
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS393_5-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          2.432
LGA    S       2      S       2          1.912
LGA    F       3      F       3          0.909
LGA    I       4      I       4          1.201
LGA    E       5      E       5          0.754
LGA    K       6      K       6          0.481
LGA    M       7      M       7          0.933
LGA    I       8      I       8          1.003
LGA    G       9      G       9          0.357
LGA    S      10      S      10          0.349
LGA    L      11      L      11          0.548
LGA    N      12      N      12          0.500
LGA    D      13      D      13          0.512
LGA    K      14      K      14          0.794
LGA    R      15      R      15          0.452
LGA    E      16      E      16          0.526
LGA    W      17      W      17          0.867
LGA    K      18      K      18          0.778
LGA    A      19      A      19          0.297
LGA    M      20      M      20          0.722
LGA    E      21      E      21          1.264
LGA    A      22      A      22          1.106
LGA    R      23      R      23          0.646
LGA    A      24      A      24          1.246
LGA    K      25      K      25          1.504
LGA    A      26      A      26          1.049
LGA    L      27      L      27          1.006
LGA    P      28      P      28          2.739
LGA    K      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    H      32      -       -           -
LGA    H      33      K      29          2.112
LGA    A      34      E      30          3.696
LGA    Y      35      Y      31           #
LGA    K      36      H      32           #
LGA    A      37      H      33          5.228
LGA    I      38      A      34          4.296
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      Y      35          5.618
LGA    D      63      K      36           -
LGA    -       -      A      37           -
LGA    L      64      I      38          3.446
LGA    F      65      Q      39          2.746
LGA    E      66      K      40          5.185
LGA    E      67      Y      41          3.862
LGA    G      68      M      42          2.873
LGA    A      69      W      43          3.981
LGA    A      70      T      44          1.399
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    E      71      G      47          3.794
LGA    G      72      P      48          2.487
LGA    K      73      T      49           #
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    K      74      D      53           #
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    V      75      I      57          2.795
LGA    T      76      F      58          2.862
LGA    D      77      G      59           -
LGA    L      78      G      60           -
LGA    T      79      I      61           -
LGA    G      80      L      62           -
LGA    E      81      D      63           -
LGA    D      82      L      64           -
LGA    V      83      F      65           -
LGA    A      84      E      66           -
LGA    A      85      E      67           -
LGA    F      86      G      68           -
LGA    C      87      A      69           -
LGA    D      88      A      70           -
LGA    E      89      E      71           -
LGA    L      90      G      72           -
LGA    M      91      K      73           -
LGA    K      92      K      74           -
LGA    -       -      V      75           -
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    -       -      T      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    D      93      D      82           #
LGA    T      94      V      83           #
LGA    K      95      A      84           #
LGA    T      96      A      85           #
LGA    W      97      F      86           -
LGA    -       -      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     44    2.41    63.64     35.703     1.756

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.256133 * X  +   0.894778 * Y  +   0.365743 * Z  +  22.809536
  Y_new =  -0.966615 * X  +  -0.234277 * Y  +  -0.103778 * Z  +  30.539450
  Z_new =  -0.007173 * X  +  -0.380113 * Y  +   0.924912 * Z  +  -3.649585 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.389929    2.751663  [ DEG:   -22.3413    157.6587 ]
  Theta =   0.007173    3.134420  [ DEG:     0.4110    179.5890 ]
  Phi   =  -1.829823    1.311770  [ DEG:  -104.8411     75.1589 ]
 
# 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_5-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_5-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   44   2.41   63.64  35.703
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_5-D1
PFRMAT TS
TARGET T0283
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      27.848   4.520  24.378  1.00 25.00           C
ATOM      2  CA  SER     2      26.604   7.679  22.576  1.00 25.00           C
ATOM      3  CA  PHE     3      29.461   8.591  20.168  1.00 25.00           C
ATOM      4  CA  ILE     4      27.893   6.030  17.792  1.00 25.00           C
ATOM      5  CA  GLU     5      24.755   8.206  17.480  1.00 25.00           C
ATOM      6  CA  LYS     6      26.925  11.267  16.712  1.00 25.00           C
ATOM      7  CA  MET     7      28.820   9.285  14.039  1.00 25.00           C
ATOM      8  CA  ILE     8      25.504   8.169  12.482  1.00 25.00           C
ATOM      9  CA  GLY     9      24.272  11.795  12.444  1.00 25.00           C
ATOM     10  CA  SER    10      27.528  12.908  10.760  1.00 25.00           C
ATOM     11  CA  LEU    11      27.141  10.152   8.130  1.00 25.00           C
ATOM     12  CA  ASN    12      23.531  11.252   7.473  1.00 25.00           C
ATOM     13  CA  ASP    13      24.684  14.883   7.079  1.00 25.00           C
ATOM     14  CA  LYS    14      27.404  13.778   4.621  1.00 25.00           C
ATOM     15  CA  ARG    15      24.818  11.787   2.616  1.00 25.00           C
ATOM     16  CA  GLU    16      22.507  14.840   2.518  1.00 25.00           C
ATOM     17  CA  TRP    17      25.407  17.026   1.304  1.00 25.00           C
ATOM     18  CA  LYS    18      26.222  14.471  -1.430  1.00 25.00           C
ATOM     19  CA  ALA    19      22.551  14.428  -2.518  1.00 25.00           C
ATOM     20  CA  MET    20      22.522  18.255  -2.660  1.00 25.00           C
ATOM     21  CA  GLU    21      25.716  18.225  -4.775  1.00 25.00           C
ATOM     22  CA  ALA    22      24.146  15.665  -7.151  1.00 25.00           C
ATOM     23  CA  ARG    23      21.010  17.840  -7.464  1.00 25.00           C
ATOM     24  CA  ALA    24      23.180  20.901  -8.231  1.00 25.00           C
ATOM     25  CA  LYS    25      25.075  18.918 -10.905  1.00 25.00           C
ATOM     26  CA  ALA    26      21.758  17.803 -12.462  1.00 25.00           C
ATOM     27  CA  LEU    27      21.238  21.580 -12.826  1.00 25.00           C
ATOM     28  CA  PRO    28      22.667  22.077 -16.363  1.00 25.00           C
ATOM     29  CA  LYS    29      26.376  21.859 -17.033  1.00 25.00           C
ATOM     30  CA  GLU    30      27.117  22.873 -13.415  1.00 25.00           C
ATOM     31  CA  TYR    31      28.854  26.059 -14.637  1.00 25.00           C
ATOM     32  CA  HIS    32      25.842  26.881 -16.854  1.00 25.00           C
ATOM     33  CA  HIS    33      23.482  26.352 -13.884  1.00 25.00           C
ATOM     34  CA  ALA    34      25.646  28.656 -11.721  1.00 25.00           C
ATOM     35  CA  TYR    35      25.585  31.327 -14.465  1.00 25.00           C
ATOM     36  CA  LYS    36      21.773  31.038 -14.697  1.00 25.00           C
ATOM     37  CA  ALA    37      21.489  31.409 -10.895  1.00 25.00           C
ATOM     38  CA  ILE    38      23.731  34.512 -11.007  1.00 25.00           C
ATOM     39  CA  GLN    39      21.567  36.006 -13.792  1.00 25.00           C
ATOM     40  CA  LYS    40      18.408  35.326 -11.736  1.00 25.00           C
ATOM     41  CA  TYR    41      20.000  37.010  -8.688  1.00 25.00           C
ATOM     42  CA  MET    42      20.938  40.048 -10.824  1.00 25.00           C
ATOM     43  CA  TRP    43      17.352  40.251 -12.153  1.00 25.00           C
ATOM     44  CA  THR    44      15.990  40.085  -8.578  1.00 25.00           C
ATOM     45  CA  SER    45      13.438  38.142  -6.431  1.00 25.00           C
ATOM     46  CA  GLY    46      11.793  37.515  -9.838  1.00 25.00           C
ATOM     47  CA  GLY    47      11.784  39.609 -12.946  1.00 25.00           C
ATOM     48  CA  PRO    48      14.103  38.044 -15.588  1.00 25.00           C
ATOM     49  CA  THR    49      13.922  35.990 -18.783  1.00 25.00           C
ATOM     50  CA  ASP    50      13.389  32.763 -16.839  1.00 25.00           C
ATOM     51  CA  TRP    51      10.030  31.162 -16.407  1.00 25.00           C
ATOM     52  CA  GLN    52       8.669  32.489 -13.082  1.00 25.00           C
ATOM     53  CA  ASP    53       9.545  29.175 -11.373  1.00 25.00           C
ATOM     54  CA  THR    54      13.086  29.336 -12.821  1.00 25.00           C
ATOM     55  CA  LYS    55      13.467  32.930 -11.555  1.00 25.00           C
ATOM     56  CA  ARG    56      12.278  31.858  -8.077  1.00 25.00           C
ATOM     57  CA  ILE    57      14.796  28.971  -8.079  1.00 25.00           C
ATOM     58  CA  PHE    58      17.596  31.383  -9.086  1.00 25.00           C
ATOM     59  CA  GLY    59      16.591  33.768  -6.263  1.00 25.00           C
ATOM     60  CA  GLY    60      16.626  30.865  -3.765  1.00 25.00           C
ATOM     61  CA  ILE    61      20.105  29.824  -4.985  1.00 25.00           C
ATOM     62  CA  LEU    62      21.347  33.425  -4.588  1.00 25.00           C
ATOM     63  CA  ASP    63      19.923  33.552  -1.035  1.00 25.00           C
ATOM     64  CA  LEU    64      21.660  30.243  -0.195  1.00 25.00           C
ATOM     65  CA  PHE    65      24.966  31.603  -1.569  1.00 25.00           C
ATOM     66  CA  GLU    66      24.567  34.775   0.539  1.00 25.00           C
ATOM     67  CA  GLU    67      23.884  32.650   3.652  1.00 25.00           C
ATOM     68  CA  GLY    68      27.008  30.552   2.934  1.00 25.00           C
ATOM     69  CA  ALA    69      29.091  33.742   2.541  1.00 25.00           C
ATOM     70  CA  ALA    70      27.731  35.069   5.866  1.00 25.00           C
ATOM     71  CA  GLU    71      26.741  32.065   7.949  1.00 25.00           C
ATOM     72  CA  GLY    72      23.377  30.241   8.131  1.00 25.00           C
ATOM     73  CA  LYS    73      20.033  31.728   7.035  1.00 25.00           C
ATOM     74  CA  LYS    74      19.203  29.327   4.127  1.00 25.00           C
ATOM     75  CA  VAL    75      18.697  26.429   1.702  1.00 25.00           C
ATOM     76  CA  THR    76      20.494  25.358  -1.506  1.00 25.00           C
ATOM     77  CA  ASP    77      23.860  25.446   0.320  1.00 25.00           C
ATOM     78  CA  LEU    78      26.216  24.661  -2.564  1.00 25.00           C
ATOM     79  CA  THR    79      28.922  22.043  -2.935  1.00 25.00           C
ATOM     80  CA  GLY    80      31.903  20.457  -4.719  1.00 25.00           C
ATOM     81  CA  GLU    81      34.607  23.023  -3.841  1.00 25.00           C
ATOM     82  CA  ASP    82      34.323  24.556  -7.339  1.00 25.00           C
ATOM     83  CA  VAL    83      30.517  24.768  -6.963  1.00 25.00           C
ATOM     84  CA  ALA    84      30.924  26.472  -3.558  1.00 25.00           C
ATOM     85  CA  ALA    85      33.389  28.978  -5.078  1.00 25.00           C
ATOM     86  CA  PHE    86      30.926  29.715  -7.917  1.00 25.00           C
ATOM     87  CA  CYS    87      28.117  30.262  -5.372  1.00 25.00           C
ATOM     88  CA  ASP    88      30.355  32.645  -3.377  1.00 25.00           C
ATOM     89  CA  GLU    89      31.188  34.579  -6.576  1.00 25.00           C
ATOM     90  CA  LEU    90      27.461  34.835  -7.421  1.00 25.00           C
ATOM     91  CA  MET    91      26.724  36.122  -3.890  1.00 25.00           C
ATOM     92  CA  LYS    92      29.507  38.730  -4.233  1.00 25.00           C
ATOM     93  CA  ASP    93      28.077  39.847  -7.606  1.00 25.00           C
ATOM     94  CA  THR    94      24.592  40.161  -6.053  1.00 25.00           C
ATOM     95  CA  LYS    95      26.032  42.245  -3.181  1.00 25.00           C
ATOM     96  CA  THR    96      27.819  44.518  -5.693  1.00 25.00           C
ATOM     97  CA  TRP    97      24.558  44.955  -7.654  1.00 25.00           C
TER
END
