
#######################################################
#                                                     #
#                        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 T0352TS393_3
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS393_3.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    T       3      T       3           -
LGA    H       4      H       4           -
LGA    D       5      D       5           -
LGA    R       6      R       6           -
LGA    V       7      V       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    Q      10      Q      10           -
LGA    L      11      L      11           -
LGA    Q      12      Q      12           -
LGA    A      13      A      13           -
LGA    L      14      L      14           -
LGA    E      15      E      15           -
LGA    A      16      A      16           -
LGA    L      17      L      17           -
LGA    L      18      L      18           -
LGA    R      19      R      19           -
LGA    E      20      E      20           -
LGA    H      21      H      21           -
LGA    Q      22      Q      22           -
LGA    H      23      H      23           -
LGA    W      24      W      24           -
LGA    R      25      R      25           -
LGA    N      26      N      26           -
LGA    D      27      D      27           -
LGA    E      28      E      28           -
LGA    P      29      P      29           -
LGA    Q      30      Q      30           -
LGA    P      31      P      31          4.989
LGA    H      32      H      32          4.293
LGA    Q      33      Q      33          1.485
LGA    F      34      -       -           -
LGA    N      35      F      34          2.582
LGA    S      36      -       -           -
LGA    T      37      N      35          4.461
LGA    Q      38      S      36           -
LGA    P      39      T      37           -
LGA    F      40      -       -           -
LGA    F      41      -       -           -
LGA    M      42      Q      38           #
LGA    D      43      P      39           -
LGA    T      44      -       -           -
LGA    M      45      -       -           -
LGA    E      46      -       -           -
LGA    P      47      -       -           -
LGA    L      48      -       -           -
LGA    E      49      -       -           -
LGA    W      50      F      40          2.899
LGA    L      51      F      41          2.792
LGA    Q      52      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    W      53      W      53           #
LGA    V      54      V      54           #
LGA    L      55      L      55          4.060
LGA    I      56      I      56          3.200
LGA    P      57      P      57          2.443
LGA    R      58      R      58          2.052
LGA    M      59      M      59          2.376
LGA    H      60      H      60          3.799
LGA    D      61      D      61          2.926
LGA    L      62      -       -           -
LGA    L      63      L      62          3.684
LGA    D      64      L      63          1.413
LGA    N      65      D      64          2.209
LGA    K      66      N      65          2.498
LGA    Q      67      K      66          3.089
LGA    P      68      Q      67          3.326
LGA    L      69      -       -           -
LGA    P      70      P      68          2.377
LGA    G      71      L      69          2.407
LGA    A      72      P      70          2.029
LGA    F      73      G      71          0.881
LGA    A      74      A      72          3.388
LGA    V      75      -       -           -
LGA    A      76      -       -           -
LGA    P      77      -       -           -
LGA    Y      78      F      73          2.645
LGA    Y      79      A      74          3.335
LGA    E      80      -       -           -
LGA    M      81      -       -           -
LGA    A      82      V      75          3.092
LGA    L      83      A      76          1.646
LGA    A      84      P      77          2.752
LGA    T      85      Y      78          2.212
LGA    D      86      Y      79          2.341
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    H      87      R      90          2.465
LGA    P      88      A      91          3.346
LGA    -       -      L      92           -
LGA    Q      89      I      93          1.720
LGA    R      90      L      94          2.505
LGA    A      91      A      95          2.359
LGA    L      92      E      96          0.929
LGA    I      93      L      97          0.299
LGA    L      94      E      98          0.498
LGA    A      95      K      99          1.507
LGA    E      96      L     100          1.836
LGA    L      97      D     101          1.352
LGA    E      98      A     102          1.750
LGA    K      99      L     103          1.491
LGA    L     100      F     104          1.129
LGA    D     101      A     105          0.638
LGA    A     102      D     106          0.806
LGA    L     103      D     107          4.735
LGA    F     104      -       -           -
LGA    A     105      -       -           -
LGA    D     106      A     108           #
LGA    D     107      S     109           -
LGA    A     108      -       -           -
LGA    S     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  109    5.0     49    2.67    28.57     29.696     1.772

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.571681 * X  +   0.278119 * Y  +  -0.771900 * Z  +  -7.377170
  Y_new =   0.744505 * X  +  -0.219532 * Y  +  -0.630490 * Z  +   5.441915
  Z_new =  -0.344808 * X  +  -0.935123 * Y  +  -0.081558 * Z  +   2.223627 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.657793    1.483800  [ DEG:   -94.9845     85.0155 ]
  Theta =   0.352034    2.789558  [ DEG:    20.1701    159.8299 ]
  Phi   =   2.225635   -0.915958  [ DEG:   127.5195    -52.4805 ]
 
# 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: T0352TS393_3                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS393_3.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   49   2.67   28.57  29.696
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS393_3
PFRMAT TS
TARGET T0352
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -1.931  -6.743  22.648  1.00 25.00           C
ATOM      2  CA  THR     2      -2.874  -6.644  18.956  1.00 25.00           C
ATOM      3  CA  THR     3      -4.990  -5.406  16.111  1.00 25.00           C
ATOM      4  CA  HIS     4      -6.709  -2.392  17.732  1.00 25.00           C
ATOM      5  CA  ASP     5      -3.323  -0.650  18.141  1.00 25.00           C
ATOM      6  CA  ARG     6      -2.501  -1.329  14.462  1.00 25.00           C
ATOM      7  CA  VAL     7      -5.895   0.106  13.416  1.00 25.00           C
ATOM      8  CA  ARG     8      -5.259   3.228  15.543  1.00 25.00           C
ATOM      9  CA  LEU     9      -1.809   3.649  13.935  1.00 25.00           C
ATOM     10  CA  GLN    10      -3.365   3.323  10.450  1.00 25.00           C
ATOM     11  CA  LEU    11      -5.997   5.955  11.353  1.00 25.00           C
ATOM     12  CA  GLN    12      -3.249   8.308  12.608  1.00 25.00           C
ATOM     13  CA  ALA    13      -1.293   7.801   9.355  1.00 25.00           C
ATOM     14  CA  LEU    14      -4.443   8.565   7.313  1.00 25.00           C
ATOM     15  CA  GLU    15      -5.027  11.749   9.361  1.00 25.00           C
ATOM     16  CA  ALA    16      -1.396  12.820   8.774  1.00 25.00           C
ATOM     17  CA  LEU    17      -1.796  12.205   5.015  1.00 25.00           C
ATOM     18  CA  LEU    18      -5.009  14.288   4.992  1.00 25.00           C
ATOM     19  CA  ARG    19      -3.215  17.121   6.843  1.00 25.00           C
ATOM     20  CA  GLU    20      -0.347  16.994   4.309  1.00 25.00           C
ATOM     21  CA  HIS    21      -2.859  17.147   1.422  1.00 25.00           C
ATOM     22  CA  GLN    22      -4.577  20.162   3.043  1.00 25.00           C
ATOM     23  CA  HIS    23      -1.191  21.903   3.451  1.00 25.00           C
ATOM     24  CA  TRP    24      -0.371  21.225  -0.228  1.00 25.00           C
ATOM     25  CA  ARG    25      -3.764  22.661  -1.274  1.00 25.00           C
ATOM     26  CA  ASN    26      -3.123  25.894   0.708  1.00 25.00           C
ATOM     27  CA  ASP    27      -0.388  27.369   2.946  1.00 25.00           C
ATOM     28  CA  GLU    28       1.223  28.605  -0.323  1.00 25.00           C
ATOM     29  CA  PRO    29       2.147  28.941  -3.968  1.00 25.00           C
ATOM     30  CA  GLN    30      -0.604  28.495  -6.639  1.00 25.00           C
ATOM     31  CA  PRO    31      -1.521  26.072  -9.466  1.00 25.00           C
ATOM     32  CA  HIS    32      -1.949  22.325  -8.799  1.00 25.00           C
ATOM     33  CA  GLN    33      -5.528  22.926  -7.576  1.00 25.00           C
ATOM     34  CA  PHE    34      -6.288  24.966 -10.728  1.00 25.00           C
ATOM     35  CA  ASN    35      -4.875  22.157 -12.915  1.00 25.00           C
ATOM     36  CA  SER    36      -6.940  21.944 -16.036  1.00 25.00           C
ATOM     37  CA  THR    37      -8.879  18.714 -15.255  1.00 25.00           C
ATOM     38  CA  GLN    38     -12.160  20.556 -15.792  1.00 25.00           C
ATOM     39  CA  PRO    39     -13.513  23.799 -14.332  1.00 25.00           C
ATOM     40  CA  PHE    40     -14.838  22.950 -10.931  1.00 25.00           C
ATOM     41  CA  PHE    41     -17.648  20.792  -9.599  1.00 25.00           C
ATOM     42  CA  MET    42     -17.538  21.622  -5.861  1.00 25.00           C
ATOM     43  CA  ASP    43     -19.716  24.141  -3.983  1.00 25.00           C
ATOM     44  CA  THR    44     -17.682  25.863  -1.189  1.00 25.00           C
ATOM     45  CA  MET    45     -15.259  23.883   0.988  1.00 25.00           C
ATOM     46  CA  GLU    46     -16.668  21.481   3.583  1.00 25.00           C
ATOM     47  CA  PRO    47     -15.709  17.932   2.695  1.00 25.00           C
ATOM     48  CA  LEU    48     -16.599  14.258   3.312  1.00 25.00           C
ATOM     49  CA  GLU    49     -16.026  13.472  -0.392  1.00 25.00           C
ATOM     50  CA  TRP    50     -12.628  15.233  -0.266  1.00 25.00           C
ATOM     51  CA  LEU    51     -11.674  13.223   2.851  1.00 25.00           C
ATOM     52  CA  GLN    52     -12.696   9.974   1.099  1.00 25.00           C
ATOM     53  CA  TRP    53     -10.588  10.928  -1.953  1.00 25.00           C
ATOM     54  CA  VAL    54      -7.591  11.660   0.316  1.00 25.00           C
ATOM     55  CA  LEU    55      -8.033   8.267   2.037  1.00 25.00           C
ATOM     56  CA  ILE    56      -8.170   6.528  -1.373  1.00 25.00           C
ATOM     57  CA  PRO    57      -4.973   8.341  -2.452  1.00 25.00           C
ATOM     58  CA  ARG    58      -3.239   7.264   0.789  1.00 25.00           C
ATOM     59  CA  MET    59      -4.331   3.641   0.200  1.00 25.00           C
ATOM     60  CA  HIS    60      -2.979   3.790  -3.380  1.00 25.00           C
ATOM     61  CA  ASP    61       0.350   5.177  -2.090  1.00 25.00           C
ATOM     62  CA  LEU    62       0.548   2.362   0.498  1.00 25.00           C
ATOM     63  CA  LEU    63      -0.142  -0.232  -2.234  1.00 25.00           C
ATOM     64  CA  ASP    64       2.606   1.299  -4.416  1.00 25.00           C
ATOM     65  CA  ASN    65       5.691   2.807  -2.745  1.00 25.00           C
ATOM     66  CA  LYS    66       7.437   0.135  -0.703  1.00 25.00           C
ATOM     67  CA  GLN    67       8.572   2.791   1.798  1.00 25.00           C
ATOM     68  CA  PRO    68       8.380   0.308   4.736  1.00 25.00           C
ATOM     69  CA  LEU    69       5.883   1.771   7.259  1.00 25.00           C
ATOM     70  CA  PRO    70       3.218  -0.954   7.387  1.00 25.00           C
ATOM     71  CA  GLY    71      -0.091  -0.729   5.447  1.00 25.00           C
ATOM     72  CA  ALA    72      -3.400   0.508   4.036  1.00 25.00           C
ATOM     73  CA  PHE    73      -6.087  -2.002   5.108  1.00 25.00           C
ATOM     74  CA  ALA    74      -6.618  -0.074   8.375  1.00 25.00           C
ATOM     75  CA  VAL    75      -6.952   3.200   6.417  1.00 25.00           C
ATOM     76  CA  ALA    76      -9.510   1.570   4.080  1.00 25.00           C
ATOM     77  CA  PRO    77     -11.493   0.296   7.099  1.00 25.00           C
ATOM     78  CA  TYR    78     -11.452   3.803   8.637  1.00 25.00           C
ATOM     79  CA  TYR    79     -12.689   5.294   5.334  1.00 25.00           C
ATOM     80  CA  GLU    80     -15.508   2.704   5.192  1.00 25.00           C
ATOM     81  CA  MET    81     -16.497   3.547   8.795  1.00 25.00           C
ATOM     82  CA  ALA    82     -16.541   7.279   7.935  1.00 25.00           C
ATOM     83  CA  LEU    83     -18.742   6.574   4.881  1.00 25.00           C
ATOM     84  CA  ALA    84     -21.139   4.522   7.050  1.00 25.00           C
ATOM     85  CA  THR    85     -24.015   6.949   6.448  1.00 25.00           C
ATOM     86  CA  ASP    86     -23.607   8.201   2.909  1.00 25.00           C
ATOM     87  CA  HIS    87     -25.252   6.296   0.111  1.00 25.00           C
ATOM     88  CA  PRO    88     -23.933   5.567  -3.366  1.00 25.00           C
ATOM     89  CA  GLN    89     -20.297   6.689  -2.929  1.00 25.00           C
ATOM     90  CA  ARG    90     -20.226   5.172   0.587  1.00 25.00           C
ATOM     91  CA  ALA    91     -21.639   1.883  -0.776  1.00 25.00           C
ATOM     92  CA  LEU    92     -18.970   1.849  -3.524  1.00 25.00           C
ATOM     93  CA  ILE    93     -16.237   2.455  -0.911  1.00 25.00           C
ATOM     94  CA  LEU    94     -17.606  -0.413   1.224  1.00 25.00           C
ATOM     95  CA  ALA    95     -17.616  -2.718  -1.835  1.00 25.00           C
ATOM     96  CA  GLU    96     -13.996  -1.742  -2.613  1.00 25.00           C
ATOM     97  CA  LEU    97     -12.995  -2.471   1.012  1.00 25.00           C
ATOM     98  CA  GLU    98     -14.715  -5.888   0.825  1.00 25.00           C
ATOM     99  CA  LYS    99     -12.870  -6.665  -2.439  1.00 25.00           C
ATOM    100  CA  LEU   100      -9.543  -5.673  -0.824  1.00 25.00           C
ATOM    101  CA  ASP   101     -10.295  -7.933   2.175  1.00 25.00           C
ATOM    102  CA  ALA   102     -11.114 -10.835  -0.187  1.00 25.00           C
ATOM    103  CA  LEU   103      -7.829 -10.261  -2.070  1.00 25.00           C
ATOM    104  CA  PHE   104      -5.903 -10.252   1.240  1.00 25.00           C
ATOM    105  CA  ALA   105      -7.609 -13.523   2.270  1.00 25.00           C
ATOM    106  CA  ASP   106      -6.693 -15.089  -1.104  1.00 25.00           C
ATOM    107  CA  ASP   107      -3.058 -13.968  -0.665  1.00 25.00           C
ATOM    108  CA  ALA   108      -2.987 -15.484   2.850  1.00 25.00           C
ATOM    109  CA  SER   109      -4.400 -18.773   1.487  1.00 25.00           C
ATOM    110  CA  LEU   110      -7.240 -20.001   3.641  1.00 25.00           C
ATOM    111  CA  GLU   111      -4.389 -20.776   6.099  1.00 25.00           C
ATOM    112  CA  HIS   112      -1.143 -22.826   6.106  1.00 25.00           C
ATOM    113  CA  HIS   113      -0.333 -23.604   9.741  1.00 25.00           C
ATOM    114  CA  HIS   114       2.942 -22.200  11.148  1.00 25.00           C
ATOM    115  CA  HIS   115       6.011 -20.485   9.680  1.00 25.00           C
ATOM    116  CA  HIS   116       6.794 -17.176   8.036  1.00 25.00           C
ATOM    117  CA  HIS   117       4.357 -18.362   5.399  1.00 25.00           C
TER
END
