
#######################################################
#                                                     #
#                        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  127 (  127),  selected  127 , name T0383TS393_2
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383TS393_2.T0383.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      A       3           -
LGA    N       2      M       4           -
LGA    A       3      N       5           -
LGA    M       4      L       6           -
LGA    N       5      K       7           -
LGA    L       6      R       8           -
LGA    K       7      -       -           -
LGA    R       8      -       -           -
LGA    E       9      -       -           -
LGA    Q      10      -       -           -
LGA    E      11      -       -           -
LGA    F      12      -       -           -
LGA    V      13      -       -           -
LGA    S      14      -       -           -
LGA    Q      15      -       -           -
LGA    Y      16      -       -           -
LGA    H      17      -       -           -
LGA    F      18      -       -           -
LGA    D      19      -       -           -
LGA    A      20      -       -           -
LGA    R      21      -       -           -
LGA    N      22      -       -           -
LGA    F      23      -       -           -
LGA    E      24      -       -           -
LGA    W      25      -       -           -
LGA    E      26      -       -           -
LGA    N      27      -       -           -
LGA    E      28      -       -           -
LGA    N      29      -       -           -
LGA    G      30      -       -           -
LGA    A      31      -       -           -
LGA    P      32      -       -           -
LGA    E      33      -       -           -
LGA    T      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      -       -           -
LGA    D      37      -       -           -
LGA    V      38      -       -           -
LGA    N      39      -       -           -
LGA    F      40      -       -           -
LGA    Q      41      -       -           -
LGA    L      42      -       -           -
LGA    L      43      -       -           -
LGA    Q      44      -       -           -
LGA    H      45      -       -           -
LGA    D      46      -       -           -
LGA    Q      47      -       -           -
LGA    E      48      -       -           -
LGA    N      49      -       -           -
LGA    Q      50      -       -           -
LGA    V      51      -       -           -
LGA    T      52      -       -           -
LGA    S      53      E       9           #
LGA    L      54      Q      10          1.512
LGA    -       -      E      11           -
LGA    I      55      F      12          4.463
LGA    V      56      V      13           -
LGA    I      57      S      14           -
LGA    L      58      Q      15           -
LGA    S      59      Y      16           -
LGA    F      60      H      17           -
LGA    M      61      F      18           -
LGA    I      62      D      19           -
LGA    -       -      A      20           -
LGA    -       -      R      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      E      24           -
LGA    -       -      W      25           -
LGA    -       -      E      26           -
LGA    -       -      N      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      G      30           -
LGA    -       -      A      31           -
LGA    -       -      P      32           -
LGA    -       -      E      33           -
LGA    -       -      T      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    V      63      D      37           #
LGA    F      64      V      38           -
LGA    D      65      N      39           -
LGA    K      66      F      40           -
LGA    F      67      Q      41           -
LGA    V      68      L      42           -
LGA    I      69      L      43           -
LGA    -       -      Q      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      Q      47           -
LGA    -       -      E      48           -
LGA    -       -      N      49           -
LGA    -       -      Q      50           -
LGA    -       -      V      51           -
LGA    -       -      T      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      I      55           -
LGA    -       -      V      56           -
LGA    -       -      I      57           -
LGA    -       -      L      58           -
LGA    -       -      S      59           -
LGA    S      70      F      60          2.750
LGA    -       -      M      61           -
LGA    -       -      I      62           -
LGA    -       -      V      63           -
LGA    -       -      F      64           -
LGA    -       -      D      65           -
LGA    -       -      K      66           -
LGA    -       -      F      67           -
LGA    -       -      V      68           -
LGA    -       -      I      69           -
LGA    G      71      S      70          3.857
LGA    T      72      G      71          6.245
LGA    I      73      T      72          4.583
LGA    S      74      I      73          2.715
LGA    Q      75      S      74          3.957
LGA    V      76      -       -           -
LGA    N      77      Q      75          1.993
LGA    H      78      V      76          2.612
LGA    I      79      -       -           -
LGA    D      80      -       -           -
LGA    G      81      -       -           -
LGA    R      82      -       -           -
LGA    I      83      N      77          4.923
LGA    -       -      H      78           -
LGA    V      84      I      79          3.394
LGA    N      85      D      80          3.509
LGA    E      86      -       -           -
LGA    P      87      -       -           -
LGA    S      88      -       -           -
LGA    E      89      -       -           -
LGA    L      90      G      81          3.408
LGA    N      91      R      82          1.794
LGA    Q      92      I      83           #
LGA    E      93      -       -           -
LGA    E      94      -       -           -
LGA    V      95      -       -           -
LGA    E      96      V      84           #
LGA    -       -      N      85           -
LGA    -       -      E      86           -
LGA    -       -      P      87           -
LGA    -       -      S      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      Q      92           -
LGA    T      97      E      93          4.861
LGA    L      98      E      94          4.730
LGA    A      99      V      95          4.456
LGA    R     100      E      96          2.907
LGA    P     101      T      97          1.897
LGA    C     102      L      98          3.267
LGA    L     103      A      99          2.009
LGA    N     104      R     100          3.526
LGA    M     105      P     101          2.929
LGA    L     106      C     102          1.381
LGA    N     107      L     103          2.434
LGA    R     108      N     104          2.832
LGA    L     109      M     105          1.557
LGA    T     110      L     106          1.383
LGA    Y     111      N     107          2.505
LGA    E     112      R     108          1.851
LGA    V     113      L     109          0.918
LGA    T     114      T     110          1.738
LGA    E     115      Y     111          1.881
LGA    I     116      E     112          0.975
LGA    A     117      V     113          1.246
LGA    -       -      T     114           -
LGA    -       -      E     115           -
LGA    L     118      I     116          1.933
LGA    D     119      A     117          6.258
LGA    -       -      L     118           -
LGA    L     120      D     119          3.817
LGA    P     121      L     120          2.319
LGA    G     122      P     121           -
LGA    I     123      G     122           -
LGA    N     124      I     123           -
LGA    L     125      N     124           -
LGA    E     126      L     125           -
LGA    F     127      E     126           -
LGA    -       -      F     127           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  127  125    5.0     40    3.23     2.50     21.080     1.201

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.597227 * X  +   0.789783 * Y  +   0.139864 * Z  +   9.164529
  Y_new =   0.703420 * X  +   0.431960 * Y  +   0.564456 * Z  +  29.726303
  Z_new =   0.385382 * X  +   0.435492 * Y  +  -0.813528 * Z  +  11.602165 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.650096   -0.491497  [ DEG:   151.8393    -28.1607 ]
  Theta =  -0.395622   -2.745970  [ DEG:   -22.6675   -157.3325 ]
  Phi   =   2.274729   -0.866864  [ DEG:   130.3324    -49.6677 ]
 
# 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: T0383TS393_2                                  
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383TS393_2.T0383.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  127  125   5.0   40   3.23    2.50  21.080
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS393_2
PFRMAT TS
TARGET T0383
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1       8.072   9.035   1.165  1.00 25.00           C
ATOM      2  CA  ASN     2       4.435   9.514   2.196  1.00 25.00           C
ATOM      3  CA  ALA     3       3.908  13.225   1.819  1.00 25.00           C
ATOM      4  CA  MET     4       4.979  16.518   3.398  1.00 25.00           C
ATOM      5  CA  ASN     5       5.275  18.796   6.432  1.00 25.00           C
ATOM      6  CA  LEU     6       8.055  19.971   8.665  1.00 25.00           C
ATOM      7  CA  LYS     7       7.169  23.710   8.823  1.00 25.00           C
ATOM      8  CA  ARG     8       6.182  27.411   8.790  1.00 25.00           C
ATOM      9  CA  GLU     9       3.022  26.017   7.095  1.00 25.00           C
ATOM     10  CA  GLN    10       0.319  28.549   7.827  1.00 25.00           C
ATOM     11  CA  GLU    11      -1.402  25.969  10.074  1.00 25.00           C
ATOM     12  CA  PHE    12       0.181  27.573  13.171  1.00 25.00           C
ATOM     13  CA  VAL    13      -1.017  31.026  12.025  1.00 25.00           C
ATOM     14  CA  SER    14      -4.554  29.652  11.504  1.00 25.00           C
ATOM     15  CA  GLN    15      -4.498  28.106  15.008  1.00 25.00           C
ATOM     16  CA  TYR    16      -2.119  26.607  17.653  1.00 25.00           C
ATOM     17  CA  HIS    17      -3.834  23.191  17.977  1.00 25.00           C
ATOM     18  CA  PHE    18      -6.809  25.288  18.870  1.00 25.00           C
ATOM     19  CA  ASP    19      -8.656  24.996  22.231  1.00 25.00           C
ATOM     20  CA  ALA    20      -8.572  28.670  23.213  1.00 25.00           C
ATOM     21  CA  ARG    21     -10.549  30.288  20.394  1.00 25.00           C
ATOM     22  CA  ASN    22      -8.215  30.883  17.525  1.00 25.00           C
ATOM     23  CA  PHE    23      -4.722  31.222  18.943  1.00 25.00           C
ATOM     24  CA  GLU    24      -4.834  34.758  20.411  1.00 25.00           C
ATOM     25  CA  TRP    25      -2.063  35.868  18.012  1.00 25.00           C
ATOM     26  CA  GLU    26      -3.985  34.369  15.058  1.00 25.00           C
ATOM     27  CA  ASN    27      -7.161  36.202  16.164  1.00 25.00           C
ATOM     28  CA  GLU    28      -5.209  39.486  16.414  1.00 25.00           C
ATOM     29  CA  ASN    29      -8.572  41.308  16.210  1.00 25.00           C
ATOM     30  CA  GLY    30      -9.168  40.748  12.477  1.00 25.00           C
ATOM     31  CA  ALA    31      -5.491  40.593  11.308  1.00 25.00           C
ATOM     32  CA  PRO    32      -2.570  43.002  11.749  1.00 25.00           C
ATOM     33  CA  GLU    33      -0.541  40.931   9.282  1.00 25.00           C
ATOM     34  CA  THR    34       0.896  37.649   8.068  1.00 25.00           C
ATOM     35  CA  LYS    35       0.340  33.877   7.850  1.00 25.00           C
ATOM     36  CA  VAL    36       3.998  32.887   7.904  1.00 25.00           C
ATOM     37  CA  ASP    37       4.234  32.039  11.622  1.00 25.00           C
ATOM     38  CA  VAL    38       5.131  28.649  13.212  1.00 25.00           C
ATOM     39  CA  ASN    39       7.676  25.791  13.530  1.00 25.00           C
ATOM     40  CA  PHE    40       9.461  22.565  14.502  1.00 25.00           C
ATOM     41  CA  GLN    41      12.698  22.149  12.472  1.00 25.00           C
ATOM     42  CA  LEU    42      15.453  20.879  14.767  1.00 25.00           C
ATOM     43  CA  LEU    43      16.656  18.432  17.428  1.00 25.00           C
ATOM     44  CA  GLN    44      19.028  16.168  15.557  1.00 25.00           C
ATOM     45  CA  HIS    45      21.661  13.487  15.339  1.00 25.00           C
ATOM     46  CA  ASP    46      21.208  11.969  18.782  1.00 25.00           C
ATOM     47  CA  GLN    47      18.429  13.681  20.784  1.00 25.00           C
ATOM     48  CA  GLU    48      21.032  15.791  22.640  1.00 25.00           C
ATOM     49  CA  ASN    49      22.634  16.788  19.307  1.00 25.00           C
ATOM     50  CA  GLN    50      25.382  17.933  16.992  1.00 25.00           C
ATOM     51  CA  VAL    51      24.746  21.338  18.657  1.00 25.00           C
ATOM     52  CA  THR    52      20.912  21.507  18.714  1.00 25.00           C
ATOM     53  CA  SER    53      18.714  24.020  16.890  1.00 25.00           C
ATOM     54  CA  LEU    54      15.110  25.285  17.193  1.00 25.00           C
ATOM     55  CA  ILE    55      11.474  26.408  17.377  1.00 25.00           C
ATOM     56  CA  VAL    56       8.370  28.527  17.750  1.00 25.00           C
ATOM     57  CA  ILE    57       5.415  30.998  17.858  1.00 25.00           C
ATOM     58  CA  LEU    58       7.710  32.836  15.454  1.00 25.00           C
ATOM     59  CA  SER    59       5.868  35.981  14.352  1.00 25.00           C
ATOM     60  CA  PHE    60       4.822  38.260  11.423  1.00 25.00           C
ATOM     61  CA  MET    61       7.574  36.357   9.599  1.00 25.00           C
ATOM     62  CA  ILE    62       5.756  37.571   6.507  1.00 25.00           C
ATOM     63  CA  VAL    63       4.395  36.041   3.318  1.00 25.00           C
ATOM     64  CA  PHE    64       2.707  35.177   0.035  1.00 25.00           C
ATOM     65  CA  ASP    65       0.515  35.414  -3.038  1.00 25.00           C
ATOM     66  CA  LYS    66      -1.826  32.680  -4.295  1.00 25.00           C
ATOM     67  CA  PHE    67       0.852  30.190  -3.354  1.00 25.00           C
ATOM     68  CA  VAL    68       1.584  28.938   0.216  1.00 25.00           C
ATOM     69  CA  ILE    69       2.968  30.417   3.419  1.00 25.00           C
ATOM     70  CA  SER    70       5.904  31.349   1.124  1.00 25.00           C
ATOM     71  CA  GLY    71       8.027  29.662   3.849  1.00 25.00           C
ATOM     72  CA  THR    72       8.266  33.162   5.231  1.00 25.00           C
ATOM     73  CA  ILE    73       9.436  31.817   8.623  1.00 25.00           C
ATOM     74  CA  SER    74       9.858  30.017  11.910  1.00 25.00           C
ATOM     75  CA  GLN    75      12.076  27.036  11.186  1.00 25.00           C
ATOM     76  CA  VAL    76      14.051  29.037  13.773  1.00 25.00           C
ATOM     77  CA  ASN    77      12.474  31.235  16.492  1.00 25.00           C
ATOM     78  CA  HIS    78      11.283  32.232  19.992  1.00 25.00           C
ATOM     79  CA  ILE    79      11.440  29.022  22.034  1.00 25.00           C
ATOM     80  CA  ASP    80      10.767  29.762  25.721  1.00 25.00           C
ATOM     81  CA  GLY    81       9.375  31.099  29.065  1.00 25.00           C
ATOM     82  CA  ARG    82       9.843  34.890  29.134  1.00 25.00           C
ATOM     83  CA  ILE    83      11.994  35.235  25.992  1.00 25.00           C
ATOM     84  CA  VAL    84      14.743  35.778  28.564  1.00 25.00           C
ATOM     85  CA  ASN    85      16.223  36.115  32.051  1.00 25.00           C
ATOM     86  CA  GLU    86      19.837  36.188  33.136  1.00 25.00           C
ATOM     87  CA  PRO    87      21.917  39.307  33.411  1.00 25.00           C
ATOM     88  CA  SER    88      20.026  42.406  32.124  1.00 25.00           C
ATOM     89  CA  GLU    89      17.552  45.071  31.161  1.00 25.00           C
ATOM     90  CA  LEU    90      16.042  42.951  28.391  1.00 25.00           C
ATOM     91  CA  ASN    91      12.263  43.075  27.859  1.00 25.00           C
ATOM     92  CA  GLN    92       9.967  44.832  25.492  1.00 25.00           C
ATOM     93  CA  GLU    93      11.886  46.621  22.700  1.00 25.00           C
ATOM     94  CA  GLU    94      14.838  44.225  23.161  1.00 25.00           C
ATOM     95  CA  VAL    95      12.464  41.226  22.982  1.00 25.00           C
ATOM     96  CA  GLU    96      10.905  42.620  19.773  1.00 25.00           C
ATOM     97  CA  THR    97      14.391  43.092  18.256  1.00 25.00           C
ATOM     98  CA  LEU    98      15.309  39.491  19.181  1.00 25.00           C
ATOM     99  CA  ALA    99      12.074  38.227  17.566  1.00 25.00           C
ATOM    100  CA  ARG   100      12.849  40.224  14.392  1.00 25.00           C
ATOM    101  CA  PRO   101      16.384  38.752  14.300  1.00 25.00           C
ATOM    102  CA  CYS   102      14.951  35.222  14.695  1.00 25.00           C
ATOM    103  CA  LEU   103      12.484  35.877  11.841  1.00 25.00           C
ATOM    104  CA  ASN   104      15.342  37.136   9.625  1.00 25.00           C
ATOM    105  CA  MET   105      17.386  34.001  10.439  1.00 25.00           C
ATOM    106  CA  LEU   106      14.387  31.788   9.561  1.00 25.00           C
ATOM    107  CA  ASN   107      13.954  33.649   6.241  1.00 25.00           C
ATOM    108  CA  ARG   108      17.674  33.173   5.462  1.00 25.00           C
ATOM    109  CA  LEU   109      17.384  29.435   6.241  1.00 25.00           C
ATOM    110  CA  THR   110      14.334  29.165   3.940  1.00 25.00           C
ATOM    111  CA  TYR   111      16.252  30.954   1.149  1.00 25.00           C
ATOM    112  CA  GLU   112      19.205  28.558   1.610  1.00 25.00           C
ATOM    113  CA  VAL   113      16.831  25.559   1.430  1.00 25.00           C
ATOM    114  CA  THR   114      15.272  26.953  -1.778  1.00 25.00           C
ATOM    115  CA  GLU   115      18.758  27.425  -3.295  1.00 25.00           C
ATOM    116  CA  ILE   116      19.676  23.824  -2.371  1.00 25.00           C
ATOM    117  CA  ALA   117      16.441  22.560  -3.985  1.00 25.00           C
ATOM    118  CA  LEU   118      18.690  19.952  -5.544  1.00 25.00           C
ATOM    119  CA  ASP   119      22.046  21.543  -6.251  1.00 25.00           C
ATOM    120  CA  LEU   120      23.643  22.672  -9.551  1.00 25.00           C
ATOM    121  CA  PRO   121      21.799  23.832 -12.655  1.00 25.00           C
ATOM    122  CA  GLY   122      20.485  21.299 -15.168  1.00 25.00           C
ATOM    123  CA  ILE   123      19.400  18.440 -12.999  1.00 25.00           C
ATOM    124  CA  ASN   124      16.974  15.842 -14.213  1.00 25.00           C
ATOM    125  CA  LEU   125      13.717  17.602 -13.348  1.00 25.00           C
ATOM    126  CA  GLU   126      10.508  18.426 -15.209  1.00 25.00           C
ATOM    127  CA  PHE   127      10.334  22.253 -14.740  1.00 25.00           C
TER
END
