
#######################################################
#                                                     #
#                        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 T0352TS168_2
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS168_2.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    T       3      -       -           -
LGA    H       4      M       1          2.554
LGA    D       5      T       2          0.778
LGA    R       6      T       3          0.578
LGA    V       7      H       4          0.486
LGA    R       8      D       5          0.218
LGA    L       9      R       6          0.435
LGA    Q      10      V       7          0.621
LGA    L      11      R       8          0.614
LGA    Q      12      L       9          0.553
LGA    A      13      Q      10          0.399
LGA    L      14      L      11          1.354
LGA    E      15      Q      12          1.679
LGA    A      16      A      13          0.959
LGA    L      17      L      14          1.032
LGA    L      18      E      15          1.567
LGA    R      19      A      16          1.124
LGA    E      20      L      17          0.656
LGA    H      21      L      18          1.510
LGA    Q      22      R      19          1.420
LGA    H      23      E      20          0.646
LGA    W      24      H      21          1.147
LGA    R      25      Q      22          1.409
LGA    -       -      H      23           -
LGA    N      26      W      24          5.662
LGA    D      27      R      25           -
LGA    E      28      N      26           -
LGA    P      29      D      27           -
LGA    Q      30      E      28           -
LGA    P      31      P      29           -
LGA    H      32      Q      30           -
LGA    Q      33      P      31           -
LGA    F      34      H      32           -
LGA    N      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      -       -           -
LGA    Q      38      -       -           -
LGA    P      39      -       -           -
LGA    F      40      -       -           -
LGA    F      41      -       -           -
LGA    M      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    M      45      Q      33           #
LGA    E      46      F      34           #
LGA    P      47      N      35          4.591
LGA    L      48      S      36          2.768
LGA    E      49      -       -           -
LGA    W      50      T      37          3.199
LGA    L      51      Q      38          4.234
LGA    Q      52      P      39           #
LGA    W      53      F      40          3.525
LGA    V      54      F      41           #
LGA    -       -      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           -
LGA    -       -      V      54           -
LGA    -       -      L      55           -
LGA    L      55      I      56          5.146
LGA    I      56      P      57           #
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      A      74           -
LGA    P      57      V      75           #
LGA    R      58      A      76           -
LGA    M      59      P      77           -
LGA    -       -      Y      78           -
LGA    -       -      Y      79           -
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    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    H      60      E      96           #
LGA    D      61      L      97          1.332
LGA    -       -      E      98           -
LGA    L      62      K      99          3.701
LGA    L      63      L     100          4.367
LGA    D      64      D     101          4.080
LGA    N      65      A     102           #
LGA    K      66      -       -           -
LGA    Q      67      -       -           -
LGA    P      68      L     103          5.080
LGA    L      69      F     104          3.771
LGA    P      70      A     105          2.134
LGA    G      71      D     106           -
LGA    A      72      D     107           -
LGA    F      73      A     108           -
LGA    A      74      S     109           -
LGA    V      75      -       -           -
LGA    A      76      -       -           -
LGA    P      77      -       -           -
LGA    Y      78      -       -           -
LGA    Y      79      -       -           -
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    R      90      -       -           -
LGA    A      91      -       -           -
LGA    L      92      -       -           -
LGA    I      93      -       -           -
LGA    L      94      -       -           -
LGA    A      95      -       -           -
LGA    E      96      -       -           -
LGA    L      97      -       -           -
LGA    E      98      -       -           -
LGA    K      99      -       -           -
LGA    L     100      -       -           -
LGA    D     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    F     104      -       -           -
LGA    A     105      -       -           -
LGA    D     106      -       -           -
LGA    D     107      -       -           -
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     36    2.64    13.89     24.507     1.312

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.276765 * X  +  -0.203892 * Y  +   0.939057 * Z  + -11.276997
  Y_new =   0.808497 * X  +   0.478756 * Y  +   0.342235 * Z  +   8.413441
  Z_new =  -0.519359 * X  +   0.853944 * Y  +   0.032343 * Z  +  -0.146238 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.532940   -1.608653  [ DEG:    87.8310    -92.1690 ]
  Theta =   0.546100    2.595492  [ DEG:    31.2892    148.7108 ]
  Phi   =   1.900614   -1.240979  [ DEG:   108.8971    -71.1029 ]
 
# 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: T0352TS168_2                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS168_2.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   36   2.64   13.89  24.507
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS168_2
PFRMAT TS
TARGET T0352
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1       5.982 -10.159  -0.981  1.00 25.00           C
ATOM      2  CA  THR     2       4.818  -9.269  -4.509  1.00 25.00           C
ATOM      3  CA  THR     3       1.871  -6.896  -4.346  1.00 25.00           C
ATOM      4  CA  HIS     4       2.248  -5.140  -7.728  1.00 25.00           C
ATOM      5  CA  ASP     5      -1.055  -6.671  -8.918  1.00 25.00           C
ATOM      6  CA  ARG     6      -2.786  -5.490  -5.714  1.00 25.00           C
ATOM      7  CA  VAL     7      -1.384  -1.963  -6.228  1.00 25.00           C
ATOM      8  CA  ARG     8      -2.642  -1.964  -9.845  1.00 25.00           C
ATOM      9  CA  LEU     9      -6.109  -3.085  -8.666  1.00 25.00           C
ATOM     10  CA  GLN    10      -6.149  -0.289  -6.048  1.00 25.00           C
ATOM     11  CA  LEU    11      -5.172   2.266  -8.728  1.00 25.00           C
ATOM     12  CA  GLN    12      -7.972   0.989 -11.005  1.00 25.00           C
ATOM     13  CA  ALA    13     -10.481   1.282  -8.125  1.00 25.00           C
ATOM     14  CA  LEU    14      -9.310   4.863  -7.439  1.00 25.00           C
ATOM     15  CA  GLU    15      -9.711   5.732 -11.148  1.00 25.00           C
ATOM     16  CA  ALA    16     -13.245   4.254 -11.137  1.00 25.00           C
ATOM     17  CA  LEU    17     -14.119   6.305  -8.023  1.00 25.00           C
ATOM     18  CA  LEU    18     -12.784   9.476  -9.706  1.00 25.00           C
ATOM     19  CA  ARG    19     -14.875   8.730 -12.826  1.00 25.00           C
ATOM     20  CA  GLU    20     -17.986   8.223 -10.650  1.00 25.00           C
ATOM     21  CA  HIS    21     -17.317  11.551  -8.876  1.00 25.00           C
ATOM     22  CA  GLN    22     -16.941  13.307 -12.259  1.00 25.00           C
ATOM     23  CA  HIS    23     -20.244  11.775 -13.449  1.00 25.00           C
ATOM     24  CA  TRP    24     -21.975  12.957 -10.243  1.00 25.00           C
ATOM     25  CA  ARG    25     -20.573  16.484 -10.758  1.00 25.00           C
ATOM     26  CA  ASN    26     -22.826  16.386 -13.821  1.00 25.00           C
ATOM     27  CA  ASP    27     -25.113  13.852 -15.419  1.00 25.00           C
ATOM     28  CA  GLU    28     -27.691  16.625 -15.351  1.00 25.00           C
ATOM     29  CA  PRO    29     -29.546  17.974 -12.353  1.00 25.00           C
ATOM     30  CA  GLN    30     -28.393  21.103 -10.452  1.00 25.00           C
ATOM     31  CA  PRO    31     -27.142  20.069  -6.951  1.00 25.00           C
ATOM     32  CA  HIS    32     -27.488  17.724  -3.941  1.00 25.00           C
ATOM     33  CA  GLN    33     -23.677  17.402  -3.723  1.00 25.00           C
ATOM     34  CA  PHE    34     -23.323  21.214  -3.843  1.00 25.00           C
ATOM     35  CA  ASN    35     -25.925  21.567  -1.055  1.00 25.00           C
ATOM     36  CA  SER    36     -26.875  20.426   2.490  1.00 25.00           C
ATOM     37  CA  THR    37     -24.240  21.825   4.897  1.00 25.00           C
ATOM     38  CA  GLN    38     -22.442  24.991   3.872  1.00 25.00           C
ATOM     39  CA  PRO    39     -20.864  28.120   2.376  1.00 25.00           C
ATOM     40  CA  PHE    40     -20.181  28.571  -1.364  1.00 25.00           C
ATOM     41  CA  PHE    41     -16.590  29.109  -2.483  1.00 25.00           C
ATOM     42  CA  MET    42     -15.754  26.610  -5.277  1.00 25.00           C
ATOM     43  CA  ASP    43     -13.818  29.375  -7.061  1.00 25.00           C
ATOM     44  CA  THR    44     -12.710  26.761  -9.589  1.00 25.00           C
ATOM     45  CA  MET    45     -11.514  23.273 -10.303  1.00 25.00           C
ATOM     46  CA  GLU    46      -8.373  23.850  -8.309  1.00 25.00           C
ATOM     47  CA  PRO    47      -8.065  20.139  -7.527  1.00 25.00           C
ATOM     48  CA  LEU    48      -5.444  18.187  -5.531  1.00 25.00           C
ATOM     49  CA  GLU    49      -7.734  18.203  -2.461  1.00 25.00           C
ATOM     50  CA  TRP    50     -10.646  16.929  -4.597  1.00 25.00           C
ATOM     51  CA  LEU    51      -8.431  14.138  -5.998  1.00 25.00           C
ATOM     52  CA  GLN    52      -7.375  13.162  -2.449  1.00 25.00           C
ATOM     53  CA  TRP    53     -11.043  13.074  -1.354  1.00 25.00           C
ATOM     54  CA  VAL    54     -11.913  10.862  -4.357  1.00 25.00           C
ATOM     55  CA  LEU    55      -9.028   8.499  -3.483  1.00 25.00           C
ATOM     56  CA  ILE    56     -10.247   8.313   0.143  1.00 25.00           C
ATOM     57  CA  PRO    57     -13.795   7.522  -1.064  1.00 25.00           C
ATOM     58  CA  ARG    58     -12.430   4.764  -3.344  1.00 25.00           C
ATOM     59  CA  MET    59     -10.442   3.294  -0.419  1.00 25.00           C
ATOM     60  CA  HIS    60     -13.584   3.344   1.771  1.00 25.00           C
ATOM     61  CA  ASP    61     -15.566   1.578  -0.988  1.00 25.00           C
ATOM     62  CA  LEU    62     -12.823  -1.077  -1.294  1.00 25.00           C
ATOM     63  CA  LEU    63     -12.880  -1.607   2.498  1.00 25.00           C
ATOM     64  CA  ASP    64     -16.690  -1.986   2.413  1.00 25.00           C
ATOM     65  CA  ASN    65     -18.568  -2.807  -0.792  1.00 25.00           C
ATOM     66  CA  LYS    66     -18.361  -6.388  -1.905  1.00 25.00           C
ATOM     67  CA  GLN    67     -15.307  -8.722  -2.029  1.00 25.00           C
ATOM     68  CA  PRO    68     -13.291 -11.073   0.225  1.00 25.00           C
ATOM     69  CA  LEU    69     -11.180  -8.113   1.484  1.00 25.00           C
ATOM     70  CA  PRO    70      -8.813  -7.451   4.350  1.00 25.00           C
ATOM     71  CA  GLY    71      -8.383  -3.620   4.179  1.00 25.00           C
ATOM     72  CA  ALA    72      -7.278   0.008   3.603  1.00 25.00           C
ATOM     73  CA  PHE    73      -3.634  -1.111   3.233  1.00 25.00           C
ATOM     74  CA  ALA    74      -3.649  -0.028  -0.441  1.00 25.00           C
ATOM     75  CA  VAL    75      -5.085   3.383   0.547  1.00 25.00           C
ATOM     76  CA  ALA    76      -2.369   3.780   3.217  1.00 25.00           C
ATOM     77  CA  PRO    77       0.326   2.899   0.643  1.00 25.00           C
ATOM     78  CA  TYR    78      -1.124   5.474  -1.793  1.00 25.00           C
ATOM     79  CA  TYR    79      -1.113   8.128   0.967  1.00 25.00           C
ATOM     80  CA  GLU    80       2.535   7.299   1.786  1.00 25.00           C
ATOM     81  CA  MET    81       3.460   7.600  -1.919  1.00 25.00           C
ATOM     82  CA  ALA    82       1.693  10.992  -2.110  1.00 25.00           C
ATOM     83  CA  LEU    83       3.584  12.180   1.001  1.00 25.00           C
ATOM     84  CA  ALA    84       6.896  11.042  -0.548  1.00 25.00           C
ATOM     85  CA  THR    85       6.401  10.972  -4.262  1.00 25.00           C
ATOM     86  CA  ASP    86       4.726  14.435  -4.199  1.00 25.00           C
ATOM     87  CA  HIS    87       3.794  16.669  -1.266  1.00 25.00           C
ATOM     88  CA  PRO    88       2.120  19.382   0.808  1.00 25.00           C
ATOM     89  CA  GLN    89      -1.372  18.890  -0.686  1.00 25.00           C
ATOM     90  CA  ARG    90      -0.951  15.089  -0.479  1.00 25.00           C
ATOM     91  CA  ALA    91       0.138  15.385   3.181  1.00 25.00           C
ATOM     92  CA  LEU    92      -2.918  17.565   3.939  1.00 25.00           C
ATOM     93  CA  ILE    93      -5.202  14.995   2.253  1.00 25.00           C
ATOM     94  CA  LEU    94      -3.609  12.190   4.317  1.00 25.00           C
ATOM     95  CA  ALA    95      -4.135  14.216   7.523  1.00 25.00           C
ATOM     96  CA  GLU    96      -7.801  14.800   6.583  1.00 25.00           C
ATOM     97  CA  LEU    97      -8.258  11.054   5.940  1.00 25.00           C
ATOM     98  CA  GLU    98      -6.689  10.253   9.341  1.00 25.00           C
ATOM     99  CA  LYS    99      -9.033  12.761  11.039  1.00 25.00           C
ATOM    100  CA  LEU   100     -12.044  11.173   9.286  1.00 25.00           C
ATOM    101  CA  ASP   101     -10.911   7.699  10.432  1.00 25.00           C
ATOM    102  CA  ALA   102     -10.550   8.977  14.025  1.00 25.00           C
ATOM    103  CA  LEU   103     -14.064  10.489  13.868  1.00 25.00           C
ATOM    104  CA  PHE   104     -15.461   7.169  12.567  1.00 25.00           C
ATOM    105  CA  ALA   105     -13.718   5.292  15.413  1.00 25.00           C
ATOM    106  CA  ASP   106     -15.183   7.747  17.963  1.00 25.00           C
ATOM    107  CA  ASP   107     -18.674   7.253  16.467  1.00 25.00           C
ATOM    108  CA  ALA   108     -18.253   3.453  16.675  1.00 25.00           C
ATOM    109  CA  SER   109     -17.164   3.749  20.334  1.00 25.00           C
ATOM    110  CA  LEU   110     -20.303   5.605  21.189  1.00 25.00           C
ATOM    111  CA  GLU   111     -22.204   2.580  19.939  1.00 25.00           C
ATOM    112  CA  HIS   112     -23.175  -0.222  17.515  1.00 25.00           C
ATOM    113  CA  HIS   113     -23.186  -2.461  20.612  1.00 25.00           C
ATOM    114  CA  HIS   114     -22.527  -5.468  18.280  1.00 25.00           C
ATOM    115  CA  HIS   115     -19.504  -7.085  19.947  1.00 25.00           C
ATOM    116  CA  HIS   116     -16.029  -8.387  20.795  1.00 25.00           C
ATOM    117  CA  HIS   117     -14.300  -5.771  18.703  1.00 25.00           C
TER
END
