
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0367TS393_4
# Molecule2: number of CA atoms  125 ( 1016),  selected  125 , name T0367.pdb
# PARAMETERS: T0367TS393_4.T0367.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    D       2      D       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    E       5      E       5           -
LGA    L       6      L       6           -
LGA    R       7      R       7           -
LGA    I       8      I       8           -
LGA    R       9      R       9           -
LGA    K      10      K      10           -
LGA    A      11      A      11           -
LGA    E      12      E      12           -
LGA    -       -      K      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      Q      16           -
LGA    -       -      D      17           -
LGA    -       -      A      18           -
LGA    -       -      K      19           -
LGA    -       -      K      20           -
LGA    -       -      E      21           -
LGA    -       -      F      22           -
LGA    -       -      E      23           -
LGA    K      13      M      24          5.539
LGA    L      14      G      25          2.115
LGA    V      15      -       -           -
LGA    Q      16      L      26          1.971
LGA    D      17      -       -           -
LGA    A      18      Y      27          3.297
LGA    K      19      E      28          2.877
LGA    K      20      R      29          2.448
LGA    E      21      C      30          2.613
LGA    F      22      C      31          2.447
LGA    E      23      S      32          1.976
LGA    M      24      T      33          1.613
LGA    G      25      A      34          1.272
LGA    L      26      Y      35          0.913
LGA    Y      27      Y      36          0.615
LGA    E      28      A      37          0.693
LGA    R      29      M      38          0.414
LGA    C      30      F      39          0.754
LGA    C      31      H      40          0.839
LGA    S      32      A      41          1.131
LGA    T      33      A      42          1.344
LGA    A      34      K      43          1.597
LGA    Y      35      A      44          1.816
LGA    Y      36      M      45          1.999
LGA    A      37      L      46          2.257
LGA    M      38      L      47          2.225
LGA    F      39      G      48          2.596
LGA    H      40      Y      49          3.055
LGA    A      41      G      50          2.751
LGA    A      42      R      51          5.708
LGA    K      43      -       -           -
LGA    A      44      -       -           -
LGA    M      45      -       -           -
LGA    L      46      -       -           -
LGA    L      47      -       -           -
LGA    G      48      -       -           -
LGA    Y      49      -       -           -
LGA    G      50      -       -           -
LGA    R      51      -       -           -
LGA    D      52      D      52           #
LGA    S      53      -       -           -
LGA    K      54      -       -           -
LGA    T      55      -       -           -
LGA    H      56      S      53           #
LGA    R      57      K      54          3.869
LGA    G      58      T      55          3.907
LGA    T      59      H      56          3.641
LGA    I      60      R      57          2.393
LGA    Y      61      G      58          1.755
LGA    L      62      T      59          2.287
LGA    I      63      I      60          1.060
LGA    W      64      Y      61          0.623
LGA    E      65      L      62          1.533
LGA    C      66      I      63          2.649
LGA    R      67      W      64          2.674
LGA    E      68      E      65          3.045
LGA    E      69      C      66          4.285
LGA    L      70      -       -           -
LGA    G      71      R      67           #
LGA    L      72      E      68          1.265
LGA    S      73      E      69          1.605
LGA    D      74      L      70          2.005
LGA    D      75      G      71          1.189
LGA    D      76      -       -           -
LGA    C      77      -       -           -
LGA    S      78      -       -           -
LGA    K      79      L      72          3.630
LGA    L      80      S      73           -
LGA    S      81      D      74           -
LGA    -       -      D      75           -
LGA    -       -      D      76           -
LGA    R      82      C      77          1.397
LGA    -       -      S      78           -
LGA    A      83      K      79          3.919
LGA    F      84      L      80          2.927
LGA    D      85      S      81          1.988
LGA    L      86      R      82          2.441
LGA    R      87      A      83          2.314
LGA    E      88      F      84          2.763
LGA    E      89      D      85          3.154
LGA    S      90      -       -           -
LGA    D      91      -       -           -
LGA    Y      92      -       -           -
LGA    G      93      -       -           -
LGA    I      94      -       -           -
LGA    Y      95      -       -           -
LGA    K      96      -       -           -
LGA    E      97      -       -           -
LGA    V      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    D     101      -       -           -
LGA    L     102      L      86          5.229
LGA    A     103      R      87           #
LGA    -       -      E      88           -
LGA    -       -      E      89           -
LGA    -       -      S      90           -
LGA    -       -      D      91           -
LGA    -       -      Y      92           -
LGA    -       -      G      93           -
LGA    -       -      I      94           -
LGA    -       -      Y      95           -
LGA    -       -      K      96           -
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    I     104      L     102          2.949
LGA    K     105      A     103           -
LGA    -       -      I     104           -
LGA    -       -      K     105           -
LGA    I     106      I     106          3.651
LGA    L     107      L     107          3.306
LGA    K     108      K     108          3.094
LGA    D     109      D     109          1.152
LGA    A     110      A     110          0.756
LGA    E     111      E     111          2.773
LGA    I     112      I     112          2.746
LGA    F     113      F     113          3.194
LGA    V     114      V     114          4.833
LGA    Q     115      -       -           -
LGA    K     116      -       -           -
LGA    A     117      Q     115          2.953
LGA    K     118      K     116           -
LGA    N     119      A     117           -
LGA    A     120      K     118           #
LGA    -       -      N     119           -
LGA    -       -      A     120           -
LGA    -       -      V     121           -
LGA    -       -      N     122           -
LGA    -       -      K     123           -
LGA    V     121      N     124          4.855
LGA    N     122      R     125           -
LGA    K     123      -       -           -
LGA    N     124      -       -           -
LGA    R     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125  125    5.0     67    2.75    19.40     34.693     2.355

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.221759 * X  +   0.833187 * Y  +  -0.506579 * Z  +  39.064095
  Y_new =   0.348148 * X  +   0.552926 * Y  +   0.757011 * Z  +  34.491112
  Z_new =   0.910832 * X  +  -0.008491 * Y  +  -0.412689 * Z  +  28.766613 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.121022    0.020571  [ DEG:  -178.8214      1.1786 ]
  Theta =  -1.145296   -1.996296  [ DEG:   -65.6206   -114.3794 ]
  Phi   =   2.137955   -1.003638  [ DEG:   122.4958    -57.5042 ]
 
# 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: T0367TS393_4                                  
REMARK     2: T0367.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0367TS393_4.T0367.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125  125   5.0   67   2.75   19.40  34.693
REMARK  ---------------------------------------------------------- 
MOLECULE T0367TS393_4
PFRMAT TS
TARGET T0367
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       0.065  31.265  42.440  1.00 25.00           C
ATOM      2  CA  ASP     2       2.786  29.866  44.746  1.00 25.00           C
ATOM      3  CA  GLU     3       3.598  27.812  41.618  1.00 25.00           C
ATOM      4  CA  LEU     4       4.475  31.017  39.712  1.00 25.00           C
ATOM      5  CA  GLU     5       6.753  32.131  42.582  1.00 25.00           C
ATOM      6  CA  LEU     6       8.479  28.712  42.571  1.00 25.00           C
ATOM      7  CA  ARG     7       8.996  28.958  38.784  1.00 25.00           C
ATOM      8  CA  ILE     8      10.484  32.463  39.190  1.00 25.00           C
ATOM      9  CA  ARG     9      12.845  31.173  41.916  1.00 25.00           C
ATOM     10  CA  LYS    10      13.930  28.288  39.643  1.00 25.00           C
ATOM     11  CA  ALA    11      14.588  30.754  36.787  1.00 25.00           C
ATOM     12  CA  GLU    12      16.667  32.954  39.132  1.00 25.00           C
ATOM     13  CA  LYS    13      18.683  29.898  40.253  1.00 25.00           C
ATOM     14  CA  LEU    14      19.297  28.931  36.599  1.00 25.00           C
ATOM     15  CA  VAL    15      20.462  32.496  35.827  1.00 25.00           C
ATOM     16  CA  GLN    16      22.838  32.397  38.830  1.00 25.00           C
ATOM     17  CA  ASP    17      24.241  29.039  37.639  1.00 25.00           C
ATOM     18  CA  ALA    18      24.773  30.477  34.130  1.00 25.00           C
ATOM     19  CA  LYS    19      26.579  33.509  35.619  1.00 25.00           C
ATOM     20  CA  LYS    20      28.814  31.190  37.692  1.00 25.00           C
ATOM     21  CA  GLU    21      29.627  29.136  34.563  1.00 25.00           C
ATOM     22  CA  PHE    22      30.503  32.340  32.657  1.00 25.00           C
ATOM     23  CA  GLU    23      32.781  33.454  35.527  1.00 25.00           C
ATOM     24  CA  MET    24      34.508  30.036  35.516  1.00 25.00           C
ATOM     25  CA  GLY    25      35.025  30.282  31.730  1.00 25.00           C
ATOM     26  CA  LEU    26      36.512  33.788  32.136  1.00 25.00           C
ATOM     27  CA  TYR    27      38.873  32.497  34.861  1.00 25.00           C
ATOM     28  CA  GLU    28      39.959  29.612  32.588  1.00 25.00           C
ATOM     29  CA  ARG    29      40.616  32.077  29.732  1.00 25.00           C
ATOM     30  CA  CYS    30      42.696  34.278  32.077  1.00 25.00           C
ATOM     31  CA  CYS    31      44.711  31.221  33.198  1.00 25.00           C
ATOM     32  CA  SER    32      45.326  30.255  29.544  1.00 25.00           C
ATOM     33  CA  THR    33      46.491  33.820  28.772  1.00 25.00           C
ATOM     34  CA  ALA    34      48.866  33.721  31.775  1.00 25.00           C
ATOM     35  CA  TYR    35      50.270  30.362  30.584  1.00 25.00           C
ATOM     36  CA  TYR    36      50.801  31.801  27.075  1.00 25.00           C
ATOM     37  CA  ALA    37      52.607  34.832  28.564  1.00 25.00           C
ATOM     38  CA  MET    38      54.843  32.513  30.637  1.00 25.00           C
ATOM     39  CA  PHE    39      55.655  30.460  27.508  1.00 25.00           C
ATOM     40  CA  HIS    40      56.532  33.665  25.602  1.00 25.00           C
ATOM     41  CA  ALA    41      58.809  34.778  28.473  1.00 25.00           C
ATOM     42  CA  ALA    42      60.536  31.359  28.461  1.00 25.00           C
ATOM     43  CA  LYS    43      61.053  31.606  24.674  1.00 25.00           C
ATOM     44  CA  ALA    44      62.541  35.112  25.081  1.00 25.00           C
ATOM     45  CA  MET    45      64.901  33.819  27.807  1.00 25.00           C
ATOM     46  CA  LEU    46      65.988  30.936  25.534  1.00 25.00           C
ATOM     47  CA  LEU    47      66.645  33.401  22.677  1.00 25.00           C
ATOM     48  CA  GLY    48      68.724  35.602  25.022  1.00 25.00           C
ATOM     49  CA  TYR    49      66.521  38.435  26.249  1.00 25.00           C
ATOM     50  CA  GLY    50      64.395  40.603  28.626  1.00 25.00           C
ATOM     51  CA  ARG    51      61.531  42.606  30.203  1.00 25.00           C
ATOM     52  CA  ASP    52      60.050  45.250  32.440  1.00 25.00           C
ATOM     53  CA  SER    53      58.164  47.889  34.448  1.00 25.00           C
ATOM     54  CA  LYS    54      55.114  47.053  36.549  1.00 25.00           C
ATOM     55  CA  THR    55      51.912  45.404  35.259  1.00 25.00           C
ATOM     56  CA  HIS    56      48.308  44.875  34.400  1.00 25.00           C
ATOM     57  CA  ARG    57      47.699  41.419  35.732  1.00 25.00           C
ATOM     58  CA  GLY    58      49.317  38.471  33.901  1.00 25.00           C
ATOM     59  CA  THR    59      46.116  37.946  31.866  1.00 25.00           C
ATOM     60  CA  ILE    60      46.052  41.667  30.961  1.00 25.00           C
ATOM     61  CA  TYR    61      49.718  41.489  29.868  1.00 25.00           C
ATOM     62  CA  LEU    62      48.952  38.420  27.709  1.00 25.00           C
ATOM     63  CA  ILE    63      45.994  40.253  26.109  1.00 25.00           C
ATOM     64  CA  TRP    64      48.231  43.276  25.381  1.00 25.00           C
ATOM     65  CA  GLU    65      50.854  40.983  23.791  1.00 25.00           C
ATOM     66  CA  CYS    66      48.150  39.347  21.629  1.00 25.00           C
ATOM     67  CA  ARG    67      46.908  42.799  20.527  1.00 25.00           C
ATOM     68  CA  GLU    68      50.487  43.826  19.629  1.00 25.00           C
ATOM     69  CA  GLU    69      50.928  40.608  17.600  1.00 25.00           C
ATOM     70  CA  LEU    70      47.795  40.228  15.507  1.00 25.00           C
ATOM     71  CA  GLY    71      49.904  38.316  12.988  1.00 25.00           C
ATOM     72  CA  LEU    72      49.613  35.523  15.570  1.00 25.00           C
ATOM     73  CA  SER    73      52.124  32.695  15.386  1.00 25.00           C
ATOM     74  CA  ASP    74      51.779  30.217  18.251  1.00 25.00           C
ATOM     75  CA  ASP    75      48.155  29.919  17.046  1.00 25.00           C
ATOM     76  CA  ASP    76      47.089  28.637  20.495  1.00 25.00           C
ATOM     77  CA  CYS    77      48.890  31.572  22.171  1.00 25.00           C
ATOM     78  CA  SER    78      47.139  34.027  19.809  1.00 25.00           C
ATOM     79  CA  LYS    79      43.754  32.432  20.622  1.00 25.00           C
ATOM     80  CA  LEU    80      44.488  32.724  24.370  1.00 25.00           C
ATOM     81  CA  SER    81      45.426  36.410  23.924  1.00 25.00           C
ATOM     82  CA  ARG    82      42.173  37.030  22.000  1.00 25.00           C
ATOM     83  CA  ALA    83      40.172  35.321  24.782  1.00 25.00           C
ATOM     84  CA  PHE    84      41.928  37.486  27.409  1.00 25.00           C
ATOM     85  CA  ASP    85      41.127  40.636  25.383  1.00 25.00           C
ATOM     86  CA  LEU    86      37.458  39.569  25.129  1.00 25.00           C
ATOM     87  CA  ARG    87      37.341  38.982  28.912  1.00 25.00           C
ATOM     88  CA  GLU    88      38.858  42.445  29.520  1.00 25.00           C
ATOM     89  CA  GLU    89      36.256  44.021  27.195  1.00 25.00           C
ATOM     90  CA  SER    90      37.512  47.281  28.608  1.00 25.00           C
ATOM     91  CA  ASP    91      38.186  50.256  30.853  1.00 25.00           C
ATOM     92  CA  TYR    92      35.912  48.472  33.282  1.00 25.00           C
ATOM     93  CA  GLY    93      35.996  51.407  35.755  1.00 25.00           C
ATOM     94  CA  ILE    94      32.187  52.027  35.758  1.00 25.00           C
ATOM     95  CA  TYR    95      28.447  52.135  34.879  1.00 25.00           C
ATOM     96  CA  LYS    96      27.611  52.779  31.194  1.00 25.00           C
ATOM     97  CA  GLU    97      24.876  50.862  29.418  1.00 25.00           C
ATOM     98  CA  VAL    98      27.619  48.254  28.990  1.00 25.00           C
ATOM     99  CA  SER    99      28.194  45.330  31.394  1.00 25.00           C
ATOM    100  CA  LYS   100      26.810  42.438  29.355  1.00 25.00           C
ATOM    101  CA  ASP   101      27.003  41.798  25.584  1.00 25.00           C
ATOM    102  CA  LEU   102      30.828  41.849  25.745  1.00 25.00           C
ATOM    103  CA  ALA   103      30.763  39.367  28.661  1.00 25.00           C
ATOM    104  CA  ILE   104      28.415  37.073  26.688  1.00 25.00           C
ATOM    105  CA  LYS   105      30.752  37.248  23.658  1.00 25.00           C
ATOM    106  CA  ILE   106      33.744  36.377  25.884  1.00 25.00           C
ATOM    107  CA  LEU   107      31.825  33.400  27.341  1.00 25.00           C
ATOM    108  CA  LYS   108      30.955  32.200  23.810  1.00 25.00           C
ATOM    109  CA  ASP   109      34.633  32.489  22.779  1.00 25.00           C
ATOM    110  CA  ALA   110      35.681  30.484  25.869  1.00 25.00           C
ATOM    111  CA  GLU   111      33.096  27.787  25.027  1.00 25.00           C
ATOM    112  CA  ILE   112      34.401  27.624  21.430  1.00 25.00           C
ATOM    113  CA  PHE   113      37.989  27.273  22.722  1.00 25.00           C
ATOM    114  CA  VAL   114      36.893  24.453  25.071  1.00 25.00           C
ATOM    115  CA  GLN   115      35.142  22.679  22.163  1.00 25.00           C
ATOM    116  CA  LYS   116      38.302  23.011  20.025  1.00 25.00           C
ATOM    117  CA  ALA   117      40.411  21.565  22.876  1.00 25.00           C
ATOM    118  CA  LYS   118      37.975  18.631  23.224  1.00 25.00           C
ATOM    119  CA  ASN   119      38.167  17.991  19.454  1.00 25.00           C
ATOM    120  CA  ALA   120      41.993  18.042  19.616  1.00 25.00           C
ATOM    121  CA  VAL   121      41.927  15.560  22.530  1.00 25.00           C
ATOM    122  CA  ASN   122      39.580  13.266  20.557  1.00 25.00           C
ATOM    123  CA  LYS   123      40.470   9.536  20.345  1.00 25.00           C
ATOM    124  CA  ASN   124      38.569   8.861  23.586  1.00 25.00           C
ATOM    125  CA  ARG   125      35.416   8.391  25.682  1.00 25.00           C
TER
END
