
#######################################################
#                                                     #
#                        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   27 (  132),  selected   27 , name T0306TS239_3_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_3_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    S      69      H      17          2.042
LGA    E      70      G      18          2.575
LGA    T      71      L      19          4.131
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    S      72      I      44          3.766
LGA    P      73      D      45          2.989
LGA    V      74      N      46          3.387
LGA    -       -      I      47           -
LGA    D      75      G      48           #
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    L      76      E      53           #
LGA    C      77      W      54          3.714
LGA    V      78      V      55          4.228
LGA    I      79      L      56           -
LGA    G      80      -       -           -
LGA    I      81      -       -           -
LGA    V      82      -       -           -
LGA    D      83      -       -           -
LGA    E      84      L      57          1.486
LGA    V      85      V      58          5.324
LGA    V      86      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    S      87      R      64           #
LGA    -       -      Q      65           -
LGA    G      88      A      66          4.631
LGA    G      89      H      67          3.444
LGA    Q      90      K      68          2.573
LGA    V      91      S      69          1.563
LGA    I      92      E      70          2.210
LGA    F      93      T      71          3.729
LGA    -       -      S      72           -
LGA    H      94      P      73          4.602
LGA    K      95      V      74          3.562
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   95    5.0     18    3.49    11.11     10.907     0.501

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.304400 * X  +   0.354713 * Y  +  -0.884036 * Z  +  97.304787
  Y_new =   0.624693 * X  +   0.774965 * Y  +   0.095849 * Z  +  26.528549
  Z_new =   0.719096 * X  +  -0.523075 * Y  +  -0.457486 * Z  +  70.210556 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.289405    0.852187  [ DEG:  -131.1733     48.8267 ]
  Theta =  -0.802500   -2.339092  [ DEG:   -45.9799   -134.0201 ]
  Phi   =   2.024216   -1.117377  [ DEG:   115.9790    -64.0210 ]
 
# 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: T0306TS239_3_2                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_3_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   95   5.0   18   3.49   11.11  10.907
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0306
PARENT 1fnf
ATOM      1  N   SER    69      19.815  23.206  61.545  1.00  9.99
ATOM      2  CA  SER    69      21.024  23.046  62.384  1.00  9.99
ATOM      3  C   SER    69      22.094  24.003  61.902  1.00  9.99
ATOM      4  O   SER    69      21.896  24.708  60.911  1.00  9.99
ATOM      5  CB  SER    69      21.487  21.595  62.280  1.00  9.99
ATOM      6  N   GLU    70      23.206  24.047  62.624  1.00  9.99
ATOM      7  CA  GLU    70      24.305  24.936  62.279  1.00  9.99
ATOM      8  C   GLU    70      25.507  24.110  61.843  1.00  9.99
ATOM      9  O   GLU    70      25.759  23.032  62.389  1.00  9.99
ATOM     10  CB  GLU    70      24.681  25.785  63.498  1.00  9.99
ATOM     11  N   THR    71      26.193  24.567  60.806  1.00  9.99
ATOM     12  CA  THR    71      27.382  23.885  60.324  1.00  9.99
ATOM     13  C   THR    71      28.514  24.498  61.139  1.00  9.99
ATOM     14  O   THR    71      28.546  25.711  61.362  1.00  9.99
ATOM     15  CB  THR    71      27.590  24.142  58.839  1.00  9.99
ATOM     16  N   SER    72      29.411  23.663  61.664  1.00  9.99
ATOM     17  CA  SER    72      30.533  24.141  62.471  1.00  9.99
ATOM     18  C   SER    72      31.615  24.849  61.657  1.00  9.99
ATOM     19  O   SER    72      31.547  24.907  60.422  1.00  9.99
ATOM     20  CB  SER    72      31.080  22.844  63.056  1.00  9.99
ATOM     21  N   PRO    73      32.585  25.482  62.346  1.00  9.99
ATOM     22  CA  PRO    73      33.644  26.149  61.587  1.00  9.99
ATOM     23  C   PRO    73      34.508  25.016  61.028  1.00  9.99
ATOM     24  O   PRO    73      34.367  23.849  61.437  1.00  9.99
ATOM     25  CB  PRO    73      34.407  26.913  62.671  1.00  9.99
ATOM     26  N   VAL    74      35.351  25.327  60.057  1.00  9.99
ATOM     27  CA  VAL    74      36.241  24.324  59.496  1.00  9.99
ATOM     28  C   VAL    74      37.595  24.993  59.427  1.00  9.99
ATOM     29  O   VAL    74      37.713  26.164  59.771  1.00  9.99
ATOM     30  CB  VAL    74      35.868  23.965  58.072  1.00  9.99
ATOM     31  N   ASP    75      38.610  24.248  59.002  1.00  9.99
ATOM     32  CA  ASP    75      39.953  24.795  58.839  1.00  9.99
ATOM     33  C   ASP    75      40.415  25.509  60.099  1.00  9.99
ATOM     34  O   ASP    75      40.683  26.712  60.084  1.00  9.99
ATOM     35  CB  ASP    75      39.960  25.766  57.657  1.00  9.99
ATOM     36  N   LEU    76      40.463  24.762  61.196  1.00  9.99
ATOM     37  CA  LEU    76      40.878  25.310  62.482  1.00  9.99
ATOM     38  C   LEU    76      42.403  25.383  62.524  1.00  9.99
ATOM     39  O   LEU    76      43.088  24.438  62.112  1.00  9.99
ATOM     40  CB  LEU    76      40.361  24.412  63.610  1.00  9.99
ATOM     41  N   CYS    77      42.926  26.525  62.959  1.00  9.99
ATOM     42  CA  CYS    77      44.371  26.722  63.070  1.00  9.99
ATOM     43  C   CYS    77      44.719  27.191  64.474  1.00  9.99
ATOM     44  O   CYS    77      44.068  28.082  65.019  1.00  9.99
ATOM     45  CB  CYS    77      44.889  27.722  62.024  1.00  9.99
ATOM     46  N   VAL    78      45.713  26.546  65.073  1.00  9.99
ATOM     47  CA  VAL    78      46.163  26.877  66.424  1.00  9.99
ATOM     48  C   VAL    78      47.613  27.350  66.372  1.00  9.99
ATOM     49  O   VAL    78      48.489  26.606  65.927  1.00  9.99
ATOM     50  CB  VAL    78      46.050  25.646  67.326  1.00  9.99
ATOM     51  N   ILE    79      47.857  28.585  66.809  1.00  9.99
ATOM     52  CA  ILE    79      49.204  29.157  66.795  1.00  9.99
ATOM     53  C   ILE    79      49.617  29.634  68.176  1.00  9.99
ATOM     54  O   ILE    79      49.128  30.654  68.657  1.00  9.99
ATOM     55  CB  ILE    79      49.277  30.326  65.812  1.00  9.99
ATOM     56  N   GLY    80      50.514  28.887  68.811  1.00  9.99
ATOM     57  CA  GLY    80      51.000  29.229  70.145  1.00  9.99
ATOM     58  C   GLY    80      52.356  29.914  70.065  1.00  9.99
ATOM     59  O   GLY    80      53.291  29.401  69.444  1.00  9.99
ATOM     60  N   ILE    81      52.449  31.088  70.679  1.00  9.99
ATOM     61  CA  ILE    81      53.689  31.846  70.698  1.00  9.99
ATOM     62  C   ILE    81      54.713  31.055  71.506  1.00  9.99
ATOM     63  O   ILE    81      54.397  30.569  72.592  1.00  9.99
ATOM     64  CB  ILE    81      53.449  33.202  71.358  1.00  9.99
ATOM     65  N   VAL    82      55.938  30.882  70.971  1.00  9.99
ATOM     66  CA  VAL    82      57.034  30.147  71.620  1.00  9.99
ATOM     67  C   VAL    82      57.136  30.471  73.106  1.00  9.99
ATOM     68  O   VAL    82      57.152  29.575  73.952  1.00  9.99
ATOM     69  CB  VAL    82      58.250  30.626  70.843  1.00  9.99
ATOM     70  N   ASP    83      57.241  31.756  73.413  1.00  9.99
ATOM     71  CA  ASP    83      57.282  32.219  74.793  1.00  9.99
ATOM     72  C   ASP    83      55.800  32.317  75.152  1.00  9.99
ATOM     73  O   ASP    83      55.190  33.389  75.093  1.00  9.99
ATOM     74  CB  ASP    83      57.988  33.578  74.897  1.00  9.99
ATOM     75  N   GLU    84      42.260  30.433  64.814  1.00  9.99
ATOM     76  CA  GLU    84      41.645  30.902  63.575  1.00  9.99
ATOM     77  C   GLU    84      40.849  29.784  62.898  1.00  9.99
ATOM     78  O   GLU    84      41.185  28.598  63.016  1.00  9.99
ATOM     79  CB  GLU    84      42.707  31.446  62.618  1.00  9.99
ATOM     80  N   VAL    85      39.802  30.155  62.176  1.00  9.99
ATOM     81  CA  VAL    85      38.978  29.157  61.515  1.00  9.99
ATOM     82  C   VAL    85      38.259  29.717  60.300  1.00  9.99
ATOM     83  O   VAL    85      38.165  30.934  60.103  1.00  9.99
ATOM     84  CB  VAL    85      37.929  28.614  62.499  1.00  9.99
ATOM     85  N   VAL    86      37.803  28.807  59.458  1.00  9.99
ATOM     86  CA  VAL    86      37.033  29.157  58.285  1.00  9.99
ATOM     87  C   VAL    86      35.630  29.306  58.875  1.00  9.99
ATOM     88  O   VAL    86      35.205  28.502  59.711  1.00  9.99
ATOM     89  CB  VAL    86      37.081  28.012  57.278  1.00  9.99
ATOM     90  N   SER    87      34.923  30.353  58.484  1.00  9.99
ATOM     91  CA  SER    87      33.593  30.590  59.025  1.00  9.99
ATOM     92  C   SER    87      32.576  29.516  58.630  1.00  9.99
ATOM     93  O   SER    87      32.746  28.853  57.600  1.00  9.99
ATOM     94  CB  SER    87      33.098  31.950  58.563  1.00  9.99
ATOM     95  N   GLY    88      31.530  29.357  59.447  1.00  9.99
ATOM     96  CA  GLY    88      30.443  28.405  59.184  1.00  9.99
ATOM     97  C   GLY    88      29.803  28.792  57.852  1.00  9.99
ATOM     98  O   GLY    88      29.920  29.939  57.409  1.00  9.99
ATOM     99  N   GLY    89      29.170  27.831  57.189  1.00  9.99
ATOM    100  CA  GLY    89      28.510  28.102  55.922  1.00  9.99
ATOM    101  C   GLY    89      27.003  28.271  56.127  1.00  9.99
ATOM    102  O   GLY    89      26.229  28.297  55.163  1.00  9.99
ATOM    103  N   GLN    90      26.598  28.360  57.392  1.00  9.99
ATOM    104  CA  GLN    90      25.198  28.559  57.760  1.00  9.99
ATOM    105  C   GLN    90      25.000  30.054  57.901  1.00  9.99
ATOM    106  O   GLN    90      25.772  30.715  58.609  1.00  9.99
ATOM    107  CB  GLN    90      24.884  27.929  59.135  1.00  9.99
ATOM    108  N   VAL    91      24.015  30.628  57.189  1.00  9.99
ATOM    109  CA  VAL    91      23.807  32.073  57.326  1.00  9.99
ATOM    110  C   VAL    91      22.933  32.400  58.550  1.00  9.99
ATOM    111  O   VAL    91      22.386  31.505  59.198  1.00  9.99
ATOM    112  CB  VAL    91      23.096  32.429  56.027  1.00  9.99
ATOM    113  N   ILE    92      22.881  33.675  58.913  1.00  9.99
ATOM    114  CA  ILE    92      22.053  34.142  60.018  1.00  9.99
ATOM    115  C   ILE    92      22.414  33.694  61.433  1.00  9.99
ATOM    116  O   ILE    92      21.542  33.614  62.313  1.00  9.99
ATOM    117  CB  ILE    92      20.582  33.832  59.713  1.00  9.99
ATOM    118  N   PHE    93      23.698  33.433  61.660  1.00  9.99
ATOM    119  CA  PHE    93      24.172  33.034  62.975  1.00  9.99
ATOM    120  C   PHE    93      24.607  34.295  63.756  1.00  9.99
ATOM    121  O   PHE    93      24.772  35.377  63.179  1.00  9.99
ATOM    122  CB  PHE    93      25.288  31.955  62.868  1.00  9.99
ATOM    123  N   HIS    94      24.783  34.171  65.065  1.00  9.99
ATOM    124  CA  HIS    94      25.139  35.322  65.899  1.00  9.99
ATOM    125  C   HIS    94      26.562  35.416  66.472  1.00  9.99
ATOM    126  O   HIS    94      26.902  36.403  67.124  1.00  9.99
ATOM    127  CB  HIS    94      24.163  35.424  67.051  1.00  9.99
ATOM    128  N   LYS    95      27.376  34.388  66.275  1.00  9.99
ATOM    129  CA  LYS    95      28.727  34.440  66.791  1.00  9.99
ATOM    130  C   LYS    95      29.437  33.110  66.813  1.00  9.99
ATOM    131  O   LYS    95      29.043  32.161  66.128  1.00  9.99
ATOM    132  CB  LYS    95      28.682  35.045  68.204  1.00  9.99
TER
END
