
#######################################################
#                                                     #
#                        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  156 (  156),  selected  156 , name T0364TS393_4
# Molecule2: number of CA atoms  153 ( 1220),  selected  153 , name T0364.pdb
# PARAMETERS: T0364TS393_4.T0364.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    P       2      P       2           #
LGA    A       3      A       3          3.038
LGA    L       4      L       4          1.427
LGA    I       5      I       5          1.963
LGA    T       6      T       6          2.478
LGA    Y       7      Y       7          1.610
LGA    R       8      R       8          2.748
LGA    T       9      T       9          4.102
LGA    T      10      T      10          3.285
LGA    V      11      V      11          1.658
LGA    Q      12      Q      12          4.507
LGA    E      13      E      13          2.786
LGA    D      14      D      14          2.673
LGA    W      15      W      15          2.626
LGA    V      16      V      16          2.394
LGA    D      17      D      17          2.410
LGA    Y      18      Y      18          2.229
LGA    N      19      N      19           #
LGA    G      20      -       -           -
LGA    H      21      G      20           #
LGA    L      22      H      21          2.488
LGA    R      23      L      22          4.613
LGA    D      24      -       -           -
LGA    A      25      -       -           -
LGA    F      26      R      23          2.927
LGA    Y      27      D      24          2.476
LGA    L      28      A      25          2.508
LGA    L      29      -       -           -
LGA    I      30      F      26          1.817
LGA    F      31      Y      27          2.174
LGA    S      32      L      28          2.400
LGA    Y      33      L      29          2.312
LGA    A      34      I      30          1.799
LGA    T      35      F      31          1.928
LGA    D      36      S      32          2.611
LGA    A      37      Y      33          2.441
LGA    L      38      A      34          2.141
LGA    M      39      T      35          2.683
LGA    D      40      D      36          3.042
LGA    R      41      A      37          2.753
LGA    I      42      L      38          2.724
LGA    G      43      M      39          1.721
LGA    L      44      D      40          4.720
LGA    D      45      R      41           -
LGA    A      46      I      42           -
LGA    -       -      G      43           -
LGA    D      47      L      44          4.494
LGA    S      48      -       -           -
LGA    R      49      -       -           -
LGA    G      50      -       -           -
LGA    Q      51      -       -           -
LGA    S      52      -       -           -
LGA    G      53      D      45           #
LGA    N      54      A      46           -
LGA    -       -      D      47           -
LGA    -       -      S      48           -
LGA    -       -      R      49           -
LGA    S      55      G      50          5.710
LGA    -       -      Q      51           -
LGA    -       -      S      52           -
LGA    -       -      G      53           -
LGA    -       -      N      54           -
LGA    L      56      S      55          2.767
LGA    F      57      L      56          3.903
LGA    -       -      F      57           -
LGA    T      58      T      58          1.349
LGA    L      59      L      59          0.977
LGA    E      60      E      60          1.664
LGA    A      61      A      61          1.423
LGA    H      62      H      62           #
LGA    I      63      I      63          3.450
LGA    N      64      N      64          3.145
LGA    Y      65      Y      65          2.885
LGA    L      66      L      66          3.237
LGA    H      67      H      67          1.285
LGA    E      68      E      68          2.753
LGA    V      69      V      69          2.230
LGA    K      70      K      70           #
LGA    L      71      L      71           -
LGA    G      72      G      72          3.417
LGA    T      73      T      73          1.934
LGA    E      74      E      74          1.919
LGA    V      75      V      75          1.428
LGA    W      76      W      76          0.414
LGA    V      77      V      77          1.273
LGA    Q      78      Q      78          2.663
LGA    T      79      T      79          3.390
LGA    Q      80      Q      80          4.892
LGA    I      81      I      81          3.273
LGA    L      82      -       -           -
LGA    G      83      L      82          2.128
LGA    F      84      G      83          0.117
LGA    D      85      F      84          5.372
LGA    R      86      D      85          4.533
LGA    K      87      R      86           #
LGA    -       -      K      87           -
LGA    R      88      R      88          3.287
LGA    L      89      L      89          1.695
LGA    H      90      H      90          1.617
LGA    V      91      V      91          1.650
LGA    Y      92      Y      92          1.570
LGA    H      93      H      93          1.334
LGA    S      94      S      94          0.779
LGA    L      95      L      95          1.245
LGA    H      96      H      96          1.472
LGA    R      97      R      97          2.051
LGA    A      98      A      98          3.119
LGA    G      99      G      99          3.296
LGA    F     100      F     100           #
LGA    D     101      D     101          2.244
LGA    E     102      E     102          2.122
LGA    V     103      V     103          1.952
LGA    L     104      L     104          1.625
LGA    A     105      A     105          3.030
LGA    A     106      A     106          1.771
LGA    S     107      S     107          1.056
LGA    E     108      E     108           #
LGA    Q     109      Q     109           #
LGA    M     110      -       -           -
LGA    L     111      M     110           #
LGA    L     112      L     111          1.141
LGA    H     113      L     112          2.144
LGA    V     114      H     113          2.041
LGA    D     115      V     114          2.556
LGA    -       -      D     115           -
LGA    -       -      L     116           -
LGA    L     116      Q     120          1.532
LGA    A     117      S     121           #
LGA    G     118      -       -           -
LGA    P     119      -       -           -
LGA    Q     120      -       -           -
LGA    S     121      -       -           -
LGA    A     122      -       -           -
LGA    P     123      A     122           #
LGA    F     124      P     123          5.031
LGA    G     125      F     124           #
LGA    H     126      G     125          4.977
LGA    T     127      H     126          0.428
LGA    T     128      T     127          3.930
LGA    -       -      T     128           -
LGA    V     129      V     129          0.658
LGA    C     130      C     130          1.193
LGA    R     131      R     131          2.889
LGA    L     132      L     132          2.524
LGA    N     133      N     133          2.674
LGA    H     134      H     134          3.933
LGA    L     135      -       -           -
LGA    V     136      -       -           -
LGA    E     137      L     135          5.404
LGA    -       -      V     136           -
LGA    -       -      E     137           -
LGA    -       -      Q     138           -
LGA    Q     138      Q     139           #
LGA    Q     139      E     140           -
LGA    E     140      G     141           -
LGA    G     141      A     142           -
LGA    A     142      Q     143           -
LGA    Q     143      A     144           -
LGA    A     144      P     145           -
LGA    P     145      Q     146           -
LGA    Q     146      Y     147           -
LGA    Y     147      M     148           -
LGA    M     148      G     149           -
LGA    G     149      R     150           -
LGA    R     150      T     151           -
LGA    T     151      I     152           -
LGA    I     152      K     153           -
LGA    K     153      L     154           -
LGA    L     154      P     155           -
LGA    P     155      A     156           -
LGA    A     156      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  156  153    5.0    100    2.78    65.00     39.756     3.474

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.930321 * X  +  -0.305655 * Y  +  -0.202677 * Z  +  45.337288
  Y_new =   0.022913 * X  +  -0.599996 * Y  +   0.799675 * Z  +  10.047151
  Z_new =  -0.366029 * X  +   0.739310 * Y  +   0.565193 * Z  +   4.801100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.918088   -2.223505  [ DEG:    52.6026   -127.3974 ]
  Theta =   0.374739    2.766854  [ DEG:    21.4710    158.5291 ]
  Phi   =   3.116969   -0.024624  [ DEG:   178.5891     -1.4109 ]
 
# 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: T0364TS393_4                                  
REMARK     2: T0364.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0364TS393_4.T0364.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  156  153   5.0  100   2.78   65.00  39.756
REMARK  ---------------------------------------------------------- 
MOLECULE T0364TS393_4
PFRMAT TS
TARGET T0364
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      29.624   9.921  14.709  1.00 25.00           C
ATOM      2  CA  PRO     2      31.804  12.833  13.409  1.00 25.00           C
ATOM      3  CA  ALA     3      34.907  13.034  11.164  1.00 25.00           C
ATOM      4  CA  LEU     4      37.054  11.951   8.290  1.00 25.00           C
ATOM      5  CA  ILE     5      38.279  12.009   4.644  1.00 25.00           C
ATOM      6  CA  THR     6      38.923   9.856   1.576  1.00 25.00           C
ATOM      7  CA  TYR     7      40.530   8.375  -1.539  1.00 25.00           C
ATOM      8  CA  ARG     8      41.397   4.858  -2.494  1.00 25.00           C
ATOM      9  CA  THR     9      43.684   1.875  -2.953  1.00 25.00           C
ATOM     10  CA  THR    10      42.867   0.922  -6.572  1.00 25.00           C
ATOM     11  CA  VAL    11      43.464  -2.845  -6.340  1.00 25.00           C
ATOM     12  CA  GLN    12      42.139  -6.469  -6.205  1.00 25.00           C
ATOM     13  CA  GLU    13      43.715  -8.095  -9.272  1.00 25.00           C
ATOM     14  CA  ASP    14      47.014  -6.166  -9.503  1.00 25.00           C
ATOM     15  CA  TRP    15      47.859  -7.130  -5.894  1.00 25.00           C
ATOM     16  CA  VAL    16      47.132 -10.613  -4.545  1.00 25.00           C
ATOM     17  CA  ASP    17      49.747 -12.605  -6.415  1.00 25.00           C
ATOM     18  CA  TYR    18      50.056 -16.341  -7.145  1.00 25.00           C
ATOM     19  CA  ASN    19      51.513 -17.442  -3.826  1.00 25.00           C
ATOM     20  CA  GLY    20      48.986 -17.881  -0.995  1.00 25.00           C
ATOM     21  CA  HIS    21      47.622 -14.329  -0.396  1.00 25.00           C
ATOM     22  CA  LEU    22      45.381 -11.432   0.755  1.00 25.00           C
ATOM     23  CA  ARG    23      48.689  -9.747   1.634  1.00 25.00           C
ATOM     24  CA  ASP    24      51.481  -8.575   3.999  1.00 25.00           C
ATOM     25  CA  ALA    25      54.157  -6.128   2.764  1.00 25.00           C
ATOM     26  CA  PHE    26      52.065  -5.375  -0.354  1.00 25.00           C
ATOM     27  CA  TYR    27      48.984  -4.751   1.834  1.00 25.00           C
ATOM     28  CA  LEU    28      51.015  -2.390   4.062  1.00 25.00           C
ATOM     29  CA  LEU    29      52.259  -0.502   0.971  1.00 25.00           C
ATOM     30  CA  ILE    30      48.665  -0.188  -0.314  1.00 25.00           C
ATOM     31  CA  PHE    31      47.537   1.148   3.094  1.00 25.00           C
ATOM     32  CA  SER    32      50.392   3.702   3.065  1.00 25.00           C
ATOM     33  CA  TYR    33      49.396   4.811  -0.462  1.00 25.00           C
ATOM     34  CA  ALA    34      45.756   5.204   0.662  1.00 25.00           C
ATOM     35  CA  THR    35      46.885   7.289   3.669  1.00 25.00           C
ATOM     36  CA  ASP    36      49.002   9.504   1.371  1.00 25.00           C
ATOM     37  CA  ALA    37      46.006   9.981  -0.968  1.00 25.00           C
ATOM     38  CA  LEU    38      43.799  10.932   2.013  1.00 25.00           C
ATOM     39  CA  MET    39      46.429  13.457   3.187  1.00 25.00           C
ATOM     40  CA  ASP    40      46.592  14.960  -0.332  1.00 25.00           C
ATOM     41  CA  ARG    41      42.773  15.246  -0.413  1.00 25.00           C
ATOM     42  CA  ILE    42      42.805  16.974   3.004  1.00 25.00           C
ATOM     43  CA  GLY    43      46.217  18.653   3.121  1.00 25.00           C
ATOM     44  CA  LEU    44      49.737  17.408   2.362  1.00 25.00           C
ATOM     45  CA  ASP    45      49.804  16.010   5.868  1.00 25.00           C
ATOM     46  CA  ALA    46      52.944  17.543   7.262  1.00 25.00           C
ATOM     47  CA  ASP    47      53.711  20.416   4.848  1.00 25.00           C
ATOM     48  CA  SER    48      50.484  22.191   5.898  1.00 25.00           C
ATOM     49  CA  ARG    49      51.418  21.762   9.588  1.00 25.00           C
ATOM     50  CA  GLY    50      54.901  23.197   8.897  1.00 25.00           C
ATOM     51  CA  GLN    51      53.336  26.188   7.088  1.00 25.00           C
ATOM     52  CA  SER    52      54.784  25.755   3.612  1.00 25.00           C
ATOM     53  CA  GLY    53      58.259  25.154   4.945  1.00 25.00           C
ATOM     54  CA  ASN    54      59.267  21.602   6.017  1.00 25.00           C
ATOM     55  CA  SER    55      59.004  18.284   4.105  1.00 25.00           C
ATOM     56  CA  LEU    56      56.928  15.556   2.456  1.00 25.00           C
ATOM     57  CA  PHE    57      57.700  12.176   4.086  1.00 25.00           C
ATOM     58  CA  THR    58      57.434   9.712   6.980  1.00 25.00           C
ATOM     59  CA  LEU    59      58.838   9.356  10.467  1.00 25.00           C
ATOM     60  CA  GLU    60      56.030   7.006  11.668  1.00 25.00           C
ATOM     61  CA  ALA    61      53.970   3.982  10.652  1.00 25.00           C
ATOM     62  CA  HIS    62      53.913   2.141   7.319  1.00 25.00           C
ATOM     63  CA  ILE    63      51.872  -0.745   8.858  1.00 25.00           C
ATOM     64  CA  ASN    64      49.940  -2.397  11.697  1.00 25.00           C
ATOM     65  CA  TYR    65      47.842  -3.943   8.950  1.00 25.00           C
ATOM     66  CA  LEU    66      45.182  -6.569   9.577  1.00 25.00           C
ATOM     67  CA  HIS    67      41.995  -8.004   8.106  1.00 25.00           C
ATOM     68  CA  GLU    68      40.012  -7.907   4.889  1.00 25.00           C
ATOM     69  CA  VAL    69      39.098  -6.359   1.526  1.00 25.00           C
ATOM     70  CA  LYS    70      35.405  -7.101   1.264  1.00 25.00           C
ATOM     71  CA  LEU    71      34.358  -6.864  -2.436  1.00 25.00           C
ATOM     72  CA  GLY    72      35.277  -5.317  -5.773  1.00 25.00           C
ATOM     73  CA  THR    73      37.077  -2.307  -4.206  1.00 25.00           C
ATOM     74  CA  GLU    74      36.037   0.415  -1.698  1.00 25.00           C
ATOM     75  CA  VAL    75      39.195   1.211   0.202  1.00 25.00           C
ATOM     76  CA  TRP    76      37.941   4.481   1.758  1.00 25.00           C
ATOM     77  CA  VAL    77      41.176   5.555   3.371  1.00 25.00           C
ATOM     78  CA  GLN    78      41.367   8.100   6.168  1.00 25.00           C
ATOM     79  CA  THR    79      44.314  10.320   7.156  1.00 25.00           C
ATOM     80  CA  GLN    80      43.492  13.834   8.453  1.00 25.00           C
ATOM     81  CA  ILE    81      45.130  15.959  11.185  1.00 25.00           C
ATOM     82  CA  LEU    82      42.551  16.413  13.949  1.00 25.00           C
ATOM     83  CA  GLY    83      43.905  14.698  17.082  1.00 25.00           C
ATOM     84  CA  PHE    84      47.446  15.951  17.976  1.00 25.00           C
ATOM     85  CA  ASP    85      48.160  17.181  21.522  1.00 25.00           C
ATOM     86  CA  ARG    86      51.942  17.327  20.989  1.00 25.00           C
ATOM     87  CA  LYS    87      52.706  16.186  17.442  1.00 25.00           C
ATOM     88  CA  ARG    88      51.686  18.194  14.377  1.00 25.00           C
ATOM     89  CA  LEU    89      49.763  15.274  12.958  1.00 25.00           C
ATOM     90  CA  HIS    90      48.623  11.955  14.308  1.00 25.00           C
ATOM     91  CA  VAL    91      46.647   9.728  11.863  1.00 25.00           C
ATOM     92  CA  TYR    92      43.766   7.763  13.274  1.00 25.00           C
ATOM     93  CA  HIS    93      43.378   5.483  10.261  1.00 25.00           C
ATOM     94  CA  SER    94      40.985   2.931   8.730  1.00 25.00           C
ATOM     95  CA  LEU    95      39.220   1.566   5.732  1.00 25.00           C
ATOM     96  CA  HIS    96      35.499   0.911   5.716  1.00 25.00           C
ATOM     97  CA  ARG    97      33.346  -1.709   4.041  1.00 25.00           C
ATOM     98  CA  ALA    98      29.798  -3.139   3.770  1.00 25.00           C
ATOM     99  CA  GLY    99      27.961  -4.980   6.529  1.00 25.00           C
ATOM    100  CA  PHE   100      28.016  -4.407  10.289  1.00 25.00           C
ATOM    101  CA  ASP   101      31.583  -3.658  11.167  1.00 25.00           C
ATOM    102  CA  GLU   102      35.142  -4.624  10.458  1.00 25.00           C
ATOM    103  CA  VAL   103      37.705  -2.649   8.461  1.00 25.00           C
ATOM    104  CA  LEU   104      41.168  -3.075   6.953  1.00 25.00           C
ATOM    105  CA  ALA   105      44.369  -1.104   6.308  1.00 25.00           C
ATOM    106  CA  ALA   106      45.172   0.271   9.700  1.00 25.00           C
ATOM    107  CA  SER   107      48.066   2.565  10.572  1.00 25.00           C
ATOM    108  CA  GLU   108      48.993   5.430   8.188  1.00 25.00           C
ATOM    109  CA  GLN   109      51.197   7.960   6.305  1.00 25.00           C
ATOM    110  CA  MET   110      51.223   9.682   9.695  1.00 25.00           C
ATOM    111  CA  LEU   111      52.851  12.514   7.753  1.00 25.00           C
ATOM    112  CA  LEU   112      54.596  13.845  10.823  1.00 25.00           C
ATOM    113  CA  HIS   113      57.504  14.882   8.615  1.00 25.00           C
ATOM    114  CA  VAL   114      58.815  18.256   9.781  1.00 25.00           C
ATOM    115  CA  ASP   115      62.358  18.267   8.434  1.00 25.00           C
ATOM    116  CA  LEU   116      65.318  19.891  10.165  1.00 25.00           C
ATOM    117  CA  ALA   117      67.327  21.961   7.617  1.00 25.00           C
ATOM    118  CA  GLY   118      69.840  23.110  10.229  1.00 25.00           C
ATOM    119  CA  PRO   119      67.994  25.865  12.116  1.00 25.00           C
ATOM    120  CA  GLN   120      65.488  27.517  14.419  1.00 25.00           C
ATOM    121  CA  SER   121      63.230  25.400  16.677  1.00 25.00           C
ATOM    122  CA  ALA   122      59.774  25.936  18.173  1.00 25.00           C
ATOM    123  CA  PRO   123      56.072  25.487  17.471  1.00 25.00           C
ATOM    124  CA  PHE   124      53.542  24.048  15.122  1.00 25.00           C
ATOM    125  CA  GLY   125      50.734  25.620  17.124  1.00 25.00           C
ATOM    126  CA  HIS   126      50.541  28.546  14.758  1.00 25.00           C
ATOM    127  CA  THR   127      49.217  29.920  11.437  1.00 25.00           C
ATOM    128  CA  THR   128      49.374  26.417   9.898  1.00 25.00           C
ATOM    129  CA  VAL   129      47.473  24.986  12.899  1.00 25.00           C
ATOM    130  CA  CYS   130      44.808  27.712  12.542  1.00 25.00           C
ATOM    131  CA  ARG   131      44.464  26.923   8.811  1.00 25.00           C
ATOM    132  CA  LEU   132      44.080  23.196   9.609  1.00 25.00           C
ATOM    133  CA  ASN   133      41.388  24.006  12.210  1.00 25.00           C
ATOM    134  CA  HIS   134      39.537  26.177   9.654  1.00 25.00           C
ATOM    135  CA  LEU   135      39.703  23.340   7.088  1.00 25.00           C
ATOM    136  CA  VAL   136      38.326  20.881   9.680  1.00 25.00           C
ATOM    137  CA  GLU   137      35.469  23.298  10.492  1.00 25.00           C
ATOM    138  CA  GLN   138      34.669  23.644   6.763  1.00 25.00           C
ATOM    139  CA  GLN   139      34.634  19.832   6.392  1.00 25.00           C
ATOM    140  CA  GLU   140      30.811  20.298   6.061  1.00 25.00           C
ATOM    141  CA  GLY   141      28.181  22.942   6.622  1.00 25.00           C
ATOM    142  CA  ALA   142      28.155  25.887   4.305  1.00 25.00           C
ATOM    143  CA  GLN   143      24.639  24.976   3.031  1.00 25.00           C
ATOM    144  CA  ALA   144      25.229  27.045  -0.122  1.00 25.00           C
ATOM    145  CA  PRO   145      27.287  25.005  -2.650  1.00 25.00           C
ATOM    146  CA  GLN   146      28.005  23.969  -6.194  1.00 25.00           C
ATOM    147  CA  TYR   147      26.998  22.904  -9.654  1.00 25.00           C
ATOM    148  CA  MET   148      24.913  19.833 -10.656  1.00 25.00           C
ATOM    149  CA  GLY   149      27.156  16.759 -10.892  1.00 25.00           C
ATOM    150  CA  ARG   150      29.602  19.107 -12.619  1.00 25.00           C
ATOM    151  CA  THR   151      33.043  17.905 -13.648  1.00 25.00           C
ATOM    152  CA  ILE   152      36.011  20.287 -13.478  1.00 25.00           C
ATOM    153  CA  LYS   153      39.654  19.951 -14.352  1.00 25.00           C
ATOM    154  CA  LEU   154      42.114  17.742 -12.587  1.00 25.00           C
ATOM    155  CA  PRO   155      45.309  17.551 -14.631  1.00 25.00           C
ATOM    156  CA  ALA   156      48.076  15.861 -12.577  1.00 25.00           C
TER
END
