47.152  27.024  1.00  0.00              
ATOM    110  CA  THR    50       2.745  47.794  26.358  1.00  0.00              
ATOM    111  C   THR    50       2.574  47.178  24.986  1.00  0.00              
ATOM    112  O   THR    50       1.488  47.192  24.421  1.00  0.00              
ATOM    113  N   HIS    51       3.666  46.663  24.426  1.00  0.00              
ATOM    114  CA  HIS    51       3.632  46.124  23.078  1.00  0.00              
ATOM    115  C   HIS    51       3.125  44.696  23.027  1.00  0.00              
ATOM    116  O   HIS    51       2.508  44.276  22.054  1.00  0.00              
ATOM    117  N   PHE    52       3.377  43.957  24.092  1.00  0.00              
ATOM    118  CA  PHE    52       2.993  42.576  24.165  1.00  0.00              
ATOM    119  C   PHE    52       1.529  42.307  24.332  1.00  0.00              
ATOM    120  O   PHE    52       0.972  42.616  25.358  1.00  0.00              
ATOM    121  N   TYR    53       0.883  41.661  23.360  1.00  0.00              
ATOM    122  CA  TYR    53      -0.543  41.373  23.484  1.00  0.00              
ATOM    123  C   TYR    53      -0.815  40.237  24.470  1.00  0.00              
ATOM    124  O   TYR    53      -1.895  40.130  25.016  1.00  0.00              
ATOM    125  N   ASP    54       0.194  39.414  24.710  1.00  0.00              
ATOM    126  CA  ASP    54       0.100  38.304  25.618  1.00  0.00              
ATOM    127  C   ASP    54       0.014  38.825  27.028  1.00  0.00              
ATOM    128  O   ASP    54      -0.684  38.241  27.861  1.00  0.00              
ATOM    129  N   GLN    55       0.736  39.905  27.304  1.00  0.00              
ATOM    130  CA  GLN    55       0.700  40.504  28.626  1.00  0.00              
ATOM    131  C   GLN    55      -0.660  41.192  28.842  1.00  0.00              
ATOM    132  O   GLN    55      -1.226  41.143  29.932  1.00  0.00              
ATOM    133  N   LEU    56      -1.186  41.823  27.803  1.00  0.00              
ATOM    134  CA  LEU    56      -2.483  42.446  27.896  1.00  0.00              
ATOM    135  C   LEU    56      -3.575  41.403  28.099  1.00  0.00              
ATOM    136  O   LEU    56      -4.637  41.725  28.599  1.00  0.00              
ATOM    137  N   MET    57      -3.346  40.156  27.708  1.00  0.00              
ATOM    138  CA  MET    57      -4.363  39.129  27.836  1.00  0.00              
ATOM    139  C   MET    57      -4.126  38.365  29.108  1.00  0.00              
ATOM    140  O   MET    57      -5.035  37.726  29.605  1.00  0.00              
ATOM    141  N   GLY    58      -2.902  38.414  29.619  1.00  0.00              
ATOM    142  CA  GLY    58      -2.530  37.676  30.821  1.00  0.00              
ATOM    143  C   GLY    58      -1.646  38.531  31.723  1.00  0.00              
ATOM    144  O   GLY    58      -0.412  38.424  31.736  1.00  0.00              
END
