
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0283AL044_1-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283AL044_1-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    K       6      M       1           -
LGA    M       7      -       -           -
LGA    I       8      -       -           -
LGA    G       9      -       -           -
LGA    L      11      -       -           -
LGA    N      12      S       2           #
LGA    D      13      -       -           -
LGA    K      14      F       3          2.884
LGA    R      15      I       4          2.431
LGA    E      16      -       -           -
LGA    W      17      E       5          3.089
LGA    K      18      K       6          4.059
LGA    A      19      M       7          4.451
LGA    -       -      I       8           -
LGA    M      20      G       9          1.791
LGA    L      27      S      10          1.682
LGA    -       -      L      11           -
LGA    -       -      N      12           -
LGA    P      28      D      13          1.572
LGA    K      29      K      14          2.324
LGA    -       -      R      15           -
LGA    -       -      E      16           -
LGA    E      30      W      17          0.592
LGA    Y      31      K      18          2.984
LGA    -       -      A      19           -
LGA    -       -      M      20           -
LGA    H      32      E      21          1.693
LGA    -       -      A      22           -
LGA    -       -      R      23           -
LGA    -       -      A      24           -
LGA    H      33      K      25          1.879
LGA    -       -      A      26           -
LGA    A      34      L      27          3.950
LGA    Y      35      P      28           -
LGA    K      40      K      29           -
LGA    Y      41      E      30           -
LGA    R      56      Y      31           -
LGA    I      57      H      32           -
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
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    F      58      W      51          2.568
LGA    G      59      Q      52          4.649
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           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    -       -      K      74           -
LGA    G      60      V      75          1.516
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    I      61      L      78          1.683
LGA    L      62      T      79          5.524
LGA    D      63      -       -           -
LGA    L      64      -       -           -
LGA    F      65      -       -           -
LGA    K      74      -       -           -
LGA    V      75      G      80          2.474
LGA    T      76      E      81          2.801
LGA    D      77      -       -           -
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    D      82      -       -           -
LGA    V      83      D      82           #
LGA    A      84      V      83           -
LGA    A      85      A      84           -
LGA    F      86      A      85           -
LGA    -       -      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)   46   97    5.0     21    2.95     9.52     13.948     0.688

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.105083 * X  +   0.869548 * Y  +  -0.482539 * Z  +  11.182634
  Y_new =  -0.978818 * X  +   0.004707 * Y  +  -0.204677 * Z  +  43.048790
  Z_new =  -0.175705 * X  +   0.493826 * Y  +   0.851624 * Z  + -46.212383 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.525482   -2.616110  [ DEG:    30.1079   -149.8921 ]
  Theta =   0.176622    2.964971  [ DEG:    10.1197    169.8803 ]
  Phi   =  -1.463849    1.677744  [ DEG:   -83.8724     96.1276 ]
 
# 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: T0283AL044_1-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL044_1-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   97   5.0   21   2.95    9.52  13.948
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL044_1-D1
REMARK Aligment from pdb entry: 1h6s_1
ATOM      1  N   LYS     6      36.696  39.979  11.916  1.00  0.00              
ATOM      2  CA  LYS     6      36.179  40.738  13.044  1.00  0.00              
ATOM      3  C   LYS     6      34.890  41.425  12.589  1.00  0.00              
ATOM      4  O   LYS     6      34.741  41.802  11.419  1.00  0.00              
ATOM      5  N   MET     7      33.960  41.569  13.524  1.00  0.00              
ATOM      6  CA  MET     7      32.691  42.238  13.271  1.00  0.00              
ATOM      7  C   MET     7      32.437  43.181  14.433  1.00  0.00              
ATOM      8  O   MET     7      32.900  42.935  15.549  1.00  0.00              
ATOM      9  N   ILE     8      30.488  15.759  10.102  1.00  0.00              
ATOM     10  CA  ILE     8      30.328  15.117  11.397  1.00  0.00              
ATOM     11  C   ILE     8      30.659  16.163  12.478  1.00  0.00              
ATOM     12  O   ILE     8      31.812  16.569  12.630  1.00  0.00              
ATOM     13  N   GLY     9      29.646  16.612  13.244  1.00  0.00              
ATOM     14  CA  GLY     9      29.820  17.611  14.306  1.00  0.00              
ATOM     15  C   GLY     9      30.756  17.205  15.445  1.00  0.00              
ATOM     16  O   GLY     9      31.188  18.048  16.237  1.00  0.00              
ATOM     17  N   LEU    11      31.060  15.917  15.539  1.00  0.00              
ATOM     18  CA  LEU    11      31.972  15.422  16.563  1.00  0.00              
ATOM     19  C   LEU    11      32.507  14.097  16.048  1.00  0.00              
ATOM     20  O   LEU    11      31.915  13.046  16.280  1.00  0.00              
ATOM     21  N   ASN    12      33.630  14.161  15.347  1.00  0.00              
ATOM     22  CA  ASN    12      34.242  12.981  14.755  1.00  0.00              
ATOM     23  C   ASN    12      34.952  12.060  15.745  1.00  0.00              
ATOM     24  O   ASN    12      35.334  10.950  15.387  1.00  0.00              
ATOM     25  N   ASP    13      35.136  12.500  16.982  1.00  0.00              
ATOM     26  CA  ASP    13      35.831  11.658  17.950  1.00  0.00              
ATOM     27  C   ASP    13      34.886  10.616  18.510  1.00  0.00              
ATOM     28  O   ASP    13      35.301   9.517  18.869  1.00  0.00              
ATOM     29  N   LYS    14      33.610  10.970  18.588  1.00  0.00              
ATOM     30  CA  LYS    14      32.596  10.062  19.111  1.00  0.00              
ATOM     31  C   LYS    14      32.167   9.013  18.085  1.00  0.00              
ATOM     32  O   LYS    14      32.176   9.260  16.879  1.00  0.00              
ATOM     33  N   ARG    15      31.785   7.841  18.575  1.00  0.00              
ATOM     34  CA  ARG    15      31.338   6.755  17.707  1.00  0.00              
ATOM     35  C   ARG    15      30.201   7.245  16.799  1.00  0.00              
ATOM     36  O   ARG    15      29.205   7.789  17.280  1.00  0.00              
ATOM     37  N   GLU    16      30.359   7.044  15.491  1.00  0.00              
ATOM     38  CA  GLU    16      29.376   7.475  14.492  1.00  0.00              
ATOM     39  C   GLU    16      27.920   7.369  14.932  1.00  0.00              
ATOM     40  O   GLU    16      27.240   8.378  15.108  1.00  0.00              
ATOM     41  N   TRP    17      27.451   6.136  15.088  1.00  0.00              
ATOM     42  CA  TRP    17      26.077   5.855  15.494  1.00  0.00              
ATOM     43  C   TRP    17      25.538   6.751  16.617  1.00  0.00              
ATOM     44  O   TRP    17      24.328   6.864  16.803  1.00  0.00              
ATOM     45  N   LYS    18      26.433   7.388  17.362  1.00  0.00              
ATOM     46  CA  LYS    18      26.017   8.253  18.456  1.00  0.00              
ATOM     47  C   LYS    18      25.718   9.685  18.027  1.00  0.00              
ATOM     48  O   LYS    18      25.005  10.407  18.722  1.00  0.00              
ATOM     49  N   ALA    19      26.260  10.104  16.889  1.00  0.00              
ATOM     50  CA  ALA    19      26.036  11.462  16.405  1.00  0.00              
ATOM     51  C   ALA    19      25.296  11.474  15.079  1.00  0.00              
ATOM     52  O   ALA    19      25.250  10.463  14.375  1.00  0.00              
ATOM     53  N   MET    20      24.720  12.625  14.747  1.00  0.00              
ATOM     54  CA  MET    20      23.970  12.794  13.507  1.00  0.00              
ATOM     55  C   MET    20      24.791  13.567  12.483  1.00  0.00              
ATOM     56  O   MET    20      25.129  14.727  12.708  1.00  0.00              
ATOM     57  N   LEU    27      25.112  12.942  11.358  1.00  0.00              
ATOM     58  CA  LEU    27      25.884  13.641  10.338  1.00  0.00              
ATOM     59  C   LEU    27      24.981  14.304   9.294  1.00  0.00              
ATOM     60  O   LEU    27      23.857  13.862   9.056  1.00  0.00              
ATOM     61  N   PRO    28      25.480  15.371   8.681  1.00  0.00              
ATOM     62  CA  PRO    28      24.741  16.082   7.647  1.00  0.00              
ATOM     63  C   PRO    28      25.323  15.641   6.308  1.00  0.00              
ATOM     64  O   PRO    28      26.545  15.556   6.157  1.00  0.00              
ATOM     65  N   LYS    29      24.459  15.332   5.347  1.00  0.00              
ATOM     66  CA  LYS    29      24.916  14.930   4.023  1.00  0.00              
ATOM     67  C   LYS    29      24.162  15.781   3.017  1.00  0.00              
ATOM     68  O   LYS    29      22.936  15.901   3.095  1.00  0.00              
ATOM     69  N   GLU    30      24.883  16.378   2.075  1.00  0.00              
ATOM     70  CA  GLU    30      24.214  17.222   1.107  1.00  0.00              
ATOM     71  C   GLU    30      24.724  17.080  -0.308  1.00  0.00              
ATOM     72  O   GLU    30      25.929  16.999  -0.547  1.00  0.00              
ATOM     73  N   TYR    31      23.786  17.047  -1.249  1.00  0.00              
ATOM     74  CA  TYR    31      24.094  16.926  -2.668  1.00  0.00              
ATOM     75  C   TYR    31      23.555  18.203  -3.284  1.00  0.00              
ATOM     76  O   TYR    31      22.591  18.776  -2.773  1.00  0.00              
ATOM     77  N   HIS    32      24.165  18.643  -4.378  1.00  0.00              
ATOM     78  CA  HIS    32      23.731  19.863  -5.042  1.00  0.00              
ATOM     79  C   HIS    32      24.360  19.999  -6.427  1.00  0.00              
ATOM     80  O   HIS    32      25.493  19.557  -6.663  1.00  0.00              
ATOM     81  N   HIS    33      23.621  20.616  -7.343  1.00  0.00              
ATOM     82  CA  HIS    33      24.115  20.804  -8.695  1.00  0.00              
ATOM     83  C   HIS    33      23.474  22.004  -9.362  1.00  0.00              
ATOM     84  O   HIS    33      22.322  22.324  -9.088  1.00  0.00              
ATOM     85  N   ALA    34      24.229  22.684 -10.214  1.00  0.00              
ATOM     86  CA  ALA    34      23.686  23.810 -10.959  1.00  0.00              
ATOM     87  C   ALA    34      24.242  23.762 -12.385  1.00  0.00              
ATOM     88  O   ALA    34      25.271  23.123 -12.655  1.00  0.00              
ATOM     89  N   TYR    35      19.239  21.438  -4.813  1.00  0.00              
ATOM     90  CA  TYR    35      20.062  20.987  -3.706  1.00  0.00              
ATOM     91  C   TYR    35      19.228  20.225  -2.688  1.00  0.00              
ATOM     92  O   TYR    35      18.051  20.525  -2.477  1.00  0.00              
ATOM     93  N   LYS    40      19.848  19.239  -2.052  1.00  0.00              
ATOM     94  CA  LYS    40      19.166  18.437  -1.046  1.00  0.00              
ATOM     95  C   LYS    40      20.129  18.104   0.097  1.00  0.00              
ATOM     96  O   LYS    40      21.266  17.692  -0.141  1.00  0.00              
ATOM     97  N   TYR    41      19.678  18.288   1.334  1.00  0.00              
ATOM     98  CA  TYR    41      20.514  17.998   2.493  1.00  0.00              
ATOM     99  C   TYR    41      19.702  17.302   3.576  1.00  0.00              
ATOM    100  O   TYR    41      18.667  17.804   3.998  1.00  0.00              
ATOM    101  N   ARG    56      20.175  16.148   4.033  1.00  0.00              
ATOM    102  CA  ARG    56      19.478  15.414   5.083  1.00  0.00              
ATOM    103  C   ARG    56      20.146  15.648   6.426  1.00  0.00              
ATOM    104  O   ARG    56      21.370  15.738   6.517  1.00  0.00              
ATOM    105  N   ILE    57      19.333  15.748   7.470  1.00  0.00              
ATOM    106  CA  ILE    57      19.841  15.983   8.814  1.00  0.00              
ATOM    107  C   ILE    57      20.662  17.256   8.815  1.00  0.00              
ATOM    108  O   ILE    57      21.737  17.309   9.388  1.00  0.00              
ATOM    109  N   PHE    58      20.133  18.279   8.156  1.00  0.00              
ATOM    110  CA  PHE    58      20.796  19.571   8.060  1.00  0.00              
ATOM    111  C   PHE    58      21.123  20.069   9.451  1.00  0.00              
ATOM    112  O   PHE    58      20.345  19.876  10.386  1.00  0.00              
ATOM    113  N   GLY    59      22.283  20.706   9.581  1.00  0.00              
ATOM    114  CA  GLY    59      22.701  21.234  10.867  1.00  0.00              
ATOM    115  C   GLY    59      22.856  20.179  11.940  1.00  0.00              
ATOM    116  O   GLY    59      22.938  20.503  13.117  1.00  0.00              
ATOM    117  N   GLY    60      16.495  30.768 -13.074  1.00  0.00              
ATOM    118  CA  GLY    60      16.668  32.184 -13.355  1.00  0.00              
ATOM    119  C   GLY    60      16.760  32.408 -14.846  1.00  0.00              
ATOM    120  O   GLY    60      17.258  31.557 -15.593  1.00  0.00              
ATOM    121  N   ILE    61      13.464  32.667  -9.572  1.00  0.00              
ATOM    122  CA  ILE    61      12.471  32.144  -8.663  1.00  0.00              
ATOM    123  C   ILE    61      13.083  30.997  -7.874  1.00  0.00              
ATOM    124  O   ILE    61      13.555  30.019  -8.457  1.00  0.00              
ATOM    125  N   LEU    62      13.097  31.123  -6.548  1.00  0.00              
ATOM    126  CA  LEU    62      13.638  30.068  -5.692  1.00  0.00              
ATOM    127  C   LEU    62      12.544  29.468  -4.813  1.00  0.00              
ATOM    128  O   LEU    62      11.738  30.200  -4.224  1.00  0.00              
ATOM    129  N   ASP    63      12.506  28.140  -4.736  1.00  0.00              
ATOM    130  CA  ASP    63      11.533  27.458  -3.900  1.00  0.00              
ATOM    131  C   ASP    63      12.290  26.637  -2.862  1.00  0.00              
ATOM    132  O   ASP    63      13.240  25.923  -3.192  1.00  0.00              
ATOM    133  N   LEU    64      11.854  26.716  -1.612  1.00  0.00              
ATOM    134  CA  LEU    64      12.518  25.983  -0.545  1.00  0.00              
ATOM    135  C   LEU    64      11.626  25.094   0.300  1.00  0.00              
ATOM    136  O   LEU    64      10.444  25.380   0.510  1.00  0.00              
ATOM    137  N   PHE    65      12.534  21.175   9.231  1.00  0.00              
ATOM    138  CA  PHE    65      11.802  21.409  10.471  1.00  0.00              
ATOM    139  C   PHE    65      11.629  22.872  10.870  1.00  0.00              
ATOM    140  O   PHE    65      11.214  23.171  11.988  1.00  0.00              
ATOM    141  N   LYS    74      11.933  23.793   9.970  1.00  0.00              
ATOM    142  CA  LYS    74      11.774  25.201  10.311  1.00  0.00              
ATOM    143  C   LYS    74      10.289  25.531  10.413  1.00  0.00              
ATOM    144  O   LYS    74       9.472  24.998   9.654  1.00  0.00              
ATOM    145  N   VAL    75      14.754  40.015  -8.663  1.00  0.00              
ATOM    146  CA  VAL    75      15.205  40.517  -9.937  1.00  0.00              
ATOM    147  C   VAL    75      16.099  41.722  -9.745  1.00  0.00              
ATOM    148  O   VAL    75      16.041  42.409  -8.724  1.00  0.00              
ATOM    149  N   THR    76      16.946  41.973 -10.729  1.00  0.00              
ATOM    150  CA  THR    76      17.840  43.110 -10.678  1.00  0.00              
ATOM    151  C   THR    76      18.055  43.609 -12.093  1.00  0.00              
ATOM    152  O   THR    76      17.828  42.884 -13.064  1.00  0.00              
ATOM    153  N   ASP    77      18.496  44.852 -12.202  1.00  0.00              
ATOM    154  CA  ASP    77      18.740  45.454 -13.492  1.00  0.00              
ATOM    155  C   ASP    77      19.948  46.370 -13.350  1.00  0.00              
ATOM    156  O   ASP    77      20.082  47.087 -12.350  1.00  0.00              
ATOM    157  N   GLY    80      20.823  46.342 -14.352  1.00  0.00              
ATOM    158  CA  GLY    80      22.028  47.158 -14.342  1.00  0.00              
ATOM    159  C   GLY    80      22.009  48.290 -15.371  1.00  0.00              
ATOM    160  O   GLY    80      21.965  48.046 -16.572  1.00  0.00              
ATOM    161  N   GLU    81      22.041  49.525 -14.879  1.00  0.00              
ATOM    162  CA  GLU    81      22.061  50.726 -15.712  1.00  0.00              
ATOM    163  C   GLU    81      23.505  51.205 -15.768  1.00  0.00              
ATOM    164  O   GLU    81      23.835  52.263 -15.237  1.00  0.00              
ATOM    165  N   ASP    82      24.376  50.427 -16.388  1.00  0.00              
ATOM    166  CA  ASP    82      25.763  50.836 -16.455  1.00  0.00              
ATOM    167  C   ASP    82      26.516  50.520 -15.176  1.00  0.00              
ATOM    168  O   ASP    82      26.974  49.389 -14.988  1.00  0.00              
ATOM    169  N   VAL    83      19.885  47.954  -9.747  1.00  0.00              
ATOM    170  CA  VAL    83      18.678  48.038  -8.942  1.00  0.00              
ATOM    171  C   VAL    83      18.249  46.609  -8.651  1.00  0.00              
ATOM    172  O   VAL    83      18.264  45.765  -9.542  1.00  0.00              
ATOM    173  N   ALA    84      22.886  49.874  -0.708  1.00  0.00              
ATOM    174  CA  ALA    84      21.890  50.334   0.241  1.00  0.00              
ATOM    175  C   ALA    84      20.626  49.527   0.030  1.00  0.00              
ATOM    176  O   ALA    84      20.476  48.882  -1.008  1.00  0.00              
ATOM    177  N   ALA    85      14.085  47.116   8.179  1.00  0.00              
ATOM    178  CA  ALA    85      15.528  47.265   8.227  1.00  0.00              
ATOM    179  C   ALA    85      16.048  48.007   6.994  1.00  0.00              
ATOM    180  O   ALA    85      15.552  47.807   5.883  1.00  0.00              
ATOM    181  N   PHE    86      29.766  50.899   2.401  1.00  0.00              
ATOM    182  CA  PHE    86      30.798  50.679   1.409  1.00  0.00              
ATOM    183  C   PHE    86      31.488  49.355   1.656  1.00  0.00              
ATOM    184  O   PHE    86      31.548  48.872   2.789  1.00  0.00              
END
