
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0351TS168_3
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS168_3.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    L       3      L       3           -
LGA    Y       4      Y       4           -
LGA    D       5      D       5           -
LGA    A       6      A       6           -
LGA    I       7      I       7           -
LGA    M       8      M       8          5.278
LGA    Y       9      Y       9           #
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    -       -      A      14           -
LGA    K      10      V      15          2.567
LGA    Y      11      S      16          2.270
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    P      12      F      20          1.841
LGA    N      13      E      21          3.785
LGA    A      14      -       -           -
LGA    V      15      -       -           -
LGA    S      16      -       -           -
LGA    R      17      -       -           -
LGA    K      18      -       -           -
LGA    D      19      -       -           -
LGA    F      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    D      25      -       -           -
LGA    G      26      -       -           -
LGA    N      27      -       -           -
LGA    G      28      -       -           -
LGA    S      29      -       -           -
LGA    Y      30      -       -           -
LGA    I      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    W      34      -       -           -
LGA    N      35      L      22           #
LGA    L      36      -       -           -
LGA    R      37      -       -           -
LGA    A      38      -       -           -
LGA    P      39      R      23           #
LGA    L      40      N      24          2.938
LGA    P      41      D      25          4.061
LGA    T      42      G      26          3.055
LGA    Q      43      N      27          2.993
LGA    A      44      G      28          3.711
LGA    E      45      S      29          1.747
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    T      48      Y      30          3.143
LGA    W      49      I      31          2.556
LGA    W      50      -       -           -
LGA    E      51      E      32          2.125
LGA    E      52      K      33          3.028
LGA    L      53      W      34           #
LGA    Q      54      N      35           -
LGA    K      55      L      36           -
LGA    N      56      R      37           -
LGA    P      57      A      38           -
LGA    P      58      P      39           -
LGA    Y      59      -       -           -
LGA    E      60      -       -           -
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    V      65      -       -           -
LGA    E      66      -       -           -
LGA    L      67      -       -           -
LGA    L      68      -       -           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      -       -           -
LGA    L      72      L      40          5.027
LGA    S      73      -       -           -
LGA    Q      74      P      41          4.586
LGA    E      75      T      42          2.608
LGA    K      76      Q      43          2.701
LGA    L      77      A      44          1.634
LGA    A      78      E      45          1.043
LGA    R      79      L      46          1.720
LGA    K      80      E      47          0.792
LGA    Q      81      T      48          0.578
LGA    L      82      W      49          1.223
LGA    E      83      W      50          1.259
LGA    E      84      E      51          1.047
LGA    L      85      E      52          1.321
LGA    N      86      L      53          1.841
LGA    K      87      Q      54          2.489
LGA    T      88      K      55          2.540
LGA    L      89      N      56          1.871
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      -       -           -
LGA    S     102      -       -           -
LGA    L     103      -       -           -
LGA    K     104      -       -           -
LGA    G     105      -       -           -
LGA    D     106      -       -           -
LGA    Y     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117   56    5.0     32    2.75    12.50     39.008     1.125

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.585625 * X  +  -0.541035 * Y  +   0.603593 * Z  +   0.947083
  Y_new =  -0.262791 * X  +  -0.577697 * Y  +  -0.772792 * Z  +  -1.086229
  Z_new =   0.766801 * X  +  -0.611185 * Y  +   0.196135 * Z  +   3.372928 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.260269    1.881323  [ DEG:   -72.2081    107.7919 ]
  Theta =  -0.873843   -2.267750  [ DEG:   -50.0675   -129.9325 ]
  Phi   =  -2.719790    0.421802  [ DEG:  -155.8325     24.1675 ]
 
# 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: T0351TS168_3                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS168_3.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117   56   5.0   32   2.75   12.50  39.008
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS168_3
PFRMAT TS
TARGET T0351
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      11.855 -10.589  -4.194  1.00 25.00           C
ATOM      2  CA  ILE     2      11.584  -7.482  -2.001  1.00 25.00           C
ATOM      3  CA  LEU     3      12.543  -6.050   1.324  1.00 25.00           C
ATOM      4  CA  TYR     4      13.871  -5.931   4.867  1.00 25.00           C
ATOM      5  CA  ASP     5      15.052  -2.356   4.153  1.00 25.00           C
ATOM      6  CA  ALA     6      11.828  -0.466   4.953  1.00 25.00           C
ATOM      7  CA  ILE     7       8.640   1.501   5.887  1.00 25.00           C
ATOM      8  CA  MET     8       6.385   3.930   7.770  1.00 25.00           C
ATOM      9  CA  TYR     9       5.129   5.111   4.377  1.00 25.00           C
ATOM     10  CA  LYS    10       2.697   7.900   3.594  1.00 25.00           C
ATOM     11  CA  TYR    11      -0.912   7.487   4.773  1.00 25.00           C
ATOM     12  CA  PRO    12      -1.766   9.900   1.978  1.00 25.00           C
ATOM     13  CA  ASN    13      -2.899  13.219   3.494  1.00 25.00           C
ATOM     14  CA  ALA    14      -0.520  14.232   6.348  1.00 25.00           C
ATOM     15  CA  VAL    15      -0.404  16.646   9.331  1.00 25.00           C
ATOM     16  CA  SER    16      -0.543  20.375   8.544  1.00 25.00           C
ATOM     17  CA  ARG    17      -3.190  19.814   5.816  1.00 25.00           C
ATOM     18  CA  LYS    18      -0.710  19.782   2.933  1.00 25.00           C
ATOM     19  CA  ASP    19       1.298  16.630   2.184  1.00 25.00           C
ATOM     20  CA  PHE    20       4.122  14.286   3.067  1.00 25.00           C
ATOM     21  CA  GLU    21       3.034  12.218   0.117  1.00 25.00           C
ATOM     22  CA  LEU    22       2.367   9.418  -2.350  1.00 25.00           C
ATOM     23  CA  ARG    23       3.039   7.404  -5.466  1.00 25.00           C
ATOM     24  CA  ASN    24       0.131   9.392  -7.002  1.00 25.00           C
ATOM     25  CA  ASP    25       0.169   6.593  -9.626  1.00 25.00           C
ATOM     26  CA  GLY    26       0.177   3.407  -7.548  1.00 25.00           C
ATOM     27  CA  ASN    27       3.353   2.089  -5.856  1.00 25.00           C
ATOM     28  CA  GLY    28       1.278   0.328  -3.189  1.00 25.00           C
ATOM     29  CA  SER    29       2.404   2.985  -0.754  1.00 25.00           C
ATOM     30  CA  TYR    30      -1.037   4.036   0.624  1.00 25.00           C
ATOM     31  CA  ILE    31      -2.567   0.611   1.396  1.00 25.00           C
ATOM     32  CA  GLU    32       0.720  -0.524   2.998  1.00 25.00           C
ATOM     33  CA  LYS    33       0.813   2.662   5.122  1.00 25.00           C
ATOM     34  CA  TRP    34      -2.801   2.057   6.233  1.00 25.00           C
ATOM     35  CA  ASN    35      -1.997   2.736   9.881  1.00 25.00           C
ATOM     36  CA  LEU    36      -5.772   2.654  10.372  1.00 25.00           C
ATOM     37  CA  ARG    37      -5.400   6.130  11.996  1.00 25.00           C
ATOM     38  CA  ALA    38      -7.622   7.453   9.198  1.00 25.00           C
ATOM     39  CA  PRO    39      -9.827   8.517  12.086  1.00 25.00           C
ATOM     40  CA  LEU    40     -12.745   6.906  10.280  1.00 25.00           C
ATOM     41  CA  PRO    41     -15.805   4.671  10.387  1.00 25.00           C
ATOM     42  CA  THR    42     -16.536   1.398   8.639  1.00 25.00           C
ATOM     43  CA  GLN    43     -13.663  -0.559   7.071  1.00 25.00           C
ATOM     44  CA  ALA    44     -11.510   2.540   7.723  1.00 25.00           C
ATOM     45  CA  GLU    45      -9.005   1.389   5.065  1.00 25.00           C
ATOM     46  CA  LEU    46     -11.859   0.860   2.568  1.00 25.00           C
ATOM     47  CA  GLU    47     -13.205   4.365   3.327  1.00 25.00           C
ATOM     48  CA  THR    48      -9.714   5.847   2.793  1.00 25.00           C
ATOM     49  CA  TRP    49      -9.413   3.999  -0.547  1.00 25.00           C
ATOM     50  CA  TRP    50     -12.840   5.329  -1.621  1.00 25.00           C
ATOM     51  CA  GLU    51     -11.782   8.886  -0.675  1.00 25.00           C
ATOM     52  CA  GLU    52      -8.555   8.491  -2.697  1.00 25.00           C
ATOM     53  CA  LEU    53     -10.564   7.242  -5.708  1.00 25.00           C
ATOM     54  CA  GLN    54     -12.926  10.242  -5.407  1.00 25.00           C
ATOM     55  CA  LYS    55     -13.419  13.649  -3.857  1.00 25.00           C
ATOM     56  CA  ASN    56     -11.653  15.567  -6.693  1.00 25.00           C
ATOM     57  CA  PRO    57     -14.225  17.477  -8.719  1.00 25.00           C
ATOM     58  CA  PRO    58     -12.644  16.628 -12.117  1.00 25.00           C
ATOM     59  CA  TYR    59     -15.456  15.689 -14.566  1.00 25.00           C
ATOM     60  CA  GLU    60     -16.965  13.159 -16.919  1.00 25.00           C
ATOM     61  CA  PRO    61     -17.324   9.480 -17.930  1.00 25.00           C
ATOM     62  CA  PRO    62     -18.144   5.947 -18.960  1.00 25.00           C
ATOM     63  CA  ASP    63     -14.901   4.652 -20.531  1.00 25.00           C
ATOM     64  CA  GLN    64     -12.849   6.897 -18.202  1.00 25.00           C
ATOM     65  CA  VAL    65     -14.809   5.594 -15.180  1.00 25.00           C
ATOM     66  CA  GLU    66     -14.183   1.985 -16.299  1.00 25.00           C
ATOM     67  CA  LEU    67     -10.444   2.724 -16.672  1.00 25.00           C
ATOM     68  CA  LEU    68     -10.372   4.258 -13.164  1.00 25.00           C
ATOM     69  CA  ALA    69     -12.139   1.169 -11.750  1.00 25.00           C
ATOM     70  CA  GLN    70      -9.601  -1.110 -13.488  1.00 25.00           C
ATOM     71  CA  GLU    71      -6.718   0.953 -12.039  1.00 25.00           C
ATOM     72  CA  LEU    72      -8.261   0.699  -8.544  1.00 25.00           C
ATOM     73  CA  SER    73      -8.612  -3.093  -8.947  1.00 25.00           C
ATOM     74  CA  GLN    74      -4.950  -3.340 -10.042  1.00 25.00           C
ATOM     75  CA  GLU    75      -3.875  -1.279  -6.998  1.00 25.00           C
ATOM     76  CA  LYS    76      -5.913  -3.566  -4.700  1.00 25.00           C
ATOM     77  CA  LEU    77      -4.284  -6.649  -6.282  1.00 25.00           C
ATOM     78  CA  ALA    78      -0.815  -5.109  -5.771  1.00 25.00           C
ATOM     79  CA  ARG    79      -1.653  -4.378  -2.106  1.00 25.00           C
ATOM     80  CA  LYS    80      -2.834  -7.990  -1.630  1.00 25.00           C
ATOM     81  CA  GLN    81       0.410  -9.284  -3.201  1.00 25.00           C
ATOM     82  CA  LEU    82       2.462  -7.040  -0.871  1.00 25.00           C
ATOM     83  CA  GLU    83       0.502  -8.342   2.150  1.00 25.00           C
ATOM     84  CA  GLU    84       1.128 -11.952   1.032  1.00 25.00           C
ATOM     85  CA  LEU    85       4.868 -11.213   0.659  1.00 25.00           C
ATOM     86  CA  ASN    86       4.939  -9.678   4.167  1.00 25.00           C
ATOM     87  CA  LYS    87       3.171 -12.767   5.581  1.00 25.00           C
ATOM     88  CA  THR    88       5.710 -15.046   3.842  1.00 25.00           C
ATOM     89  CA  LEU    89       8.593 -12.983   5.291  1.00 25.00           C
ATOM     90  CA  GLY    90       7.050 -13.238   8.787  1.00 25.00           C
ATOM     91  CA  ASN    91       6.700 -17.030   8.383  1.00 25.00           C
ATOM     92  CA  GLU    92      10.360 -17.276   7.288  1.00 25.00           C
ATOM     93  CA  LEU    93      11.436 -15.215  10.332  1.00 25.00           C
ATOM     94  CA  SER    94       9.397 -17.503  12.630  1.00 25.00           C
ATOM     95  CA  ASP    95      11.027 -20.586  11.049  1.00 25.00           C
ATOM     96  CA  ILE    96      14.497 -19.046  11.559  1.00 25.00           C
ATOM     97  CA  LYS    97      13.659 -18.315  15.224  1.00 25.00           C
ATOM     98  CA  LEU    98      12.477 -21.926  15.700  1.00 25.00           C
ATOM     99  CA  SER    99      15.722 -23.221  14.130  1.00 25.00           C
ATOM    100  CA  LEU   100      17.773 -20.977  16.459  1.00 25.00           C
ATOM    101  CA  LEU   101      15.813 -22.280  19.480  1.00 25.00           C
ATOM    102  CA  SER   102      16.439 -25.888  18.362  1.00 25.00           C
ATOM    103  CA  LEU   103      20.053 -24.832  18.766  1.00 25.00           C
ATOM    104  CA  LYS   104      22.382 -23.287  21.371  1.00 25.00           C
ATOM    105  CA  GLY   105      22.525 -20.682  24.182  1.00 25.00           C
ATOM    106  CA  ASP   106      23.847 -17.125  24.694  1.00 25.00           C
ATOM    107  CA  TYR   107      20.897 -15.515  26.484  1.00 25.00           C
ATOM    108  CA  ALA   108      23.367 -12.610  26.837  1.00 25.00           C
ATOM    109  CA  GLU   109      23.434 -12.171  23.034  1.00 25.00           C
ATOM    110  CA  LEU   110      19.605 -12.147  22.945  1.00 25.00           C
ATOM    111  CA  GLU   111      19.533  -9.511  25.724  1.00 25.00           C
ATOM    112  CA  HIS   112      22.052  -7.370  23.792  1.00 25.00           C
ATOM    113  CA  HIS   113      20.447  -4.671  21.616  1.00 25.00           C
ATOM    114  CA  HIS   114      17.640  -3.839  24.134  1.00 25.00           C
ATOM    115  CA  HIS   115      14.123  -3.762  22.644  1.00 25.00           C
ATOM    116  CA  HIS   116      10.454  -4.301  23.572  1.00 25.00           C
ATOM    117  CA  HIS   117       7.063  -4.554  21.818  1.00 25.00           C
TER
END
