
#######################################################
#                                                     #
#                        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 T0363TS168_3
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS168_3.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      L      10           -
LGA    A       2      -       -           -
LGA    H       3      -       -           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      -       -           -
LGA    N      11      N      11           #
LGA    -       -      Q      12           -
LGA    Q      12      I      13          2.207
LGA    I      13      N      14          1.636
LGA    N      14      I      15          1.857
LGA    I      15      E      16          1.478
LGA    E      16      I      17          2.631
LGA    I      17      A      18          0.939
LGA    A      18      Y      19          2.052
LGA    Y      19      A      20           #
LGA    A      20      F      21           #
LGA    F      21      -       -           -
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      P      22          4.549
LGA    Y      25      E      23          2.310
LGA    Y      26      R      24          3.418
LGA    L      27      Y      25          1.556
LGA    K      28      Y      26          2.620
LGA    S      29      L      27          1.759
LGA    F      30      K      28          1.098
LGA    Q      31      S      29          3.651
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    V      32      V      32          5.038
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    D      33      I      36          4.166
LGA    E      34      T      37          3.459
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    G      35      T      40          4.397
LGA    I      36      A      41          4.314
LGA    -       -      I      42           -
LGA    T      37      T      43           #
LGA    V      38      Q      44          4.355
LGA    Q      39      S      45          3.792
LGA    T      40      -       -           -
LGA    A      41      G      46          0.961
LGA    I      42      I      47          2.137
LGA    T      43      L      48          2.837
LGA    Q      44      S      49          2.731
LGA    S      45      Q      50          3.230
LGA    G      46      F      51          2.860
LGA    I      47      P      52           -
LGA    L      48      E      53           #
LGA    S      49      I      54          1.727
LGA    Q      50      D      55          1.279
LGA    F      51      L      56          2.416
LGA    P      52      S      57          2.531
LGA    E      53      T      58          3.202
LGA    I      54      -       -           -
LGA    D      55      N      59          3.484
LGA    L      56      K      60          1.738
LGA    S      57      -       -           -
LGA    T      58      I      61          3.563
LGA    N      59      G      62          3.287
LGA    K      60      I      63          5.588
LGA    I      61      -       -           -
LGA    G      62      -       -           -
LGA    I      63      -       -           -
LGA    F      64      -       -           -
LGA    S      65      -       -           -
LGA    R      66      -       -           -
LGA    P      67      -       -           -
LGA    I      68      -       -           -
LGA    K      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    L      74      -       -           -
LGA    K      75      -       -           -
LGA    E      76      -       -           -
LGA    G      77      -       -           -
LGA    D      78      -       -           -
LGA    R      79      -       -           -
LGA    I      80      -       -           -
LGA    E      81      -       -           -
LGA    I      82      -       -           -
LGA    Y      83      -       -           -
LGA    R      84      -       -           -
LGA    P      85      -       -           -
LGA    L      86      F      64           #
LGA    L      87      S      65           -
LGA    A      88      R      66           -
LGA    -       -      P      67           -
LGA    -       -      I      68           -
LGA    -       -      K      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      D      72           -
LGA    -       -      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    -       -      D      78           -
LGA    -       -      R      79           -
LGA    -       -      I      80           -
LGA    -       -      E      81           -
LGA    -       -      I      82           -
LGA    D      89      Y      83           #
LGA    P      90      -       -           -
LGA    K      91      -       -           -
LGA    E      92      -       -           -
LGA    I      93      -       -           -
LGA    R      94      R      84          4.144
LGA    R      95      P      85          2.724
LGA    E      96      L      86           #
LGA    G      97      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   80    5.0     40    3.07     7.50     29.665     1.262

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.915959 * X  +  -0.323107 * Y  +  -0.237951 * Z  +  23.521116
  Y_new =  -0.353873 * X  +  -0.930000 * Y  +  -0.099364 * Z  +  14.953196
  Z_new =  -0.189189 * X  +   0.175218 * Y  +  -0.966181 * Z  +   3.637301 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.962192   -0.179401  [ DEG:   169.7211    -10.2789 ]
  Theta =   0.190337    2.951256  [ DEG:    10.9055    169.0945 ]
  Phi   =  -0.368677    2.772916  [ DEG:   -21.1236    158.8764 ]
 
# 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: T0363TS168_3                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_3.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   80   5.0   40   3.07    7.50  29.665
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_3
PFRMAT TS
TARGET T0363
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       4.773   2.014  32.444  1.00 25.00           C
ATOM      2  CA  ALA     2       7.259   1.126  29.666  1.00 25.00           C
ATOM      3  CA  HIS     3       9.432   3.841  28.088  1.00 25.00           C
ATOM      4  CA  HIS     4      12.238   4.782  25.704  1.00 25.00           C
ATOM      5  CA  HIS     5      11.342   7.794  23.645  1.00 25.00           C
ATOM      6  CA  HIS     6       9.297   7.424  20.503  1.00 25.00           C
ATOM      7  CA  HIS     7       8.590  10.517  18.400  1.00 25.00           C
ATOM      8  CA  HIS     8       7.716   9.417  14.864  1.00 25.00           C
ATOM      9  CA  SER     9       6.164   6.378  13.293  1.00 25.00           C
ATOM     10  CA  LEU    10       7.767   4.379  10.425  1.00 25.00           C
ATOM     11  CA  ASN    11      11.310   4.410   8.971  1.00 25.00           C
ATOM     12  CA  GLN    12      14.790   6.051   9.011  1.00 25.00           C
ATOM     13  CA  ILE    13      17.096   8.563   7.389  1.00 25.00           C
ATOM     14  CA  ASN    14      19.678  11.287   8.287  1.00 25.00           C
ATOM     15  CA  ILE    15      21.133  13.772   5.754  1.00 25.00           C
ATOM     16  CA  GLU    16      22.459  16.835   4.050  1.00 25.00           C
ATOM     17  CA  ILE    17      25.753  18.568   3.079  1.00 25.00           C
ATOM     18  CA  ALA    18      27.954  20.245   0.470  1.00 25.00           C
ATOM     19  CA  TYR    19      30.709  17.997  -0.882  1.00 25.00           C
ATOM     20  CA  ALA    20      30.982  18.174  -4.615  1.00 25.00           C
ATOM     21  CA  PHE    21      29.583  20.958  -6.766  1.00 25.00           C
ATOM     22  CA  PRO    22      29.844  23.849  -9.266  1.00 25.00           C
ATOM     23  CA  GLU    23      32.074  26.859 -10.020  1.00 25.00           C
ATOM     24  CA  ARG    24      32.095  29.966  -7.727  1.00 25.00           C
ATOM     25  CA  TYR    25      29.088  28.587  -5.833  1.00 25.00           C
ATOM     26  CA  TYR    26      28.600  25.168  -4.235  1.00 25.00           C
ATOM     27  CA  LEU    27      25.813  22.782  -3.315  1.00 25.00           C
ATOM     28  CA  LYS    28      25.620  19.074  -4.208  1.00 25.00           C
ATOM     29  CA  SER    29      25.080  16.530  -1.452  1.00 25.00           C
ATOM     30  CA  PHE    30      23.181  13.669   0.222  1.00 25.00           C
ATOM     31  CA  GLN    31      23.984  10.820   2.688  1.00 25.00           C
ATOM     32  CA  VAL    32      24.168   8.942   6.031  1.00 25.00           C
ATOM     33  CA  ASP    33      24.322   6.883   9.237  1.00 25.00           C
ATOM     34  CA  GLU    34      27.268   7.618  11.592  1.00 25.00           C
ATOM     35  CA  GLY    35      28.852   4.177  11.231  1.00 25.00           C
ATOM     36  CA  ILE    36      29.838   5.540   7.813  1.00 25.00           C
ATOM     37  CA  THR    37      28.024   5.668   4.504  1.00 25.00           C
ATOM     38  CA  VAL    38      28.726   9.146   3.251  1.00 25.00           C
ATOM     39  CA  GLN    39      30.556  10.418   6.365  1.00 25.00           C
ATOM     40  CA  THR    40      33.740   8.591   5.270  1.00 25.00           C
ATOM     41  CA  ALA    41      33.457  10.141   1.778  1.00 25.00           C
ATOM     42  CA  ILE    42      33.025  13.616   3.329  1.00 25.00           C
ATOM     43  CA  THR    43      36.112  13.046   5.525  1.00 25.00           C
ATOM     44  CA  GLN    44      38.125  11.956   2.455  1.00 25.00           C
ATOM     45  CA  SER    45      36.994  15.091   0.569  1.00 25.00           C
ATOM     46  CA  GLY    46      35.015  18.098   1.756  1.00 25.00           C
ATOM     47  CA  ILE    47      32.351  19.847   3.772  1.00 25.00           C
ATOM     48  CA  LEU    48      35.074  22.170   5.173  1.00 25.00           C
ATOM     49  CA  SER    49      38.486  20.694   4.253  1.00 25.00           C
ATOM     50  CA  GLN    50      38.700  18.989   7.675  1.00 25.00           C
ATOM     51  CA  PHE    51      35.301  19.082   9.457  1.00 25.00           C
ATOM     52  CA  PRO    52      36.990  20.091  12.713  1.00 25.00           C
ATOM     53  CA  GLU    53      39.229  22.721  11.052  1.00 25.00           C
ATOM     54  CA  ILE    54      37.175  25.102   8.900  1.00 25.00           C
ATOM     55  CA  ASP    55      33.803  26.125  10.258  1.00 25.00           C
ATOM     56  CA  LEU    56      32.748  23.007  12.260  1.00 25.00           C
ATOM     57  CA  SER    57      31.575  20.013  14.280  1.00 25.00           C
ATOM     58  CA  THR    58      27.776  19.951  14.523  1.00 25.00           C
ATOM     59  CA  ASN    59      27.574  21.039  10.832  1.00 25.00           C
ATOM     60  CA  LYS    60      25.534  20.864   7.617  1.00 25.00           C
ATOM     61  CA  ILE    61      25.674  17.122   8.179  1.00 25.00           C
ATOM     62  CA  GLY    62      26.499  14.260   5.837  1.00 25.00           C
ATOM     63  CA  ILE    63      28.031  14.485   2.375  1.00 25.00           C
ATOM     64  CA  PHE    64      29.074  12.436  -0.627  1.00 25.00           C
ATOM     65  CA  SER    65      28.308  13.656  -4.159  1.00 25.00           C
ATOM     66  CA  ARG    66      29.523  10.555  -5.939  1.00 25.00           C
ATOM     67  CA  PRO    67      26.455  11.244  -8.164  1.00 25.00           C
ATOM     68  CA  ILE    68      22.755  10.632  -8.715  1.00 25.00           C
ATOM     69  CA  LYS    69      21.691  10.649 -12.407  1.00 25.00           C
ATOM     70  CA  LEU    70      18.131  10.427 -10.970  1.00 25.00           C
ATOM     71  CA  THR    71      18.057   6.782 -10.005  1.00 25.00           C
ATOM     72  CA  ASP    72      20.811   4.442  -8.732  1.00 25.00           C
ATOM     73  CA  VAL    73      24.209   5.228 -10.164  1.00 25.00           C
ATOM     74  CA  LEU    74      24.987   6.220  -6.594  1.00 25.00           C
ATOM     75  CA  LYS    75      28.516   4.946  -7.317  1.00 25.00           C
ATOM     76  CA  GLU    76      27.366   1.475  -6.161  1.00 25.00           C
ATOM     77  CA  GLY    77      27.171   3.204  -2.749  1.00 25.00           C
ATOM     78  CA  ASP    78      26.951   6.917  -1.933  1.00 25.00           C
ATOM     79  CA  ARG    79      24.813   9.950  -2.839  1.00 25.00           C
ATOM     80  CA  ILE    80      22.851  12.948  -4.278  1.00 25.00           C
ATOM     81  CA  GLU    81      20.473  15.879  -3.689  1.00 25.00           C
ATOM     82  CA  ILE    82      20.762  19.075  -1.611  1.00 25.00           C
ATOM     83  CA  TYR    83      22.618  21.681   0.446  1.00 25.00           C
ATOM     84  CA  ARG    84      22.408  23.112   3.963  1.00 25.00           C
ATOM     85  CA  PRO    85      20.293  22.847   7.077  1.00 25.00           C
ATOM     86  CA  LEU    86      17.485  24.696   5.393  1.00 25.00           C
ATOM     87  CA  LEU    87      18.115  28.162   3.835  1.00 25.00           C
ATOM     88  CA  ALA    88      17.550  26.650   0.437  1.00 25.00           C
ATOM     89  CA  ASP    89      13.826  26.306   1.112  1.00 25.00           C
ATOM     90  CA  PRO    90      12.301  22.996  -0.026  1.00 25.00           C
ATOM     91  CA  LYS    91       9.874  24.125  -2.764  1.00 25.00           C
ATOM     92  CA  GLU    92       8.726  20.508  -3.274  1.00 25.00           C
ATOM     93  CA  ILE    93       8.174  20.126   0.497  1.00 25.00           C
ATOM     94  CA  ARG    94       6.137  23.369   0.552  1.00 25.00           C
ATOM     95  CA  ARG    95       5.499  24.048   4.170  1.00 25.00           C
ATOM     96  CA  GLU    96       2.421  22.046   5.064  1.00 25.00           C
ATOM     97  CA  GLY    97       2.625  18.837   7.074  1.00 25.00           C
TER
END
