
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283TS383_1.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    -       -      E       5           -
LGA    -       -      K       6           -
LGA    -       -      M       7           -
LGA    S       2      I       8          3.772
LGA    F       3      G       9          2.710
LGA    I       4      S      10          0.913
LGA    E       5      L      11          1.679
LGA    K       6      N      12          1.792
LGA    M       7      D      13          1.655
LGA    I       8      K      14          1.105
LGA    G       9      R      15          0.538
LGA    -       -      E      16           -
LGA    S      10      W      17          2.630
LGA    L      11      K      18          2.029
LGA    N      12      A      19          1.535
LGA    D      13      M      20          3.398
LGA    K      14      E      21          3.923
LGA    R      15      A      22          2.838
LGA    E      16      R      23          3.093
LGA    W      17      A      24          4.389
LGA    K      18      K      25          3.991
LGA    A      19      A      26          2.995
LGA    M      20      L      27          3.001
LGA    E      21      -       -           -
LGA    A      22      -       -           -
LGA    R      23      -       -           -
LGA    A      24      P      28          4.954
LGA    K      25      -       -           -
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      K      29          3.590
LGA    K      29      E      30          5.978
LGA    E      30      Y      31           -
LGA    Y      31      H      32           -
LGA    H      32      -       -           -
LGA    H      33      -       -           -
LGA    A      34      H      33          5.616
LGA    Y      35      A      34          5.244
LGA    -       -      Y      35           -
LGA    K      36      K      36          5.224
LGA    A      37      A      37          4.716
LGA    I      38      -       -           -
LGA    Q      39      -       -           -
LGA    K      40      I      38          3.400
LGA    Y      41      Q      39          4.112
LGA    T      44      K      40           #
LGA    S      45      Y      41          2.941
LGA    G      46      M      42          2.052
LGA    G      47      W      43          2.514
LGA    P      48      T      44          3.544
LGA    T      49      S      45          4.214
LGA    D      50      G      46           -
LGA    W      51      G      47           -
LGA    Q      52      P      48           #
LGA    D      53      T      49          5.069
LGA    T      54      D      50          4.383
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      W      51          2.403
LGA    F      58      Q      52          0.763
LGA    G      59      D      53          1.796
LGA    G      60      T      54          2.567
LGA    I      61      K      55          2.165
LGA    L      62      R      56          0.946
LGA    D      63      I      57          2.266
LGA    L      64      F      58          2.176
LGA    F      65      G      59          1.111
LGA    E      66      G      60          1.973
LGA    E      67      I      61          3.476
LGA    G      68      L      62          2.944
LGA    A      69      D      63          1.823
LGA    A      70      L      64          2.728
LGA    E      71      F      65          3.219
LGA    G      72      E      66          2.609
LGA    K      73      E      67          2.526
LGA    K      74      G      68          3.120
LGA    V      75      A      69          3.066
LGA    T      76      A      70          2.674
LGA    D      77      E      71          3.267
LGA    L      78      G      72           #
LGA    T      79      K      73           #
LGA    G      80      K      74           -
LGA    E      81      V      75           -
LGA    D      82      T      76           -
LGA    V      83      D      77           -
LGA    A      84      L      78           -
LGA    A      85      T      79           -
LGA    F      86      G      80           -
LGA    C      87      E      81           -
LGA    D      88      D      82           -
LGA    E      89      V      83           -
LGA    L      90      A      84           -
LGA    M      91      A      85           -
LGA    K      92      F      86           -
LGA    D      93      C      87           -
LGA    T      94      D      88           -
LGA    K      95      E      89           -
LGA    T      96      L      90           -
LGA    W      97      M      91           -
LGA    M      98      K      92           -
LGA    D      99      D      93           -
LGA    K     100      T      94           -
LGA    Y     101      K      95           -
LGA    R     102      T      96           -
LGA    T     103      W      97           -
LGA    K     104      M      98           -
LGA    L     105      D      99           -
LGA    N     106      K     100           -
LGA    D     107      Y     101           -
LGA    S     108      R     102           -
LGA    I     109      T     103           -
LGA    G     110      K     104           -
LGA    R     111      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     56    3.21     7.14     32.633     1.692

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.827588 * X  +   0.370669 * Y  +  -0.421548 * Z  +  30.545952
  Y_new =  -0.095231 * X  +  -0.832798 * Y  +  -0.545324 * Z  +  -8.185966
  Z_new =  -0.553199 * X  +  -0.411159 * Y  +   0.724513 * Z  +  -5.522990 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.516178    2.625415  [ DEG:   -29.5748    150.4252 ]
  Theta =   0.586199    2.555394  [ DEG:    33.5867    146.4133 ]
  Phi   =  -3.027026    0.114567  [ DEG:  -173.4358      6.5642 ]
 
# 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_1                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS383_1.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  112   5.0   56   3.21    7.14  32.633
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS383_1
PFRMAT TS
TARGET T0283
MODEL 1
PARENT 1ji5A
ATOM      1  CA  SER     2      23.551  10.529  13.171  1.00  0.00
ATOM      2  CA  PHE     3      23.688  14.127  11.852  1.00  0.00
ATOM      3  CA  ILE     4      27.406  13.985  10.957  1.00  0.00
ATOM      4  CA  GLU     5      26.336  11.104   8.770  1.00  0.00
ATOM      5  CA  LYS     6      23.170  12.576   7.285  1.00  0.00
ATOM      6  CA  MET     7      24.963  15.717   6.070  1.00  0.00
ATOM      7  CA  ILE     8      27.595  13.632   4.234  1.00  0.00
ATOM      8  CA  GLY     9      24.725  11.760   2.581  1.00  0.00
ATOM      9  CA  SER    10      26.825  16.971   0.146  1.00  0.00
ATOM     10  CA  LEU    11      27.460  13.842  -1.945  1.00  0.00
ATOM     11  CA  ASN    12      24.054  14.518  -3.448  1.00  0.00
ATOM     12  CA  ASP    13      24.816  18.194  -4.116  1.00  0.00
ATOM     13  CA  LYS    14      28.028  17.166  -5.845  1.00  0.00
ATOM     14  CA  ARG    15      25.947  14.976  -8.178  1.00  0.00
ATOM     15  CA  GLU    16      23.325  17.674  -8.707  1.00  0.00
ATOM     16  CA  TRP    17      26.098  20.163  -9.443  1.00  0.00
ATOM     17  CA  LYS    18      27.419  17.869 -12.175  1.00  0.00
ATOM     18  CA  ALA    19      24.000  16.994 -13.661  1.00  0.00
ATOM     19  CA  MET    20      22.870  20.618 -13.844  1.00  0.00
ATOM     20  CA  GLU    21      26.097  21.626 -15.584  1.00  0.00
ATOM     21  CA  ALA    22      25.864  17.837 -18.135  1.00  0.00
ATOM     22  CA  ARG    23      22.224  18.535 -18.851  1.00  0.00
ATOM     23  CA  ALA    24      22.731  22.106 -20.002  1.00  0.00
ATOM     24  CA  LYS    25      25.831  20.745 -21.633  1.00  0.00
ATOM     25  CA  ALA    26      23.548  18.346 -23.554  1.00  0.00
ATOM     26  CA  LEU    27      21.262  21.156 -24.648  1.00  0.00
ATOM     27  CA  PRO    28      27.716  25.506 -17.449  1.00  0.00
ATOM     28  CA  LYS    29      29.003  28.039 -14.955  1.00  0.00
ATOM     29  CA  GLU    30      32.224  26.611 -13.552  1.00  0.00
ATOM     30  CA  TYR    31      33.970  28.887 -11.057  1.00  0.00
ATOM     31  CA  HIS    32      33.232  29.392  -7.398  1.00  0.00
ATOM     32  CA  HIS    33      33.435  33.082  -8.240  1.00  0.00
ATOM     33  CA  ALA    34      30.392  32.948 -10.512  1.00  0.00
ATOM     34  CA  TYR    35      28.599  30.557  -8.140  1.00  0.00
ATOM     35  CA  LYS    36      28.888  33.149  -5.401  1.00  0.00
ATOM     36  CA  ALA    37      27.543  35.968  -7.539  1.00  0.00
ATOM     37  CA  ILE    38      24.558  33.931  -8.758  1.00  0.00
ATOM     38  CA  GLN    39      23.557  31.468  -6.044  1.00  0.00
ATOM     39  CA  LYS    40      20.725  32.517  -3.739  1.00  0.00
ATOM     40  CA  TYR    41      21.783  30.137  -0.950  1.00  0.00
ATOM     41  CA  THR    44      22.806  32.132   0.855  1.00  0.00
ATOM     42  CA  SER    45      23.818  32.714   1.531  1.00  0.00
ATOM     43  CA  GLY    46      23.187  31.870   2.125  1.00  0.00
ATOM     44  CA  GLY    47      26.385  29.969   3.153  1.00  0.00
ATOM     45  CA  PRO    48      28.776  30.593   6.080  1.00  0.00
ATOM     46  CA  THR    49      27.008  31.171   9.363  1.00  0.00
ATOM     47  CA  ASP    50      29.498  29.692  11.746  1.00  0.00
ATOM     48  CA  TRP    51      28.287  29.146  15.302  1.00  0.00
ATOM     49  CA  GLN    52      25.155  27.228  14.180  1.00  0.00
ATOM     50  CA  ASP    53      23.299  24.626  16.318  1.00  0.00
ATOM     51  CA  THR    54      22.756  20.994  15.395  1.00  0.00
ATOM     52  CA  LYS    55      19.063  21.832  15.171  1.00  0.00
ATOM     53  CA  ARG    56      20.006  25.145  13.612  1.00  0.00
ATOM     54  CA  ILE    57      21.788  23.309  10.805  1.00  0.00
ATOM     55  CA  PHE    58      18.886  20.927  10.173  1.00  0.00
ATOM     56  CA  GLY    59      16.529  23.867  10.276  1.00  0.00
ATOM     57  CA  GLY    60      18.905  25.764   7.955  1.00  0.00
ATOM     58  CA  ILE    61      19.219  23.383   4.989  1.00  0.00
ATOM     59  CA  LEU    62      15.602  22.356   5.425  1.00  0.00
ATOM     60  CA  ASP    63      14.613  25.952   4.635  1.00  0.00
ATOM     61  CA  LEU    64      17.164  25.951   1.803  1.00  0.00
ATOM     62  CA  PHE    65      15.538  22.894   0.292  1.00  0.00
ATOM     63  CA  GLU    66      12.057  24.422   0.555  1.00  0.00
ATOM     64  CA  GLU    67      13.168  27.693  -0.992  1.00  0.00
ATOM     65  CA  GLY    68      14.536  25.544  -3.814  1.00  0.00
ATOM     66  CA  ALA    69      11.274  23.725  -4.374  1.00  0.00
ATOM     67  CA  ALA    70       9.711  27.008  -5.492  1.00  0.00
ATOM     68  CA  GLU    71      12.569  27.852  -7.859  1.00  0.00
ATOM     69  CA  GLY    72      12.178  24.351  -9.252  1.00  0.00
ATOM     70  CA  LYS    73       8.443  24.608  -9.936  1.00  0.00
ATOM     71  CA  LYS    74       9.193  27.864 -11.730  1.00  0.00
ATOM     72  CA  VAL    75      12.011  26.069 -13.516  1.00  0.00
ATOM     73  CA  THR    76       9.712  23.323 -14.817  1.00  0.00
ATOM     74  CA  ASP    77       7.232  25.956 -15.959  1.00  0.00
ATOM     75  CA  LEU    78       9.728  27.677 -18.246  1.00  0.00
ATOM     76  CA  THR    79      11.284  24.356 -19.306  1.00  0.00
ATOM     77  CA  GLY    80       7.854  23.176 -20.440  1.00  0.00
ATOM     78  CA  GLU    81       7.136  26.543 -22.034  1.00  0.00
ATOM     79  CA  ASP    82      11.762  20.956 -22.981  1.00  0.00
ATOM     80  CA  VAL    83      14.900  19.194 -18.446  1.00  0.00
ATOM     81  CA  ALA    84      11.560  19.474 -16.641  1.00  0.00
ATOM     82  CA  ALA    85      11.681  15.765 -15.837  1.00  0.00
ATOM     83  CA  PHE    86      15.221  16.146 -14.501  1.00  0.00
ATOM     84  CA  CYS    87      14.070  18.973 -12.279  1.00  0.00
ATOM     85  CA  ASP    88      10.974  17.039 -11.246  1.00  0.00
ATOM     86  CA  GLU    89      13.223  14.341  -9.827  1.00  0.00
ATOM     87  CA  LEU    90      15.169  16.727  -7.613  1.00  0.00
ATOM     88  CA  MET    91      11.844  18.134  -6.455  1.00  0.00
ATOM     89  CA  LYS    92      10.622  14.739  -5.351  1.00  0.00
ATOM     90  CA  ASP    93      13.965  14.100  -3.643  1.00  0.00
ATOM     91  CA  THR    94      13.984  17.298  -1.648  1.00  0.00
ATOM     92  CA  LYS    95      10.319  17.032  -0.639  1.00  0.00
ATOM     93  CA  THR    96      11.023  13.736   1.100  1.00  0.00
ATOM     94  CA  TRP    97      14.066  15.163   2.854  1.00  0.00
ATOM     95  CA  MET    98      12.113  18.211   4.004  1.00  0.00
ATOM     96  CA  ASP    99       9.584  15.892   5.619  1.00  0.00
ATOM     97  CA  LYS   100      12.202  13.826   7.454  1.00  0.00
ATOM     98  CA  TYR   101      14.191  16.903   8.414  1.00  0.00
ATOM     99  CA  ARG   102      10.977  18.543   9.593  1.00  0.00
ATOM    100  CA  THR   103       9.819  15.468  11.528  1.00  0.00
ATOM    101  CA  LYS   104      13.242  15.452  13.153  1.00  0.00
ATOM    102  CA  LEU   105      12.482  18.930  14.510  1.00  0.00
ATOM    103  CA  ASN   106       8.709  19.364  15.059  1.00  0.00
ATOM    104  CA  ASP   107       7.250  17.626  16.904  1.00  0.00
ATOM    105  CA  SER   108       9.588  17.861  19.918  1.00  0.00
ATOM    106  CA  ILE   109       4.725  19.322   9.646  1.00  0.00
ATOM    107  CA  GLY   110       6.456  19.640   6.235  1.00  0.00
ATOM    108  CA  ARG   111       4.666  22.929   5.530  1.00  0.00
TER
END
