
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0363TS168_2
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS168_2.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      L      10           -
LGA    A       2      N      11           -
LGA    H       3      Q      12           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      -       -           -
LGA    N      11      -       -           -
LGA    Q      12      I      13           #
LGA    I      13      N      14          3.622
LGA    N      14      -       -           -
LGA    I      15      I      15          1.414
LGA    E      16      E      16          2.018
LGA    I      17      I      17          2.803
LGA    A      18      A      18          3.553
LGA    Y      19      -       -           -
LGA    A      20      Y      19          4.198
LGA    F      21      A      20          2.842
LGA    P      22      F      21          1.780
LGA    E      23      P      22          2.208
LGA    R      24      E      23          3.069
LGA    Y      25      R      24          0.924
LGA    Y      26      Y      25          1.021
LGA    L      27      Y      26          3.367
LGA    K      28      L      27          2.226
LGA    S      29      K      28          2.692
LGA    F      30      S      29          1.454
LGA    Q      31      F      30          2.944
LGA    V      32      Q      31          2.598
LGA    D      33      V      32          1.748
LGA    E      34      D      33          0.707
LGA    G      35      E      34          4.413
LGA    I      36      G      35          3.131
LGA    T      37      I      36          4.757
LGA    V      38      T      37           #
LGA    Q      39      V      38          4.355
LGA    T      40      Q      39           #
LGA    A      41      T      40          4.125
LGA    I      42      A      41          2.951
LGA    T      43      I      42          4.590
LGA    Q      44      T      43          1.761
LGA    S      45      Q      44           #
LGA    G      46      S      45           -
LGA    I      47      G      46           -
LGA    L      48      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    S      49      I      54          4.994
LGA    Q      50      D      55          2.483
LGA    F      51      L      56          1.434
LGA    P      52      S      57          2.011
LGA    E      53      T      58          2.299
LGA    -       -      N      59           -
LGA    I      54      K      60          5.062
LGA    D      55      -       -           -
LGA    L      56      -       -           -
LGA    S      57      -       -           -
LGA    T      58      I      61           #
LGA    N      59      G      62          3.377
LGA    K      60      I      63          3.017
LGA    I      61      -       -           -
LGA    G      62      -       -           -
LGA    I      63      -       -           -
LGA    F      64      -       -           -
LGA    S      65      -       -           -
LGA    R      66      -       -           -
LGA    P      67      -       -           -
LGA    I      68      -       -           -
LGA    K      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    L      74      -       -           -
LGA    K      75      -       -           -
LGA    E      76      -       -           -
LGA    G      77      -       -           -
LGA    D      78      -       -           -
LGA    R      79      -       -           -
LGA    I      80      -       -           -
LGA    E      81      -       -           -
LGA    I      82      -       -           -
LGA    Y      83      -       -           -
LGA    R      84      F      64          5.036
LGA    P      85      S      65           #
LGA    L      86      R      66           #
LGA    L      87      P      67           -
LGA    A      88      I      68           -
LGA    D      89      K      69           -
LGA    P      90      L      70           -
LGA    K      91      T      71           -
LGA    E      92      D      72           -
LGA    I      93      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    -       -      D      78           -
LGA    -       -      R      79           -
LGA    -       -      I      80           -
LGA    R      94      E      81          3.766
LGA    R      95      I      82          2.454
LGA    E      96      Y      83          4.821
LGA    G      97      R      84           -
LGA    -       -      P      85           -
LGA    -       -      L      86           -
LGA    -       -      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   80    5.0     40    3.19    12.50     30.044     1.215

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.594874 * X  +   0.734850 * Y  +  -0.325762 * Z  +  22.576756
  Y_new =   0.435782 * X  +   0.045708 * Y  +   0.898891 * Z  +  13.956586
  Z_new =   0.675440 * X  +  -0.676688 * Y  +  -0.293044 * Z  +   6.135550 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.979471    1.162121  [ DEG:  -113.4153     66.5847 ]
  Theta =  -0.741561   -2.400032  [ DEG:   -42.4883   -137.5117 ]
  Phi   =   0.632247   -2.509345  [ DEG:    36.2251   -143.7749 ]
 
# 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: T0363TS168_2                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_2.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   80   5.0   40   3.19   12.50  30.044
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_2
PFRMAT TS
TARGET T0363
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1       0.257  -3.077  25.088  1.00 25.00           C
ATOM      2  CA  ALA     2      -1.093   0.477  24.813  1.00 25.00           C
ATOM      3  CA  HIS     3       0.259   2.173  21.637  1.00 25.00           C
ATOM      4  CA  HIS     4       2.992   4.328  23.168  1.00 25.00           C
ATOM      5  CA  HIS     5       2.695   8.072  22.552  1.00 25.00           C
ATOM      6  CA  HIS     6       2.530   9.666  19.166  1.00 25.00           C
ATOM      7  CA  HIS     7       2.687  10.349  15.446  1.00 25.00           C
ATOM      8  CA  HIS     8       2.171   9.676  11.710  1.00 25.00           C
ATOM      9  CA  SER     9       1.471   7.513   8.638  1.00 25.00           C
ATOM     10  CA  LEU    10       4.172   5.117   7.271  1.00 25.00           C
ATOM     11  CA  ASN    11       7.869   5.894   7.782  1.00 25.00           C
ATOM     12  CA  GLN    12      11.334   7.467   7.739  1.00 25.00           C
ATOM     13  CA  ILE    13      14.761   9.038   8.050  1.00 25.00           C
ATOM     14  CA  ASN    14      17.537  10.346  10.321  1.00 25.00           C
ATOM     15  CA  ILE    15      19.789  12.000   7.761  1.00 25.00           C
ATOM     16  CA  GLU    16      20.807  15.255   6.039  1.00 25.00           C
ATOM     17  CA  ILE    17      22.721  17.524   3.587  1.00 25.00           C
ATOM     18  CA  ALA    18      25.471  16.203   1.255  1.00 25.00           C
ATOM     19  CA  TYR    19      28.083  15.722  -1.481  1.00 25.00           C
ATOM     20  CA  ALA    20      30.322  18.723  -0.616  1.00 25.00           C
ATOM     21  CA  PHE    21      30.480  22.508  -0.954  1.00 25.00           C
ATOM     22  CA  PRO    22      32.944  23.990  -3.456  1.00 25.00           C
ATOM     23  CA  GLU    23      32.371  27.162  -5.420  1.00 25.00           C
ATOM     24  CA  ARG    24      31.667  25.016  -8.429  1.00 25.00           C
ATOM     25  CA  TYR    25      28.762  23.783  -6.330  1.00 25.00           C
ATOM     26  CA  TYR    26      26.628  21.618  -4.098  1.00 25.00           C
ATOM     27  CA  LEU    27      25.206  20.939  -0.592  1.00 25.00           C
ATOM     28  CA  LYS    28      21.996  18.915  -1.172  1.00 25.00           C
ATOM     29  CA  SER    29      21.051  15.240  -1.434  1.00 25.00           C
ATOM     30  CA  PHE    30      21.626  12.983   1.608  1.00 25.00           C
ATOM     31  CA  GLN    31      19.679  10.059   3.086  1.00 25.00           C
ATOM     32  CA  VAL    32      20.790   7.350   5.471  1.00 25.00           C
ATOM     33  CA  ASP    33      20.541   4.337   7.859  1.00 25.00           C
ATOM     34  CA  GLU    34      22.188   1.625   9.946  1.00 25.00           C
ATOM     35  CA  GLY    35      24.041   2.390  13.183  1.00 25.00           C
ATOM     36  CA  ILE    36      22.942   6.076  12.922  1.00 25.00           C
ATOM     37  CA  THR    37      22.683   8.577  10.058  1.00 25.00           C
ATOM     38  CA  VAL    38      25.717   7.281   8.201  1.00 25.00           C
ATOM     39  CA  GLN    39      27.441   8.412  11.428  1.00 25.00           C
ATOM     40  CA  THR    40      30.574   6.426  10.480  1.00 25.00           C
ATOM     41  CA  ALA    41      30.569   8.029   7.002  1.00 25.00           C
ATOM     42  CA  ILE    42      30.244  11.504   8.578  1.00 25.00           C
ATOM     43  CA  THR    43      33.170  10.738  10.928  1.00 25.00           C
ATOM     44  CA  GLN    44      35.286   9.574   7.956  1.00 25.00           C
ATOM     45  CA  SER    45      34.432  12.789   6.058  1.00 25.00           C
ATOM     46  CA  GLY    46      33.475  15.581   8.433  1.00 25.00           C
ATOM     47  CA  ILE    47      31.378  18.677   9.063  1.00 25.00           C
ATOM     48  CA  LEU    48      31.567  22.452   8.951  1.00 25.00           C
ATOM     49  CA  SER    49      35.097  23.533   7.930  1.00 25.00           C
ATOM     50  CA  GLN    50      36.413  20.010   8.658  1.00 25.00           C
ATOM     51  CA  PHE    51      35.513  18.483  12.034  1.00 25.00           C
ATOM     52  CA  PRO    52      38.249  20.597  13.552  1.00 25.00           C
ATOM     53  CA  GLU    53      35.470  23.168  14.265  1.00 25.00           C
ATOM     54  CA  ILE    54      32.688  23.004  16.834  1.00 25.00           C
ATOM     55  CA  ASP    55      34.091  19.532  17.693  1.00 25.00           C
ATOM     56  CA  LEU    56      30.953  17.994  16.090  1.00 25.00           C
ATOM     57  CA  SER    57      28.124  16.988  18.373  1.00 25.00           C
ATOM     58  CA  THR    58      26.049  19.953  17.115  1.00 25.00           C
ATOM     59  CA  ASN    59      27.029  19.959  13.473  1.00 25.00           C
ATOM     60  CA  LYS    60      24.238  17.853  12.022  1.00 25.00           C
ATOM     61  CA  ILE    61      23.906  14.222  10.883  1.00 25.00           C
ATOM     62  CA  GLY    62      25.745  15.430   7.741  1.00 25.00           C
ATOM     63  CA  ILE    63      25.366  12.431   5.388  1.00 25.00           C
ATOM     64  CA  PHE    64      25.137   9.420   3.071  1.00 25.00           C
ATOM     65  CA  SER    65      23.415   6.688   1.028  1.00 25.00           C
ATOM     66  CA  ARG    66      22.856   9.275  -1.783  1.00 25.00           C
ATOM     67  CA  PRO    67      26.163   9.821  -3.616  1.00 25.00           C
ATOM     68  CA  ILE    68      29.769   8.700  -4.206  1.00 25.00           C
ATOM     69  CA  LYS    69      33.179   7.948  -5.714  1.00 25.00           C
ATOM     70  CA  LEU    70      31.566   4.843  -7.205  1.00 25.00           C
ATOM     71  CA  THR    71      29.273   6.186  -9.886  1.00 25.00           C
ATOM     72  CA  ASP    72      26.300   4.358  -8.487  1.00 25.00           C
ATOM     73  CA  VAL    73      24.144   3.562  -5.397  1.00 25.00           C
ATOM     74  CA  LEU    74      26.651   4.759  -2.861  1.00 25.00           C
ATOM     75  CA  LYS    75      28.277   1.376  -3.447  1.00 25.00           C
ATOM     76  CA  GLU    76      29.500  -0.106  -0.147  1.00 25.00           C
ATOM     77  CA  GLY    77      31.480   2.860   0.966  1.00 25.00           C
ATOM     78  CA  ASP    78      28.373   4.791   1.911  1.00 25.00           C
ATOM     79  CA  ARG    79      30.393   7.988   1.942  1.00 25.00           C
ATOM     80  CA  ILE    80      29.358  11.651   1.476  1.00 25.00           C
ATOM     81  CA  GLU    81      29.684  14.558   3.890  1.00 25.00           C
ATOM     82  CA  ILE    82      28.430  18.121   4.329  1.00 25.00           C
ATOM     83  CA  TYR    83      26.089  20.697   5.723  1.00 25.00           C
ATOM     84  CA  ARG    84      22.976  20.274   7.782  1.00 25.00           C
ATOM     85  CA  PRO    85      19.486  20.305   6.275  1.00 25.00           C
ATOM     86  CA  LEU    86      15.925  21.147   5.247  1.00 25.00           C
ATOM     87  CA  LEU    87      13.744  20.458   2.195  1.00 25.00           C
ATOM     88  CA  ALA    88      15.931  22.849   0.313  1.00 25.00           C
ATOM     89  CA  ASP    89      15.119  26.501  -0.317  1.00 25.00           C
ATOM     90  CA  PRO    90      16.109  26.832   3.380  1.00 25.00           C
ATOM     91  CA  LYS    91      13.887  29.817   4.286  1.00 25.00           C
ATOM     92  CA  GLU    92      11.044  28.376   2.163  1.00 25.00           C
ATOM     93  CA  ILE    93      11.433  24.985   3.899  1.00 25.00           C
ATOM     94  CA  ARG    94      11.322  26.697   7.323  1.00 25.00           C
ATOM     95  CA  ARG    95       7.502  26.475   7.731  1.00 25.00           C
ATOM     96  CA  GLU    96       5.547  28.368  10.386  1.00 25.00           C
ATOM     97  CA  GLY    97       5.367  25.020  12.158  1.00 25.00           C
TER
END
