
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0283TS393_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS393_4-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.997
LGA    S       2      S       2          2.432
LGA    F       3      F       3          1.185
LGA    I       4      I       4          0.872
LGA    E       5      E       5          1.029
LGA    K       6      K       6          1.030
LGA    M       7      M       7          0.748
LGA    I       8      I       8          0.698
LGA    G       9      G       9          0.740
LGA    S      10      S      10          0.587
LGA    L      11      L      11          0.391
LGA    N      12      N      12          0.412
LGA    D      13      D      13          0.373
LGA    K      14      K      14          0.111
LGA    R      15      R      15          0.261
LGA    E      16      E      16          0.297
LGA    W      17      W      17          0.305
LGA    K      18      K      18          0.225
LGA    A      19      A      19          0.163
LGA    M      20      M      20          0.347
LGA    E      21      E      21          0.476
LGA    A      22      A      22          0.560
LGA    R      23      R      23          0.687
LGA    A      24      A      24          0.505
LGA    K      25      K      25          0.567
LGA    A      26      A      26          0.615
LGA    L      27      L      27          0.528
LGA    P      28      P      28          4.207
LGA    K      29      K      29          2.756
LGA    E      30      E      30          2.271
LGA    Y      31      -       -           -
LGA    H      32      Y      31          4.108
LGA    H      33      H      32           #
LGA    -       -      H      33           -
LGA    A      34      A      34           #
LGA    Y      35      -       -           -
LGA    K      36      -       -           -
LGA    A      37      Y      35           #
LGA    I      38      K      36           -
LGA    Q      39      -       -           -
LGA    K      40      -       -           -
LGA    Y      41      -       -           -
LGA    M      42      -       -           -
LGA    W      43      -       -           -
LGA    T      44      -       -           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      -       -           -
LGA    F      58      -       -           -
LGA    G      59      -       -           -
LGA    G      60      -       -           -
LGA    I      61      -       -           -
LGA    L      62      -       -           -
LGA    D      63      -       -           -
LGA    L      64      -       -           -
LGA    F      65      A      37           #
LGA    E      66      I      38          1.577
LGA    E      67      Q      39          2.810
LGA    G      68      K      40          4.873
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      I      57           -
LGA    A      69      F      58           #
LGA    A      70      G      59           -
LGA    E      71      G      60           -
LGA    G      72      I      61           -
LGA    K      73      -       -           -
LGA    K      74      L      62          4.301
LGA    V      75      D      63          3.918
LGA    -       -      L      64           -
LGA    T      76      F      65          2.172
LGA    D      77      E      66          1.285
LGA    L      78      E      67          2.982
LGA    T      79      G      68           -
LGA    G      80      A      69           -
LGA    E      81      A      70           -
LGA    D      82      E      71           -
LGA    V      83      G      72           -
LGA    A      84      K      73           -
LGA    A      85      K      74           -
LGA    F      86      V      75           -
LGA    C      87      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    -       -      V      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      F      86           -
LGA    -       -      C      87           -
LGA    -       -      D      88           -
LGA    D      88      E      89           #
LGA    E      89      -       -           -
LGA    L      90      -       -           -
LGA    M      91      L      90          3.673
LGA    K      92      M      91          1.699
LGA    D      93      K      92           -
LGA    T      94      D      93           -
LGA    K      95      T      94           #
LGA    T      96      K      95           #
LGA    W      97      T      96          4.643
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     42    2.23    71.43     34.458     1.803

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.740005 * X  +   0.611744 * Y  +  -0.279575 * Z  +  19.043064
  Y_new =  -0.508838 * X  +   0.237346 * Y  +  -0.827497 * Z  +  29.240568
  Z_new =  -0.439860 * X  +   0.754610 * Y  +   0.486915 * Z  +   0.338631 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.997765   -2.143828  [ DEG:    57.1677   -122.8323 ]
  Theta =   0.455442    2.686150  [ DEG:    26.0949    153.9051 ]
  Phi   =  -0.602365    2.539228  [ DEG:   -34.5130    145.4870 ]
 
# 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: T0283TS393_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_4-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   42   2.23   71.43  34.458
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_4-D1
PFRMAT TS
TARGET T0283
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      29.628   6.824  26.472  1.00 25.00           C
ATOM      2  CA  SER     2      27.709   8.031  23.437  1.00 25.00           C
ATOM      3  CA  PHE     3      29.055   8.886  20.004  1.00 25.00           C
ATOM      4  CA  ILE     4      28.256   6.205  17.388  1.00 25.00           C
ATOM      5  CA  GLU     5      24.755   7.679  16.910  1.00 25.00           C
ATOM      6  CA  LYS     6      26.260  11.174  16.469  1.00 25.00           C
ATOM      7  CA  MET     7      28.728   9.811  13.879  1.00 25.00           C
ATOM      8  CA  ILE     8      25.856   8.116  11.996  1.00 25.00           C
ATOM      9  CA  GLY     9      23.874  11.393  12.020  1.00 25.00           C
ATOM     10  CA  SER    10      26.925  13.275  10.672  1.00 25.00           C
ATOM     11  CA  LEU    11      27.337  10.671   7.895  1.00 25.00           C
ATOM     12  CA  ASN    12      23.634  11.018   6.985  1.00 25.00           C
ATOM     13  CA  ASP    13      23.997  14.828   6.856  1.00 25.00           C
ATOM     14  CA  LYS    14      27.065  14.483   4.589  1.00 25.00           C
ATOM     15  CA  ARG    15      25.125  12.118   2.284  1.00 25.00           C
ATOM     16  CA  GLU    16      22.222  14.610   2.130  1.00 25.00           C
ATOM     17  CA  TRP    17      24.659  17.435   1.267  1.00 25.00           C
ATOM     18  CA  LYS    18      26.207  15.287  -1.500  1.00 25.00           C
ATOM     19  CA  ALA    19      22.721  14.534  -2.898  1.00 25.00           C
ATOM     20  CA  MET    20      21.875  18.269  -2.868  1.00 25.00           C
ATOM     21  CA  GLU    21      25.144  19.051  -4.702  1.00 25.00           C
ATOM     22  CA  ALA    22      24.346  16.370  -7.318  1.00 25.00           C
ATOM     23  CA  ARG    23      20.843  17.845  -7.796  1.00 25.00           C
ATOM     24  CA  ALA    24      22.349  21.339  -8.237  1.00 25.00           C
ATOM     25  CA  LYS    25      24.818  19.976 -10.827  1.00 25.00           C
ATOM     26  CA  ALA    26      21.945  18.280 -12.709  1.00 25.00           C
ATOM     27  CA  LEU    27      20.585  21.862 -12.713  1.00 25.00           C
ATOM     28  CA  PRO    28      21.148  25.523 -11.773  1.00 25.00           C
ATOM     29  CA  LYS    29      22.722  27.827 -14.442  1.00 25.00           C
ATOM     30  CA  GLU    30      23.060  31.169 -12.602  1.00 25.00           C
ATOM     31  CA  TYR    31      20.166  32.617 -14.649  1.00 25.00           C
ATOM     32  CA  HIS    32      18.015  29.559 -13.819  1.00 25.00           C
ATOM     33  CA  HIS    33      18.839  29.960 -10.101  1.00 25.00           C
ATOM     34  CA  ALA    34      17.885  33.665 -10.264  1.00 25.00           C
ATOM     35  CA  TYR    35      14.575  32.764 -11.967  1.00 25.00           C
ATOM     36  CA  LYS    36      13.860  30.157  -9.253  1.00 25.00           C
ATOM     37  CA  ALA    37      14.600  32.750  -6.533  1.00 25.00           C
ATOM     38  CA  ILE    38      12.241  35.243  -8.232  1.00 25.00           C
ATOM     39  CA  GLN    39       9.502  32.570  -8.402  1.00 25.00           C
ATOM     40  CA  LYS    40       9.996  31.793  -4.685  1.00 25.00           C
ATOM     41  CA  TYR    41       9.744  35.521  -3.846  1.00 25.00           C
ATOM     42  CA  MET    42       6.521  35.790  -5.896  1.00 25.00           C
ATOM     43  CA  TRP    43       5.073  32.755  -4.064  1.00 25.00           C
ATOM     44  CA  THR    44       5.982  34.326  -0.691  1.00 25.00           C
ATOM     45  CA  SER    45       9.204  34.792   1.294  1.00 25.00           C
ATOM     46  CA  GLY    46       8.430  38.480   0.758  1.00 25.00           C
ATOM     47  CA  GLY    47       4.854  39.497   0.057  1.00 25.00           C
ATOM     48  CA  PRO    48       3.702  40.098  -3.533  1.00 25.00           C
ATOM     49  CA  THR    49       2.706  38.979  -7.014  1.00 25.00           C
ATOM     50  CA  ASP    50       6.061  40.103  -8.455  1.00 25.00           C
ATOM     51  CA  TRP    51       6.829  43.875  -8.340  1.00 25.00           C
ATOM     52  CA  GLN    52      10.394  44.915  -9.278  1.00 25.00           C
ATOM     53  CA  ASP    53      11.250  45.408  -5.578  1.00 25.00           C
ATOM     54  CA  THR    54       9.833  41.945  -4.763  1.00 25.00           C
ATOM     55  CA  LYS    55      11.913  40.402  -7.585  1.00 25.00           C
ATOM     56  CA  ARG    56      15.052  42.149  -6.258  1.00 25.00           C
ATOM     57  CA  ILE    57      14.326  40.833  -2.736  1.00 25.00           C
ATOM     58  CA  PHE    58      13.883  37.291  -4.124  1.00 25.00           C
ATOM     59  CA  GLY    59      17.208  37.585  -6.002  1.00 25.00           C
ATOM     60  CA  GLY    60      18.940  38.773  -2.800  1.00 25.00           C
ATOM     61  CA  ILE    61      17.458  35.814  -0.872  1.00 25.00           C
ATOM     62  CA  LEU    62      18.685  33.402  -3.582  1.00 25.00           C
ATOM     63  CA  ASP    63      22.185  34.945  -3.407  1.00 25.00           C
ATOM     64  CA  LEU    64      22.187  34.570   0.404  1.00 25.00           C
ATOM     65  CA  PHE    65      21.131  30.904   0.067  1.00 25.00           C
ATOM     66  CA  GLU    66      23.939  30.300  -2.465  1.00 25.00           C
ATOM     67  CA  GLU    67      26.465  31.923  -0.087  1.00 25.00           C
ATOM     68  CA  GLY    68      25.224  29.710   2.782  1.00 25.00           C
ATOM     69  CA  ALA    69      25.573  26.605   0.569  1.00 25.00           C
ATOM     70  CA  ALA    70      29.138  27.644  -0.370  1.00 25.00           C
ATOM     71  CA  GLU    71      28.431  28.674  -3.999  1.00 25.00           C
ATOM     72  CA  GLY    72      26.229  29.044  -7.091  1.00 25.00           C
ATOM     73  CA  LYS    73      22.600  27.817  -7.383  1.00 25.00           C
ATOM     74  CA  LYS    74      19.409  25.768  -7.074  1.00 25.00           C
ATOM     75  CA  VAL    75      15.726  24.853  -6.720  1.00 25.00           C
ATOM     76  CA  THR    76      15.631  24.930 -10.548  1.00 25.00           C
ATOM     77  CA  ASP    77      13.603  21.683 -10.588  1.00 25.00           C
ATOM     78  CA  LEU    78      11.101  23.395  -8.338  1.00 25.00           C
ATOM     79  CA  THR    79      10.756  20.323  -6.192  1.00 25.00           C
ATOM     80  CA  GLY    80      10.302  17.017  -4.394  1.00 25.00           C
ATOM     81  CA  GLU    81       8.197  18.562  -1.592  1.00 25.00           C
ATOM     82  CA  ASP    82      10.947  17.758   0.950  1.00 25.00           C
ATOM     83  CA  VAL    83      13.563  19.370  -1.334  1.00 25.00           C
ATOM     84  CA  ALA    84      11.372  22.492  -1.682  1.00 25.00           C
ATOM     85  CA  ALA    85      10.984  22.673   2.124  1.00 25.00           C
ATOM     86  CA  PHE    86      14.777  22.366   2.551  1.00 25.00           C
ATOM     87  CA  CYS    87      15.316  25.170  -0.003  1.00 25.00           C
ATOM     88  CA  ASP    88      12.801  27.381   1.858  1.00 25.00           C
ATOM     89  CA  GLU    89      14.604  26.688   5.166  1.00 25.00           C
ATOM     90  CA  LEU    90      17.959  27.595   3.557  1.00 25.00           C
ATOM     91  CA  MET    91      16.459  30.852   2.209  1.00 25.00           C
ATOM     92  CA  LYS    92      15.092  31.690   5.687  1.00 25.00           C
ATOM     93  CA  ASP    93      18.533  31.021   7.229  1.00 25.00           C
ATOM     94  CA  THR    94      20.172  33.293   4.616  1.00 25.00           C
ATOM     95  CA  LYS    95      17.628  36.051   5.383  1.00 25.00           C
ATOM     96  CA  THR    96      18.341  35.699   9.129  1.00 25.00           C
ATOM     97  CA  TRP    97      22.104  35.941   8.462  1.00 25.00           C
TER
END
