
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0283AL044_3
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283AL044_3.T0283  -4  -ie  -d:5  -o1  -sia  
# 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      -       -           -
LGA    M       7      -       -           -
LGA    I       8      -       -           -
LGA    G       9      -       -           -
LGA    L      11      -       -           -
LGA    N      12      -       -           -
LGA    D      13      -       -           -
LGA    K      14      -       -           -
LGA    R      15      -       -           -
LGA    E      16      -       -           -
LGA    W      17      -       -           -
LGA    K      18      M       1           #
LGA    A      19      S       2          2.056
LGA    M      20      F       3          1.448
LGA    -       -      I       4           -
LGA    -       -      E       5           -
LGA    L      27      K       6          1.546
LGA    P      28      M       7          1.100
LGA    K      29      I       8          3.241
LGA    -       -      G       9           -
LGA    -       -      S      10           -
LGA    E      30      L      11          0.901
LGA    -       -      N      12           -
LGA    -       -      D      13           -
LGA    Y      31      K      14          2.182
LGA    H      32      R      15          2.545
LGA    -       -      E      16           -
LGA    -       -      W      17           -
LGA    H      33      K      18          0.308
LGA    -       -      A      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    A      34      A      22          2.461
LGA    -       -      R      23           -
LGA    Y      35      A      24          3.833
LGA    K      40      K      25          0.484
LGA    -       -      A      26           -
LGA    Y      41      L      27          3.586
LGA    R      56      P      28          1.543
LGA    I      57      K      29          2.864
LGA    F      58      E      30          3.446
LGA    G      59      Y      31          3.151
LGA    G      60      H      32           -
LGA    I      61      H      33           -
LGA    L      62      A      34           -
LGA    D      63      Y      35           -
LGA    L      64      K      36           -
LGA    F      65      A      37           -
LGA    K      74      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    -       -      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    V      75      L      62          2.134
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    T      76      F      65          1.694
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    D      77      K      73           #
LGA    L      78      K      74          1.526
LGA    T      79      V      75           #
LGA    G      80      T      76          3.568
LGA    E      81      D      77          1.995
LGA    D      82      L      78          2.615
LGA    V      83      T      79          4.800
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    A      84      D      82          4.469
LGA    A      85      V      83           -
LGA    F      86      A      84           -
LGA    -       -      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           -
LGA    -       -      M      98           -
LGA    -       -      D      99           -
LGA    -       -      K     100           -
LGA    -       -      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)   48  112    5.0     25    2.65     8.00     15.028     0.910

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.835557 * X  +   0.367882 * Y  +  -0.408054 * Z  +  40.088322
  Y_new =  -0.522624 * X  +   0.761276 * Y  +  -0.383828 * Z  +  55.585564
  Z_new =   0.169438 * X  +   0.533969 * Y  +   0.828353 * Z  +  -0.781142 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.572580   -2.569012  [ DEG:    32.8064   -147.1936 ]
  Theta =  -0.170260   -2.971333  [ DEG:    -9.7552   -170.2448 ]
  Phi   =  -0.558944    2.582649  [ DEG:   -32.0251    147.9749 ]
 
# 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_3                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283AL044_3.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48  112   5.0   25   2.65    8.00  15.028
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL044_3
REMARK Aligment from pdb entry: 2por
ATOM      1  N   LYS     6      29.492  41.262  16.134  1.00  0.00              
ATOM      2  CA  LYS     6      30.239  40.144  16.640  1.00  0.00              
ATOM      3  C   LYS     6      31.541  40.626  17.189  1.00  0.00              
ATOM      4  O   LYS     6      32.385  39.770  17.497  1.00  0.00              
ATOM      5  N   MET     7      31.782  41.929  17.337  1.00  0.00              
ATOM      6  CA  MET     7      33.115  42.350  17.718  1.00  0.00              
ATOM      7  C   MET     7      33.581  41.862  19.088  1.00  0.00              
ATOM      8  O   MET     7      34.772  41.553  19.233  1.00  0.00              
ATOM      9  N   ILE     8      31.891  13.379  13.335  1.00  0.00              
ATOM     10  CA  ILE     8      31.640  12.756  14.621  1.00  0.00              
ATOM     11  C   ILE     8      31.859  13.660  15.831  1.00  0.00              
ATOM     12  O   ILE     8      32.604  14.654  15.775  1.00  0.00              
ATOM     13  N   GLY     9      31.127  13.383  16.936  1.00  0.00              
ATOM     14  CA  GLY     9      31.300  14.087  18.216  1.00  0.00              
ATOM     15  C   GLY     9      31.596  13.011  19.278  1.00  0.00              
ATOM     16  O   GLY     9      30.854  12.049  19.427  1.00  0.00              
ATOM     17  N   LEU    11      32.734  13.080  19.931  1.00  0.00              
ATOM     18  CA  LEU    11      33.107  12.253  21.047  1.00  0.00              
ATOM     19  C   LEU    11      32.729  12.916  22.340  1.00  0.00              
ATOM     20  O   LEU    11      33.138  14.034  22.653  1.00  0.00              
ATOM     21  N   ASN    12      31.944  12.157  23.093  1.00  0.00              
ATOM     22  CA  ASN    12      31.416  12.565  24.376  1.00  0.00              
ATOM     23  C   ASN    12      32.499  12.525  25.421  1.00  0.00              
ATOM     24  O   ASN    12      33.262  11.564  25.435  1.00  0.00              
ATOM     25  N   ASP    13      32.611  13.462  26.355  1.00  0.00              
ATOM     26  CA  ASP    13      33.529  13.335  27.465  1.00  0.00              
ATOM     27  C   ASP    13      32.990  12.277  28.425  1.00  0.00              
ATOM     28  O   ASP    13      33.812  11.737  29.149  1.00  0.00              
ATOM     29  N   LYS    14      31.686  11.926  28.480  1.00  0.00              
ATOM     30  CA  LYS    14      31.185  10.935  29.427  1.00  0.00              
ATOM     31  C   LYS    14      29.983  10.287  28.789  1.00  0.00              
ATOM     32  O   LYS    14      28.892  10.888  28.752  1.00  0.00              
ATOM     33  N   ARG    15      30.182   9.047  28.314  1.00  0.00              
ATOM     34  CA  ARG    15      29.114   8.343  27.619  1.00  0.00              
ATOM     35  C   ARG    15      27.980   7.793  28.513  1.00  0.00              
ATOM     36  O   ARG    15      26.966   7.316  27.973  1.00  0.00              
ATOM     37  N   GLU    16      28.100   7.901  29.861  1.00  0.00              
ATOM     38  CA  GLU    16      26.971   7.666  30.769  1.00  0.00              
ATOM     39  C   GLU    16      26.030   8.845  30.638  1.00  0.00              
ATOM     40  O   GLU    16      24.805   8.690  30.726  1.00  0.00              
ATOM     41  N   TRP    17      26.610  10.040  30.397  1.00  0.00              
ATOM     42  CA  TRP    17      25.812  11.244  30.265  1.00  0.00              
ATOM     43  C   TRP    17      25.394  11.656  28.845  1.00  0.00              
ATOM     44  O   TRP    17      24.309  12.232  28.674  1.00  0.00              
ATOM     45  N   LYS    18      26.185  11.381  27.799  1.00  0.00              
ATOM     46  CA  LYS    18      25.847  11.775  26.417  1.00  0.00              
ATOM     47  C   LYS    18      26.519  10.768  25.531  1.00  0.00              
ATOM     48  O   LYS    18      27.703  10.511  25.710  1.00  0.00              
ATOM     49  N   ALA    19      25.783  10.093  24.668  1.00  0.00              
ATOM     50  CA  ALA    19      26.328   9.095  23.774  1.00  0.00              
ATOM     51  C   ALA    19      27.222   9.775  22.733  1.00  0.00              
ATOM     52  O   ALA    19      27.031  10.950  22.397  1.00  0.00              
ATOM     53  N   MET    20      28.203   9.074  22.223  1.00  0.00              
ATOM     54  CA  MET    20      28.944   9.524  21.043  1.00  0.00              
ATOM     55  C   MET    20      28.031   9.627  19.828  1.00  0.00              
ATOM     56  O   MET    20      27.066   8.850  19.715  1.00  0.00              
ATOM     57  N   LEU    27      28.313  10.529  18.878  1.00  0.00              
ATOM     58  CA  LEU    27      27.433  10.703  17.738  1.00  0.00              
ATOM     59  C   LEU    27      28.273  10.633  16.449  1.00  0.00              
ATOM     60  O   LEU    27      29.486  10.888  16.491  1.00  0.00              
ATOM     61  N   PRO    28      27.695  10.269  15.312  1.00  0.00              
ATOM     62  CA  PRO    28      28.408  10.304  14.051  1.00  0.00              
ATOM     63  C   PRO    28      27.395  10.445  12.960  1.00  0.00              
ATOM     64  O   PRO    28      26.202  10.183  13.180  1.00  0.00              
ATOM     65  N   LYS    29      27.821  10.927  11.784  1.00  0.00              
ATOM     66  CA  LYS    29      26.922  11.098  10.650  1.00  0.00              
ATOM     67  C   LYS    29      27.780  11.013   9.394  1.00  0.00              
ATOM     68  O   LYS    29      28.900  11.532   9.381  1.00  0.00              
ATOM     69  N   GLU    30      27.271  10.315   8.401  1.00  0.00              
ATOM     70  CA  GLU    30      27.918  10.177   7.114  1.00  0.00              
ATOM     71  C   GLU    30      27.044  10.903   6.125  1.00  0.00              
ATOM     72  O   GLU    30      25.825  10.761   6.206  1.00  0.00              
ATOM     73  N   TYR    31      27.582  11.689   5.186  1.00  0.00              
ATOM     74  CA  TYR    31      26.771  12.407   4.207  1.00  0.00              
ATOM     75  C   TYR    31      27.241  12.108   2.769  1.00  0.00              
ATOM     76  O   TYR    31      28.450  11.919   2.552  1.00  0.00              
ATOM     77  N   HIS    32      26.292  12.093   1.833  1.00  0.00              
ATOM     78  CA  HIS    32      26.558  12.038   0.397  1.00  0.00              
ATOM     79  C   HIS    32      25.837  13.265  -0.093  1.00  0.00              
ATOM     80  O   HIS    32      24.692  13.518   0.306  1.00  0.00              
ATOM     81  N   HIS    33      26.484  14.058  -0.934  1.00  0.00              
ATOM     82  CA  HIS    33      25.858  15.252  -1.439  1.00  0.00              
ATOM     83  C   HIS    33      26.142  15.308  -2.939  1.00  0.00              
ATOM     84  O   HIS    33      27.157  14.794  -3.409  1.00  0.00              
ATOM     85  N   ALA    34      25.258  15.906  -3.689  1.00  0.00              
ATOM     86  CA  ALA    34      25.423  16.072  -5.113  1.00  0.00              
ATOM     87  C   ALA    34      24.996  17.491  -5.423  1.00  0.00              
ATOM     88  O   ALA    34      24.000  17.946  -4.847  1.00  0.00              
ATOM     89  N   TYR    35      25.685  18.239  -6.290  1.00  0.00              
ATOM     90  CA  TYR    35      25.248  19.576  -6.707  1.00  0.00              
ATOM     91  C   TYR    35      25.372  19.630  -8.243  1.00  0.00              
ATOM     92  O   TYR    35      26.350  19.122  -8.789  1.00  0.00              
ATOM     93  N   LYS    40      24.411  20.212  -8.942  1.00  0.00              
ATOM     94  CA  LYS    40      24.344  20.228 -10.380  1.00  0.00              
ATOM     95  C   LYS    40      23.844  21.566 -10.799  1.00  0.00              
ATOM     96  O   LYS    40      22.873  22.079 -10.218  1.00  0.00              
ATOM     97  N   TYR    41      24.524  22.164 -11.771  1.00  0.00              
ATOM     98  CA  TYR    41      23.986  23.371 -12.393  1.00  0.00              
ATOM     99  C   TYR    41      23.673  23.021 -13.816  1.00  0.00              
ATOM    100  O   TYR    41      24.492  22.415 -14.506  1.00  0.00              
ATOM    101  N   ARG    56      22.463  23.316 -14.248  1.00  0.00              
ATOM    102  CA  ARG    56      22.008  23.081 -15.605  1.00  0.00              
ATOM    103  C   ARG    56      21.615  24.451 -16.125  1.00  0.00              
ATOM    104  O   ARG    56      20.437  24.808 -16.294  1.00  0.00              
ATOM    105  N   ILE    57      22.647  25.278 -16.290  1.00  0.00              
ATOM    106  CA  ILE    57      22.410  26.626 -16.755  1.00  0.00              
ATOM    107  C   ILE    57      21.826  27.516 -15.654  1.00  0.00              
ATOM    108  O   ILE    57      22.443  27.673 -14.595  1.00  0.00              
ATOM    109  N   PHE    58      20.622  28.062 -15.868  1.00  0.00              
ATOM    110  CA  PHE    58      19.997  28.974 -14.912  1.00  0.00              
ATOM    111  C   PHE    58      19.466  28.279 -13.644  1.00  0.00              
ATOM    112  O   PHE    58      19.038  28.963 -12.705  1.00  0.00              
ATOM    113  N   GLY    59      19.459  26.931 -13.671  1.00  0.00              
ATOM    114  CA  GLY    59      18.981  26.016 -12.637  1.00  0.00              
ATOM    115  C   GLY    59      20.043  25.345 -11.776  1.00  0.00              
ATOM    116  O   GLY    59      20.993  24.747 -12.277  1.00  0.00              
ATOM    117  N   GLY    60      24.010   8.276  13.979  1.00  0.00              
ATOM    118  CA  GLY    60      23.346   8.131  15.258  1.00  0.00              
ATOM    119  C   GLY    60      23.630   9.320  16.130  1.00  0.00              
ATOM    120  O   GLY    60      24.685   9.948  16.047  1.00  0.00              
ATOM    121  N   ILE    61      13.110  17.886  18.803  1.00  0.00              
ATOM    122  CA  ILE    61      11.649  17.924  18.694  1.00  0.00              
ATOM    123  C   ILE    61      10.980  18.572  19.888  1.00  0.00              
ATOM    124  O   ILE    61       9.752  18.538  20.050  1.00  0.00              
ATOM    125  N   LEU    62      11.814  19.228  20.693  1.00  0.00              
ATOM    126  CA  LEU    62      11.384  19.967  21.846  1.00  0.00              
ATOM    127  C   LEU    62      10.723  19.063  22.894  1.00  0.00              
ATOM    128  O   LEU    62       9.703  19.441  23.497  1.00  0.00              
ATOM    129  N   ASP    63      11.296  17.870  23.090  1.00  0.00              
ATOM    130  CA  ASP    63      10.731  16.868  23.995  1.00  0.00              
ATOM    131  C   ASP    63      11.607  16.823  25.229  1.00  0.00              
ATOM    132  O   ASP    63      12.831  16.999  25.092  1.00  0.00              
ATOM    133  N   LEU    64      11.027  16.697  26.441  1.00  0.00              
ATOM    134  CA  LEU    64      11.850  16.596  27.670  1.00  0.00              
ATOM    135  C   LEU    64      12.771  15.379  27.608  1.00  0.00              
ATOM    136  O   LEU    64      12.413  14.364  26.980  1.00  0.00              
ATOM    137  N   PHE    65      17.517   8.561  32.450  1.00  0.00              
ATOM    138  CA  PHE    65      18.203   7.279  32.307  1.00  0.00              
ATOM    139  C   PHE    65      19.582   7.571  31.763  1.00  0.00              
ATOM    140  O   PHE    65      19.834   8.707  31.344  1.00  0.00              
ATOM    141  N   LYS    74      20.494   6.605  31.818  1.00  0.00              
ATOM    142  CA  LYS    74      21.821   6.720  31.214  1.00  0.00              
ATOM    143  C   LYS    74      21.666   6.857  29.682  1.00  0.00              
ATOM    144  O   LYS    74      20.749   6.287  29.040  1.00  0.00              
ATOM    145  N   VAL    75      15.785  23.147  -5.553  1.00  0.00              
ATOM    146  CA  VAL    75      15.864  23.541  -6.941  1.00  0.00              
ATOM    147  C   VAL    75      15.625  25.039  -6.976  1.00  0.00              
ATOM    148  O   VAL    75      14.656  25.511  -6.361  1.00  0.00              
ATOM    149  N   THR    76      16.465  25.819  -7.667  1.00  0.00              
ATOM    150  CA  THR    76      16.138  27.219  -7.907  1.00  0.00              
ATOM    151  C   THR    76      16.511  27.541  -9.348  1.00  0.00              
ATOM    152  O   THR    76      17.453  26.929  -9.883  1.00  0.00              
ATOM    153  N   ASP    77      16.749  30.861 -12.350  1.00  0.00              
ATOM    154  CA  ASP    77      16.670  32.279 -12.650  1.00  0.00              
ATOM    155  C   ASP    77      16.242  32.579 -14.081  1.00  0.00              
ATOM    156  O   ASP    77      16.833  32.070 -15.033  1.00  0.00              
ATOM    157  N   LEU    78      15.229  33.410 -14.241  1.00  0.00              
ATOM    158  CA  LEU    78      14.748  33.904 -15.530  1.00  0.00              
ATOM    159  C   LEU    78      14.716  35.442 -15.482  1.00  0.00              
ATOM    160  O   LEU    78      13.793  36.094 -14.953  1.00  0.00              
ATOM    161  N   THR    79      15.778  36.046 -16.006  1.00  0.00              
ATOM    162  CA  THR    79      15.879  37.483 -16.020  1.00  0.00              
ATOM    163  C   THR    79      16.299  38.008 -14.647  1.00  0.00              
ATOM    164  O   THR    79      17.353  37.655 -14.100  1.00  0.00              
ATOM    165  N   GLY    80      15.453  38.884 -14.114  1.00  0.00              
ATOM    166  CA  GLY    80      15.660  39.445 -12.789  1.00  0.00              
ATOM    167  C   GLY    80      15.035  38.554 -11.695  1.00  0.00              
ATOM    168  O   GLY    80      15.273  38.828 -10.520  1.00  0.00              
ATOM    169  N   GLU    81      14.261  37.509 -12.028  1.00  0.00              
ATOM    170  CA  GLU    81      13.517  36.669 -11.106  1.00  0.00              
ATOM    171  C   GLU    81      14.152  35.348 -10.811  1.00  0.00              
ATOM    172  O   GLU    81      14.412  34.578 -11.735  1.00  0.00              
ATOM    173  N   ASP    82      14.411  35.073  -9.541  1.00  0.00              
ATOM    174  CA  ASP    82      14.805  33.731  -9.149  1.00  0.00              
ATOM    175  C   ASP    82      13.619  33.172  -8.363  1.00  0.00              
ATOM    176  O   ASP    82      12.932  33.911  -7.632  1.00  0.00              
ATOM    177  N   VAL    83      13.334  31.895  -8.601  1.00  0.00              
ATOM    178  CA  VAL    83      12.262  31.143  -7.949  1.00  0.00              
ATOM    179  C   VAL    83      12.936  29.863  -7.486  1.00  0.00              
ATOM    180  O   VAL    83      13.827  29.342  -8.173  1.00  0.00              
ATOM    181  N   ALA    84      20.116  45.689  -4.523  1.00  0.00              
ATOM    182  CA  ALA    84      18.818  45.607  -3.889  1.00  0.00              
ATOM    183  C   ALA    84      17.946  44.587  -4.585  1.00  0.00              
ATOM    184  O   ALA    84      18.033  44.409  -5.804  1.00  0.00              
ATOM    185  N   ALA    85       4.605  19.063  11.251  1.00  0.00              
ATOM    186  CA  ALA    85       4.281  18.705  12.615  1.00  0.00              
ATOM    187  C   ALA    85       2.867  19.226  12.892  1.00  0.00              
ATOM    188  O   ALA    85       2.358  20.097  12.160  1.00  0.00              
ATOM    189  N   PHE    86       2.182  18.643  13.909  1.00  0.00              
ATOM    190  CA  PHE    86       0.802  18.970  14.284  1.00  0.00              
ATOM    191  C   PHE    86       0.400  20.437  14.494  1.00  0.00              
ATOM    192  O   PHE    86      -0.579  20.917  13.911  1.00  0.00              
END
