
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS168_1-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS168_1-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      -       -           -
LGA    M      11      -       -           -
LGA    T      12      I      10          4.076
LGA    F      13      -       -           -
LGA    S      14      -       -           -
LGA    G      15      M      11          4.928
LGA    Q      16      T      12          1.889
LGA    E      17      F      13          4.122
LGA    L      18      S      14          4.588
LGA    T      19      G      15           #
LGA    A      20      Q      16           #
LGA    I      21      E      17          4.353
LGA    I      22      L      18           #
LGA    K      23      -       -           -
LGA    M      24      -       -           -
LGA    A      25      -       -           -
LGA    K      26      -       -           -
LGA    S      27      -       -           -
LGA    M      28      -       -           -
LGA    V      29      -       -           -
LGA    M      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      -       -           -
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    I      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      -       -           -
LGA    A      38      -       -           -
LGA    E      39      -       -           -
LGA    I      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    M      43      -       -           -
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      -       -           -
LGA    D      58      -       -           -
LGA    L      59      -       -           -
LGA    L      60      -       -           -
LGA    L      61      -       -           -
LGA    K      62      T      19          3.906
LGA    A      63      -       -           -
LGA    S      64      A      20          4.414
LGA    D      65      I      21          4.134
LGA    S      66      I      22          3.122
LGA    I      67      K      23          1.266
LGA    E      68      M      24          0.998
LGA    A      69      A      25          3.061
LGA    S      70      K      26          2.344
LGA    Q      71      S      27          3.307
LGA    A      72      M      28          4.920
LGA    V      73      V      29           #
LGA    A      74      M      30           #
LGA    L      75      A      31           #
LGA    -       -      D      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      I      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      M      43           -
LGA    -       -      T      44           -
LGA    -       -      R      45           -
LGA    -       -      E      46           -
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    I      76      V      93          4.563
LGA    A      77      I      94          4.615
LGA    R      78      M      95          3.924
LGA    M      79      A      96          3.563
LGA    D      80      S      97          2.209
LGA    E      81      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    E      82      I     101           #
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    K      85      -       -           -
LGA    Y      86      -       -           -
LGA    V      87      -       -           -
LGA    A      88      -       -           -
LGA    S      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    G      92      -       -           -
LGA    V      93      -       -           -
LGA    I      94      -       -           -
LGA    M      95      -       -           -
LGA    A      96      -       -           -
LGA    S      97      -       -           -
LGA    D      98      -       -           -
LGA    G      99      -       -           -
LGA    D     100      -       -           -
LGA    I     101      D     102           #
LGA    D     102      D     103          3.476
LGA    D     103      N     104          3.348
LGA    N     104      E     105          3.971
LGA    E     105      L     106          2.601
LGA    L     106      A     107          1.230
LGA    A     107      L     108          2.463
LGA    L     108      W     109          1.856
LGA    W     109      T     110          0.742
LGA    T     110      L     111          1.948
LGA    L     111      I     112          1.872
LGA    I     112      S     113          1.101
LGA    S     113      T     114          3.342
LGA    T     114      L     115          3.990
LGA    L     115      C     116          2.083
LGA    C     116      -       -           -
LGA    G     117      -       -           -
LGA    L     118      -       -           -
LGA    P     119      -       -           -
LGA    T     120      -       -           -
LGA    M     121      G     117          3.921
LGA    T     122      -       -           -
LGA    V     123      -       -           -
LGA    M     124      -       -           -
LGA    E     125      L     118           #
LGA    A     126      P     119          4.285
LGA    I     127      -       -           -
LGA    N     128      -       -           -
LGA    N     129      -       -           -
LGA    M     130      T     120          4.618
LGA    K     131      M     121           #
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    N     132      A     126          4.498
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     39    3.45     5.13     19.815     1.100

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.524947 * X  +   0.850922 * Y  +  -0.019046 * Z  +  20.995844
  Y_new =   0.809095 * X  +  -0.505840 * Y  +  -0.299150 * Z  +   8.352443
  Z_new =  -0.264187 * X  +   0.141628 * Y  +  -0.954016 * Z  +  34.890671 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.994214   -0.147378  [ DEG:   171.5558     -8.4442 ]
  Theta =   0.267361    2.874231  [ DEG:    15.3187    164.6813 ]
  Phi   =   0.995260   -2.146333  [ DEG:    57.0242   -122.9758 ]
 
# 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: T0307TS168_1-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS168_1-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   39   3.45    5.13  19.815
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS168_1-D1
PFRMAT TS
TARGET T0307
MODEL 1
PARENT N/A
ATOM     10  CA  ILE    10       2.122  11.976  42.587  1.00 25.00           C
ATOM     11  CA  MET    11       3.349  12.394  39.009  1.00 25.00           C
ATOM     12  CA  THR    12       5.581  15.139  37.608  1.00 25.00           C
ATOM     13  CA  PHE    13       8.411  16.407  35.489  1.00 25.00           C
ATOM     14  CA  SER    14      10.701  19.425  36.147  1.00 25.00           C
ATOM     15  CA  GLY    15      13.470  16.781  36.033  1.00 25.00           C
ATOM     16  CA  GLN    16      12.011  15.168  39.184  1.00 25.00           C
ATOM     17  CA  GLU    17      14.093  12.014  38.563  1.00 25.00           C
ATOM     18  CA  LEU    18      17.242  14.149  38.127  1.00 25.00           C
ATOM     19  CA  THR    19      16.479  15.988  41.399  1.00 25.00           C
ATOM     20  CA  ALA    20      16.008  12.640  43.198  1.00 25.00           C
ATOM     21  CA  ILE    21      19.347  11.390  41.800  1.00 25.00           C
ATOM     22  CA  ILE    22      21.072  14.598  42.985  1.00 25.00           C
ATOM     23  CA  LYS    23      19.546  14.159  46.471  1.00 25.00           C
ATOM     24  CA  MET    24      20.765  10.530  46.574  1.00 25.00           C
ATOM     25  CA  ALA    25      24.280  11.655  45.552  1.00 25.00           C
ATOM     26  CA  LYS    26      24.254  14.320  48.303  1.00 25.00           C
ATOM     27  CA  SER    27      23.161  11.695  50.868  1.00 25.00           C
ATOM     28  CA  MET    28      25.980   9.368  49.726  1.00 25.00           C
ATOM     29  CA  VAL    29      28.506  12.227  50.056  1.00 25.00           C
ATOM     30  CA  MET    30      27.222  12.987  53.583  1.00 25.00           C
ATOM     31  CA  ALA    31      28.626  15.793  55.812  1.00 25.00           C
ATOM     32  CA  ASP    32      31.012  17.173  58.391  1.00 25.00           C
ATOM     33  CA  GLY    33      33.452  18.577  61.032  1.00 25.00           C
ATOM     34  CA  LYS    34      35.924  19.710  63.737  1.00 25.00           C
ATOM     35  CA  ILE    35      38.758  20.385  66.095  1.00 25.00           C
ATOM     36  CA  LYS    36      41.657  20.756  68.596  1.00 25.00           C
ATOM     37  CA  PRO    37      44.381  19.006  70.590  1.00 25.00           C
ATOM     38  CA  ALA    38      46.650  17.180  68.103  1.00 25.00           C
ATOM     39  CA  GLU    39      44.271  14.179  68.098  1.00 25.00           C
ATOM     40  CA  ILE    40      41.297  16.507  67.462  1.00 25.00           C
ATOM     41  CA  ALA    41      43.177  18.159  64.564  1.00 25.00           C
ATOM     42  CA  VAL    42      43.967  14.716  63.082  1.00 25.00           C
ATOM     43  CA  MET    43      40.280  13.720  63.371  1.00 25.00           C
ATOM     44  CA  THR    44      39.240  16.968  61.628  1.00 25.00           C
ATOM     45  CA  ARG    45      41.757  16.296  58.820  1.00 25.00           C
ATOM     46  CA  GLU    46      40.392  12.741  58.414  1.00 25.00           C
ATOM     47  CA  PHE    47      36.818  14.108  58.239  1.00 25.00           C
ATOM     48  CA  MET    48      37.892  16.648  55.582  1.00 25.00           C
ATOM     49  CA  ARG    49      39.561  13.859  53.556  1.00 25.00           C
ATOM     50  CA  PHE    50      36.375  11.747  53.793  1.00 25.00           C
ATOM     51  CA  GLY    51      34.282  14.728  52.612  1.00 25.00           C
ATOM     52  CA  ILE    52      36.664  15.264  49.662  1.00 25.00           C
ATOM     53  CA  LEU    53      36.399  11.557  48.743  1.00 25.00           C
ATOM     54  CA  GLN    54      32.578  11.768  48.888  1.00 25.00           C
ATOM     55  CA  ASP    55      32.639  14.862  46.632  1.00 25.00           C
ATOM     56  CA  GLN    56      34.907  13.036  44.146  1.00 25.00           C
ATOM     57  CA  VAL    57      32.527  10.035  44.141  1.00 25.00           C
ATOM     58  CA  ASP    58      29.554  12.364  43.505  1.00 25.00           C
ATOM     59  CA  LEU    59      31.435  14.015  40.607  1.00 25.00           C
ATOM     60  CA  LEU    60      32.224  10.573  39.125  1.00 25.00           C
ATOM     61  CA  LEU    61      28.537   9.576  39.414  1.00 25.00           C
ATOM     62  CA  LYS    62      27.497  12.824  37.672  1.00 25.00           C
ATOM     63  CA  ALA    63      30.014  12.152  34.864  1.00 25.00           C
ATOM     64  CA  SER    64      28.649   8.597  34.458  1.00 25.00           C
ATOM     65  CA  ASP    65      25.075   9.963  34.282  1.00 25.00           C
ATOM     66  CA  SER    66      26.150  12.504  31.625  1.00 25.00           C
ATOM     67  CA  ILE    67      27.819   9.715  29.599  1.00 25.00           C
ATOM     68  CA  GLU    68      24.633   7.603  29.835  1.00 25.00           C
ATOM     69  CA  ALA    69      22.539  10.584  28.656  1.00 25.00           C
ATOM     70  CA  SER    70      24.921  11.120  25.704  1.00 25.00           C
ATOM     71  CA  GLN    71      24.656   7.412  24.786  1.00 25.00           C
ATOM     72  CA  ALA    72      20.835   7.624  24.932  1.00 25.00           C
ATOM     73  CA  VAL    73      20.895  10.718  22.676  1.00 25.00           C
ATOM     74  CA  ALA    74      23.164   8.891  20.189  1.00 25.00           C
ATOM     75  CA  LEU    75      20.784   5.892  20.185  1.00 25.00           C
ATOM     76  CA  ILE    76      17.811   8.220  19.548  1.00 25.00           C
ATOM     77  CA  ALA    77      19.692   9.871  16.650  1.00 25.00           C
ATOM     78  CA  ARG    78      20.481   6.428  15.168  1.00 25.00           C
ATOM     79  CA  MET    79      16.795   5.432  15.458  1.00 25.00           C
ATOM     80  CA  ASP    80      15.754   8.680  13.715  1.00 25.00           C
ATOM     81  CA  GLU    81      18.271   8.008  10.907  1.00 25.00           C
ATOM     82  CA  GLU    82      16.905   4.453  10.501  1.00 25.00           C
ATOM     83  CA  ARG    83      13.332   5.819  10.326  1.00 25.00           C
ATOM     84  CA  LYS    84      14.407   8.360   7.668  1.00 25.00           C
ATOM     85  CA  LYS    85      16.076   5.571   5.642  1.00 25.00           C
ATOM     86  CA  TYR    86      12.890   3.459   5.879  1.00 25.00           C
ATOM     87  CA  VAL    87      10.796   6.440   4.699  1.00 25.00           C
ATOM     88  CA  ALA    88      13.178   6.977   1.748  1.00 25.00           C
ATOM     89  CA  SER    89      12.913   3.268   0.829  1.00 25.00           C
ATOM     90  CA  TYR    90       9.092   3.480   0.974  1.00 25.00           C
ATOM     91  CA  LEU    91       9.153   6.574  -1.281  1.00 25.00           C
ATOM     92  CA  GLY    92      11.421   4.748  -3.767  1.00 25.00           C
ATOM     93  CA  VAL    93       9.041   1.747  -3.772  1.00 25.00           C
ATOM     94  CA  ILE    94       6.068   4.075  -4.409  1.00 25.00           C
ATOM     95  CA  MET    95       7.949   5.727  -7.307  1.00 25.00           C
ATOM     96  CA  ALA    96       8.738   2.284  -8.788  1.00 25.00           C
ATOM     97  CA  SER    97      11.702   0.608  -7.092  1.00 25.00           C
ATOM     98  CA  ASP    98      13.025  -0.387  -3.731  1.00 25.00           C
ATOM     99  CA  GLY    99      14.016  -1.007  -0.130  1.00 25.00           C
ATOM    100  CA  ASP   100      14.812  -1.317   3.604  1.00 25.00           C
ATOM    101  CA  ILE   101      15.606  -1.526   7.336  1.00 25.00           C
ATOM    102  CA  ASP   102      16.343  -1.358  11.123  1.00 25.00           C
ATOM    103  CA  ASP   103      17.100  -1.219  14.856  1.00 25.00           C
ATOM    104  CA  ASN   104      15.377   1.158  17.316  1.00 25.00           C
ATOM    105  CA  GLU   105      14.365  -1.811  19.514  1.00 25.00           C
ATOM    106  CA  LEU   106      17.967  -3.110  19.463  1.00 25.00           C
ATOM    107  CA  ALA   107      19.257   0.358  20.454  1.00 25.00           C
ATOM    108  CA  LEU   108      16.736   0.500  23.332  1.00 25.00           C
ATOM    109  CA  TRP   109      17.850  -2.969  24.513  1.00 25.00           C
ATOM    110  CA  THR   110      21.513  -1.858  24.396  1.00 25.00           C
ATOM    111  CA  LEU   111      20.656   1.273  26.428  1.00 25.00           C
ATOM    112  CA  ILE   112      18.818  -0.877  29.011  1.00 25.00           C
ATOM    113  CA  SER   113      21.843  -3.214  29.253  1.00 25.00           C
ATOM    114  CA  THR   114      24.157  -0.205  29.757  1.00 25.00           C
ATOM    115  CA  LEU   115      21.858   1.134  32.511  1.00 25.00           C
ATOM    116  CA  CYS   116      22.869  -0.536  35.778  1.00 25.00           C
ATOM    117  CA  GLY   117      25.415  -2.698  37.556  1.00 25.00           C
ATOM    118  CA  LEU   118      24.201  -0.979  40.742  1.00 25.00           C
ATOM    119  CA  PRO   119      22.817  -4.355  41.762  1.00 25.00           C
ATOM    120  CA  THR   120      19.093  -4.059  40.964  1.00 25.00           C
ATOM    121  CA  MET   121      16.571  -2.917  38.287  1.00 25.00           C
ATOM    122  CA  THR   122      13.982  -2.919  41.122  1.00 25.00           C
ATOM    123  CA  VAL   123      10.320  -3.110  40.020  1.00 25.00           C
ATOM    124  CA  MET   124      10.011   0.696  40.303  1.00 25.00           C
ATOM    125  CA  GLU   125      13.189   1.135  38.212  1.00 25.00           C
ATOM    126  CA  ALA   126      11.801  -1.254  35.559  1.00 25.00           C
ATOM    127  CA  ILE   127       8.513   0.708  35.476  1.00 25.00           C
ATOM    128  CA  ASN   128      10.450   3.985  35.063  1.00 25.00           C
ATOM    129  CA  ASN   129      12.474   2.456  32.193  1.00 25.00           C
ATOM    130  CA  MET   130       9.242   1.279  30.509  1.00 25.00           C
ATOM    131  CA  LYS   131       5.755   2.821  30.616  1.00 25.00           C
ATOM    132  CA  ASN   132       7.173   5.396  28.141  1.00 25.00           C
TER
END
