
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0283TS383_3
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283TS383_3.T0283  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    S       2      E       5          2.723
LGA    F       3      K       6          2.874
LGA    I       4      M       7          1.214
LGA    E       5      I       8          2.356
LGA    -       -      G       9           -
LGA    -       -      S      10           -
LGA    K       6      L      11          2.957
LGA    M       7      N      12          4.627
LGA    I       8      D      13           #
LGA    G       9      -       -           -
LGA    S      10      K      14          1.997
LGA    L      11      R      15          4.325
LGA    N      12      E      16          4.191
LGA    -       -      W      17           -
LGA    D      13      K      18          3.084
LGA    K      14      A      19           -
LGA    R      15      M      20           #
LGA    E      16      E      21          1.038
LGA    W      17      A      22           #
LGA    K      18      R      23           -
LGA    A      19      A      24          5.325
LGA    M      20      K      25          2.274
LGA    E      21      A      26           -
LGA    A      22      L      27           -
LGA    R      23      P      28          4.171
LGA    A      24      K      29          2.022
LGA    K      25      -       -           -
LGA    A      26      E      30           #
LGA    L      27      Y      31           #
LGA    -       -      H      32           -
LGA    P      28      H      33          3.981
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    K      29      A      37          4.652
LGA    E      30      I      38           -
LGA    Y      31      Q      39           -
LGA    H      32      -       -           -
LGA    H      33      -       -           -
LGA    A      34      K      40          4.377
LGA    Y      35      Y      41          4.060
LGA    K      36      -       -           -
LGA    A      37      -       -           -
LGA    I      38      -       -           -
LGA    Q      39      M      42          1.995
LGA    K      40      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    Y      41      G      46           #
LGA    T      44      G      47          2.050
LGA    S      45      P      48          2.729
LGA    G      46      T      49          4.575
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      D      50          3.823
LGA    I      61      W      51          2.167
LGA    L      62      Q      52          2.440
LGA    D      63      D      53          2.607
LGA    L      64      T      54          2.226
LGA    F      65      K      55          1.432
LGA    E      66      R      56          1.701
LGA    E      67      I      57          1.712
LGA    G      68      F      58          1.866
LGA    A      69      G      59          2.268
LGA    A      70      G      60          1.954
LGA    E      71      I      61          1.659
LGA    G      72      L      62          1.495
LGA    K      73      D      63          1.547
LGA    K      74      L      64          1.300
LGA    V      75      F      65          1.056
LGA    T      76      E      66          1.772
LGA    D      77      E      67          1.854
LGA    L      78      G      68          1.000
LGA    T      79      A      69          1.599
LGA    G      80      A      70          2.276
LGA    E      81      E      71          2.233
LGA    D      82      G      72          4.388
LGA    V      83      K      73           -
LGA    A      84      K      74           -
LGA    A      85      V      75           -
LGA    F      86      T      76           -
LGA    C      87      D      77           -
LGA    D      88      L      78           -
LGA    E      89      T      79           -
LGA    L      90      G      80           -
LGA    M      91      E      81           -
LGA    K      92      D      82           -
LGA    D      93      V      83           -
LGA    T      94      A      84           -
LGA    K      95      A      85           -
LGA    T      96      F      86           -
LGA    W      97      C      87           -
LGA    M      98      D      88           -
LGA    D      99      E      89           -
LGA    K     100      L      90           -
LGA    Y     101      M      91           -
LGA    R     102      K      92           -
LGA    T     103      D      93           -
LGA    K     104      T      94           -
LGA    L     105      K      95           -
LGA    N     106      T      96           -
LGA    D     107      W      97           -
LGA    S     108      M      98           -
LGA    I     109      D      99           -
LGA    G     110      K     100           -
LGA    R     111      Y     101           -
LGA    -       -      R     102           -
LGA    -       -      T     103           -
LGA    -       -      K     104           -
LGA    -       -      L     105           -
LGA    -       -      N     106           -
LGA    -       -      D     107           -
LGA    -       -      S     108           -
LGA    -       -      I     109           -
LGA    -       -      G     110           -
LGA    -       -      R     111           -
LGA    -       -      D     112           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  112    5.0     46    2.86    10.87     29.428     1.556

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.866009 * X  +  -0.270972 * Y  +   0.420241 * Z  +  70.190948
  Y_new =  -0.496623 * X  +   0.368187 * Y  +  -0.786005 * Z  +  34.894772
  Z_new =   0.058258 * X  +  -0.889389 * Y  +  -0.453425 * Z  +  28.987494 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.042266    1.099327  [ DEG:  -117.0132     62.9868 ]
  Theta =  -0.058291   -3.083301  [ DEG:    -3.3398   -176.6602 ]
  Phi   =  -2.620915    0.520677  [ DEG:  -150.1674     29.8326 ]
 
# 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: T0283TS383_3                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS383_3.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  112   5.0   46   2.86   10.87  29.428
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS383_3
PFRMAT TS
TARGET T0283
MODEL 3
PARENT 2fjcA
ATOM      1  CA  SER     2      25.567   6.705  15.089  1.00  0.00
ATOM      2  CA  PHE     3      25.265  10.508  14.700  1.00  0.00
ATOM      3  CA  ILE     4      29.023  11.070  14.248  1.00  0.00
ATOM      4  CA  GLU     5      28.593   8.731  11.321  1.00  0.00
ATOM      5  CA  LYS     6      25.376  10.120   9.865  1.00  0.00
ATOM      6  CA  MET     7      26.766  13.668   9.665  1.00  0.00
ATOM      7  CA  ILE     8      29.830  12.469   7.709  1.00  0.00
ATOM      8  CA  GLY     9      27.427  10.734   5.324  1.00  0.00
ATOM      9  CA  SER    10      27.833  16.270   4.096  1.00  0.00
ATOM     10  CA  LEU    11      29.007  13.766   1.498  1.00  0.00
ATOM     11  CA  ASN    12      25.573  14.033  -0.077  1.00  0.00
ATOM     12  CA  ASP    13      25.586  17.815   0.299  1.00  0.00
ATOM     13  CA  LYS    14      28.986  18.213  -1.344  1.00  0.00
ATOM     14  CA  ARG    15      27.692  16.005  -4.154  1.00  0.00
ATOM     15  CA  GLU    16      24.760  18.344  -4.813  1.00  0.00
ATOM     16  CA  TRP    17      27.206  21.226  -4.315  1.00  0.00
ATOM     17  CA  LYS    18      29.297  19.946  -7.190  1.00  0.00
ATOM     18  CA  ALA    19      26.522  18.974  -9.625  1.00  0.00
ATOM     19  CA  MET    20      24.660  22.268  -9.237  1.00  0.00
ATOM     20  CA  GLU    21      27.861  24.298  -9.614  1.00  0.00
ATOM     21  CA  ALA    22      28.587  22.369 -12.819  1.00  0.00
ATOM     22  CA  ARG    23      25.074  22.942 -14.110  1.00  0.00
ATOM     23  CA  ALA    24      25.691  26.624 -13.538  1.00  0.00
ATOM     24  CA  LYS    25      28.871  26.339 -15.614  1.00  0.00
ATOM     25  CA  ALA    26      26.955  24.593 -18.402  1.00  0.00
ATOM     26  CA  LEU    27      24.428  27.434 -18.428  1.00  0.00
ATOM     27  CA  PRO    28      30.168  29.412 -10.077  1.00  0.00
ATOM     28  CA  LYS    29      30.766  31.224  -6.785  1.00  0.00
ATOM     29  CA  GLU    30      34.008  29.675  -5.554  1.00  0.00
ATOM     30  CA  TYR    31      35.178  31.235  -2.290  1.00  0.00
ATOM     31  CA  HIS    32      33.961  31.313   1.295  1.00  0.00
ATOM     32  CA  HIS    33      33.756  35.096   1.043  1.00  0.00
ATOM     33  CA  ALA    34      31.205  34.795  -1.759  1.00  0.00
ATOM     34  CA  TYR    35      29.336  31.990  -0.026  1.00  0.00
ATOM     35  CA  LYS    36      28.987  33.989   3.191  1.00  0.00
ATOM     36  CA  ALA    37      27.710  36.881   1.081  1.00  0.00
ATOM     37  CA  ILE    38      25.144  34.790  -0.828  1.00  0.00
ATOM     38  CA  GLN    39      24.087  32.156   1.679  1.00  0.00
ATOM     39  CA  LYS    40      20.792  32.305   3.521  1.00  0.00
ATOM     40  CA  TYR    41      22.067  29.700   5.960  1.00  0.00
ATOM     41  CA  THR    44      22.425  30.421   8.339  1.00  0.00
ATOM     42  CA  SER    45      23.560  30.840   9.264  1.00  0.00
ATOM     43  CA  GLY    46      26.827  29.221  10.311  1.00  0.00
ATOM     44  CA  GLY    47      26.963  27.272  13.567  1.00  0.00
ATOM     45  CA  PRO    48      28.958  29.356  16.039  1.00  0.00
ATOM     46  CA  THR    49      28.693  27.039  18.992  1.00  0.00
ATOM     47  CA  ASP    50      30.615  23.833  19.572  1.00  0.00
ATOM     48  CA  TRP    51      29.553  21.102  21.990  1.00  0.00
ATOM     49  CA  GLN    52      25.944  20.506  21.051  1.00  0.00
ATOM     50  CA  ASP    53      23.212  18.056  21.928  1.00  0.00
ATOM     51  CA  THR    54      22.297  15.387  19.390  1.00  0.00
ATOM     52  CA  LYS    55      18.605  16.310  19.202  1.00  0.00
ATOM     53  CA  ARG    56      19.590  19.970  19.009  1.00  0.00
ATOM     54  CA  ILE    57      21.980  19.313  16.097  1.00  0.00
ATOM     55  CA  PHE    58      19.531  17.122  14.185  1.00  0.00
ATOM     56  CA  GLY    59      16.722  19.663  14.651  1.00  0.00
ATOM     57  CA  GLY    60      18.982  22.300  13.129  1.00  0.00
ATOM     58  CA  ILE    61      19.988  20.246  10.105  1.00  0.00
ATOM     59  CA  LEU    62      16.324  19.341   9.586  1.00  0.00
ATOM     60  CA  ASP    63      15.565  23.059   9.598  1.00  0.00
ATOM     61  CA  LEU    64      18.316  23.811   7.077  1.00  0.00
ATOM     62  CA  PHE    65      17.227  20.880   4.903  1.00  0.00
ATOM     63  CA  GLU    66      13.685  22.279   4.897  1.00  0.00
ATOM     64  CA  GLU    67      14.990  25.740   4.031  1.00  0.00
ATOM     65  CA  GLY    68      16.971  24.235   1.145  1.00  0.00
ATOM     66  CA  ALA    69      13.925  22.246   0.086  1.00  0.00
ATOM     67  CA  ALA    70      11.703  25.311  -0.332  1.00  0.00
ATOM     68  CA  GLU    71      14.546  27.155  -2.057  1.00  0.00
ATOM     69  CA  GLY    72      15.187  24.260  -4.441  1.00  0.00
ATOM     70  CA  LYS    73      11.478  23.894  -5.186  1.00  0.00
ATOM     71  CA  LYS    74      11.380  27.479  -6.446  1.00  0.00
ATOM     72  CA  VAL    75      14.187  26.642  -8.851  1.00  0.00
ATOM     73  CA  THR    76      12.411  23.439  -9.911  1.00  0.00
ATOM     74  CA  ASP    77       9.341  25.510 -10.753  1.00  0.00
ATOM     75  CA  LEU    78      11.375  28.055 -12.707  1.00  0.00
ATOM     76  CA  THR    79      13.187  25.360 -14.674  1.00  0.00
ATOM     77  CA  GLY    80       9.949  23.486 -15.313  1.00  0.00
ATOM     78  CA  GLU    81       8.090  26.531 -16.609  1.00  0.00
ATOM     79  CA  ASP    82      15.037  23.765 -18.632  1.00  0.00
ATOM     80  CA  VAL    83      18.116  21.706 -14.426  1.00  0.00
ATOM     81  CA  ALA    84      14.648  20.487 -13.502  1.00  0.00
ATOM     82  CA  ALA    85      15.870  16.909 -13.236  1.00  0.00
ATOM     83  CA  PHE    86      18.977  17.880 -11.320  1.00  0.00
ATOM     84  CA  CYS    87      17.091  19.851  -8.686  1.00  0.00
ATOM     85  CA  ASP    88      14.303  17.287  -8.455  1.00  0.00
ATOM     86  CA  GLU    89      16.834  14.516  -7.766  1.00  0.00
ATOM     87  CA  LEU    90      18.248  16.603  -4.924  1.00  0.00
ATOM     88  CA  MET    91      14.740  17.426  -3.757  1.00  0.00
ATOM     89  CA  LYS    92      14.057  13.687  -3.541  1.00  0.00
ATOM     90  CA  ASP    93      17.004  12.958  -1.260  1.00  0.00
ATOM     91  CA  THR    94      16.166  16.020   0.859  1.00  0.00
ATOM     92  CA  LYS    95      12.599  14.845   1.261  1.00  0.00
ATOM     93  CA  THR    96      13.697  11.455   2.485  1.00  0.00
ATOM     94  CA  TRP    97      16.220  12.949   4.938  1.00  0.00
ATOM     95  CA  MET    98      13.713  15.515   6.234  1.00  0.00
ATOM     96  CA  ASP    99      11.185  12.745   6.830  1.00  0.00
ATOM     97  CA  LYS   100      13.694  10.523   8.629  1.00  0.00
ATOM     98  CA  TYR   101      14.943  13.388  10.803  1.00  0.00
ATOM     99  CA  ARG   102      11.346  14.222  11.646  1.00  0.00
ATOM    100  CA  THR   103      10.752  10.612  12.648  1.00  0.00
ATOM    101  CA  LYS   104      13.827  10.438  14.874  1.00  0.00
ATOM    102  CA  LEU   105      13.048  13.801  16.514  1.00  0.00
ATOM    103  CA  ASN   106       9.415  12.804  17.272  1.00  0.00
ATOM    104  CA  ASP   107       7.884  10.491  18.374  1.00  0.00
ATOM    105  CA  SER   108       9.863  10.280  21.637  1.00  0.00
ATOM    106  CA  ILE   109       6.007  13.544  11.567  1.00  0.00
ATOM    107  CA  GLY   110       7.947  14.936   8.563  1.00  0.00
ATOM    108  CA  ARG   111       5.714  18.021   8.434  1.00  0.00
TER
END
