
#######################################################
#                                                     #
#                        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   39 (  191),  selected   39 , name T0306TS239_5_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_5_1.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    M       1      H      17           #
LGA    K       2      G      18           -
LGA    L       3      L      19           -
LGA    A       4      -       -           -
LGA    V       5      A      20          4.723
LGA    V       6      H      21          2.772
LGA    T       7      -       -           -
LGA    G       8      D      22          3.436
LGA    Q       9      K      23          1.327
LGA    I      10      L      24          1.833
LGA    V      11      L      25          1.912
LGA    C      12      M      26          2.845
LGA    T      13      V      27          1.528
LGA    V      14      E      28          1.746
LGA    R      15      M      29          2.326
LGA    H      16      I      30          2.216
LGA    H      17      D      31          1.828
LGA    -       -      P      32           -
LGA    G      18      Q      33          3.922
LGA    L      19      G      34          3.065
LGA    A      20      N      35           -
LGA    H      21      P      36           -
LGA    D      22      D      37           -
LGA    K      23      G      38           -
LGA    L      24      Q      39           -
LGA    L      25      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    M      26      G      50          4.656
LGA    V      27      T      51          2.837
LGA    E      28      G      52          3.395
LGA    -       -      E      53           -
LGA    M      29      W      54          3.218
LGA    I      30      V      55           #
LGA    D      31      -       -           -
LGA    P      32      L      56          2.975
LGA    Q      33      L      57          2.399
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    D      37      V      58          4.826
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    G      38      A      66          1.339
LGA    Q      39      H      67          2.576
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   95    5.0     23    2.95     0.00     15.540     0.754

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.036369 * X  +   0.121519 * Y  +   0.991923 * Z  + -84.101738
  Y_new =  -0.472295 * X  +   0.872643 * Y  +  -0.124223 * Z  + -16.487574
  Z_new =  -0.880690 * X  +  -0.472998 * Y  +   0.025656 * Z  + 185.188004 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.516609    1.624984  [ DEG:   -86.8953     93.1047 ]
  Theta =   1.077317    2.064276  [ DEG:    61.7257    118.2743 ]
  Phi   =  -1.647650    1.493943  [ DEG:   -94.4034     85.5966 ]
 
# 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: T0306TS239_5_1                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_5_1.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   95   5.0   23   2.95    0.00  15.540
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0306
PARENT 1qk3_A
ATOM      1  N   MET     1      15.402  15.937  63.523  1.00  9.99
ATOM      2  CA  MET     1      15.734  16.306  62.152  1.00  9.99
ATOM      3  C   MET     1      17.159  15.867  61.820  1.00  9.99
ATOM      4  O   MET     1      17.920  16.654  61.259  1.00  9.99
ATOM      5  CB  MET     1      15.602  17.829  61.977  1.00  9.99
ATOM      6  N   LYS     2      17.518  14.635  62.179  1.00  9.99
ATOM      7  CA  LYS     2      18.843  14.069  62.014  1.00  9.99
ATOM      8  C   LYS     2      19.324  13.857  60.586  1.00  9.99
ATOM      9  O   LYS     2      20.500  13.518  60.385  1.00  9.99
ATOM     10  CB  LYS     2      18.946  12.737  62.777  1.00  9.99
ATOM     11  N   LEU     3      18.444  13.967  59.589  1.00  9.99
ATOM     12  CA  LEU     3      18.867  13.826  58.204  1.00  9.99
ATOM     13  C   LEU     3      18.944  15.182  57.501  1.00  9.99
ATOM     14  O   LEU     3      19.504  15.245  56.398  1.00  9.99
ATOM     15  CB  LEU     3      17.934  12.884  57.440  1.00  9.99
ATOM     16  N   ALA     4      18.402  16.237  58.097  1.00  9.99
ATOM     17  CA  ALA     4      18.349  17.535  57.439  1.00  9.99
ATOM     18  C   ALA     4      19.164  18.649  58.041  1.00  9.99
ATOM     19  O   ALA     4      18.988  19.816  57.660  1.00  9.99
ATOM     20  CB  ALA     4      16.864  17.961  57.355  1.00  9.99
ATOM     21  N   VAL     5      20.022  18.400  59.034  1.00  9.99
ATOM     22  CA  VAL     5      20.864  19.454  59.622  1.00  9.99
ATOM     23  C   VAL     5      22.299  18.931  59.779  1.00  9.99
ATOM     24  O   VAL     5      22.449  17.751  60.147  1.00  9.99
ATOM     25  CB  VAL     5      20.313  19.937  60.969  1.00  9.99
ATOM     26  N   VAL     6      23.322  19.697  59.477  1.00  9.99
ATOM     27  CA  VAL     6      24.718  19.283  59.616  1.00  9.99
ATOM     28  C   VAL     6      25.205  19.198  61.043  1.00  9.99
ATOM     29  O   VAL     6      24.988  20.088  61.866  1.00  9.99
ATOM     30  CB  VAL     6      25.460  20.363  58.826  1.00  9.99
ATOM     31  N   THR     7      25.803  18.065  61.471  1.00  9.99
ATOM     32  CA  THR     7      26.219  17.907  62.861  1.00  9.99
ATOM     33  C   THR     7      27.324  18.905  63.207  1.00  9.99
ATOM     34  O   THR     7      28.082  19.334  62.327  1.00  9.99
ATOM     35  CB  THR     7      26.687  16.467  62.968  1.00  9.99
ATOM     36  N   GLY     8      27.458  19.297  64.470  1.00  9.99
ATOM     37  CA  GLY     8      28.450  20.278  64.896  1.00  9.99
ATOM     38  C   GLY     8      29.883  19.802  64.714  1.00  9.99
ATOM     39  O   GLY     8      30.146  18.586  64.614  1.00  9.99
ATOM     40  N   GLN     9      30.803  20.769  64.660  1.00  9.99
ATOM     41  CA  GLN     9      32.228  20.485  64.536  1.00  9.99
ATOM     42  C   GLN     9      32.954  20.930  65.815  1.00  9.99
ATOM     43  O   GLN     9      32.632  21.942  66.459  1.00  9.99
ATOM     44  CB  GLN     9      32.842  21.346  63.386  1.00  9.99
ATOM     45  N   ILE    10      33.892  20.102  66.287  1.00  9.99
ATOM     46  CA  ILE    10      34.704  20.395  67.451  1.00  9.99
ATOM     47  C   ILE    10      36.138  20.821  67.037  1.00  9.99
ATOM     48  O   ILE    10      36.719  20.142  66.162  1.00  9.99
ATOM     49  CB  ILE    10      34.900  19.184  68.397  1.00  9.99
ATOM     50  N   VAL    11      36.587  21.895  67.647  1.00  9.99
ATOM     51  CA  VAL    11      37.976  22.348  67.397  1.00  9.99
ATOM     52  C   VAL    11      38.743  22.567  68.695  1.00  9.99
ATOM     53  O   VAL    11      38.185  22.874  69.757  1.00  9.99
ATOM     54  CB  VAL    11      37.927  23.684  66.642  1.00  9.99
ATOM     55  N   CYS    12      40.080  22.348  68.617  1.00  9.99
ATOM     56  CA  CYS    12      40.958  22.447  69.789  1.00  9.99
ATOM     57  C   CYS    12      41.970  23.578  69.585  1.00  9.99
ATOM     58  O   CYS    12      42.560  23.547  68.510  1.00  9.99
ATOM     59  CB  CYS    12      41.646  21.070  70.014  1.00  9.99
ATOM     60  N   THR    13      41.945  24.587  70.421  1.00  9.99
ATOM     61  CA  THR    13      42.746  25.803  70.118  1.00  9.99
ATOM     62  C   THR    13      43.532  26.303  71.306  1.00  9.99
ATOM     63  O   THR    13      43.102  26.166  72.474  1.00  9.99
ATOM     64  CB  THR    13      41.737  26.905  69.685  1.00  9.99
ATOM     65  N   VAL    14      44.734  26.851  71.029  1.00  9.99
ATOM     66  CA  VAL    14      45.534  27.491  72.066  1.00  9.99
ATOM     67  C   VAL    14      45.118  28.975  72.183  1.00  9.99
ATOM     68  O   VAL    14      44.733  29.594  71.223  1.00  9.99
ATOM     69  CB  VAL    14      47.027  27.485  71.744  1.00  9.99
ATOM     70  N   ARG    15      45.292  29.571  73.368  1.00  9.99
ATOM     71  CA  ARG    15      44.947  30.992  73.545  1.00  9.99
ATOM     72  C   ARG    15      45.776  31.958  72.744  1.00  9.99
ATOM     73  O   ARG    15      45.369  33.023  72.257  1.00  9.99
ATOM     74  CB  ARG    15      45.105  31.306  75.046  1.00  9.99
ATOM     75  N   HIS    16      47.087  31.676  72.678  1.00  9.99
ATOM     76  CA  HIS    16      48.011  32.571  72.007  1.00  9.99
ATOM     77  C   HIS    16      48.573  31.940  70.743  1.00  9.99
ATOM     78  O   HIS    16      48.454  30.728  70.565  1.00  9.99
ATOM     79  CB  HIS    16      49.124  33.014  72.974  1.00  9.99
ATOM     80  N   HIS    17      49.201  32.778  69.930  1.00  9.99
ATOM     81  CA  HIS    17      49.772  32.295  68.683  1.00  9.99
ATOM     82  C   HIS    17      51.178  31.742  68.891  1.00  9.99
ATOM     83  O   HIS    17      52.188  32.437  68.805  1.00  9.99
ATOM     84  CB  HIS    17      49.735  33.333  67.579  1.00  9.99
ATOM     85  N   GLY    18      51.268  30.448  69.145  1.00  9.99
ATOM     86  CA  GLY    18      52.551  29.760  69.297  1.00  9.99
ATOM     87  C   GLY    18      52.913  29.055  67.989  1.00  9.99
ATOM     88  O   GLY    18      52.023  28.971  67.137  1.00  9.99
ATOM     89  N   LEU    19      54.127  28.514  67.902  1.00  9.99
ATOM     90  CA  LEU    19      54.445  27.744  66.672  1.00  9.99
ATOM     91  C   LEU    19      53.629  26.451  66.655  1.00  9.99
ATOM     92  O   LEU    19      53.581  25.858  67.731  1.00  9.99
ATOM     93  CB  LEU    19      55.945  27.524  66.598  1.00  9.99
ATOM     94  N   ALA    20      52.968  26.100  65.549  1.00  9.99
ATOM     95  CA  ALA    20      52.164  24.868  65.519  1.00  9.99
ATOM     96  C   ALA    20      53.032  23.671  65.926  1.00  9.99
ATOM     97  O   ALA    20      54.243  23.590  65.683  1.00  9.99
ATOM     98  CB  ALA    20      51.472  24.684  64.162  1.00  9.99
ATOM     99  N   HIS    21      52.460  22.750  66.693  1.00  9.99
ATOM    100  CA  HIS    21      53.065  21.496  67.112  1.00  9.99
ATOM    101  C   HIS    21      52.330  20.306  66.501  1.00  9.99
ATOM    102  O   HIS    21      52.317  19.198  67.061  1.00  9.99
ATOM    103  CB  HIS    21      53.087  21.346  68.652  1.00  9.99
ATOM    104  N   ASP    22      51.692  20.505  65.349  1.00  9.99
ATOM    105  CA  ASP    22      50.914  19.431  64.734  1.00  9.99
ATOM    106  C   ASP    22      51.784  18.417  63.991  1.00  9.99
ATOM    107  O   ASP    22      52.911  18.727  63.620  1.00  9.99
ATOM    108  CB  ASP    22      49.886  20.056  63.781  1.00  9.99
ATOM    109  N   LYS    23      51.230  17.243  63.754  1.00  9.99
ATOM    110  CA  LYS    23      51.891  16.191  62.974  1.00  9.99
ATOM    111  C   LYS    23      50.849  15.182  62.518  1.00  9.99
ATOM    112  O   LYS    23      49.747  15.093  63.129  1.00  9.99
ATOM    113  CB  LYS    23      53.075  15.577  63.696  1.00  9.99
ATOM    114  N   LEU    24      51.153  14.443  61.464  1.00  9.99
ATOM    115  CA  LEU    24      50.233  13.455  60.885  1.00  9.99
ATOM    116  C   LEU    24      49.771  12.398  61.913  1.00  9.99
ATOM    117  O   LEU    24      50.641  11.874  62.597  1.00  9.99
ATOM    118  CB  LEU    24      50.910  12.679  59.727  1.00  9.99
ATOM    119  N   LEU    25      48.224  13.021  64.694  1.00  9.99
ATOM    120  CA  LEU    25      48.054  13.590  66.022  1.00  9.99
ATOM    121  C   LEU    25      46.913  14.611  66.035  1.00  9.99
ATOM    122  O   LEU    25      46.455  15.076  64.944  1.00  9.99
ATOM    123  CB  LEU    25      49.353  14.223  66.547  1.00  9.99
ATOM    124  N   MET    26      46.447  14.978  67.224  1.00  9.99
ATOM    125  CA  MET    26      45.313  15.927  67.317  1.00  9.99
ATOM    126  C   MET    26      45.600  17.264  66.639  1.00  9.99
ATOM    127  O   MET    26      46.727  17.785  66.821  1.00  9.99
ATOM    128  CB  MET    26      44.978  16.208  68.804  1.00  9.99
ATOM    129  N   VAL    27      44.642  17.751  65.845  1.00  9.99
ATOM    130  CA  VAL    27      44.858  19.092  65.262  1.00  9.99
ATOM    131  C   VAL    27      44.602  20.133  66.349  1.00  9.99
ATOM    132  O   VAL    27      43.494  20.277  66.889  1.00  9.99
ATOM    133  CB  VAL    27      43.906  19.346  64.078  1.00  9.99
ATOM    134  N   GLU    28      45.653  20.906  66.664  1.00  9.99
ATOM    135  CA  GLU    28      45.549  21.997  67.635  1.00  9.99
ATOM    136  C   GLU    28      45.861  23.317  66.909  1.00  9.99
ATOM    137  O   GLU    28      46.987  23.474  66.452  1.00  9.99
ATOM    138  CB  GLU    28      46.500  21.859  68.826  1.00  9.99
ATOM    139  N   MET    29      44.912  24.240  66.886  1.00  9.99
ATOM    140  CA  MET    29      45.175  25.525  66.205  1.00  9.99
ATOM    141  C   MET    29      45.802  26.516  67.158  1.00  9.99
ATOM    142  O   MET    29      45.472  26.672  68.361  1.00  9.99
ATOM    143  CB  MET    29      43.853  26.081  65.634  1.00  9.99
ATOM    144  N   ILE    30      46.773  27.297  66.636  1.00  9.99
ATOM    145  CA  ILE    30      47.390  28.350  67.444  1.00  9.99
ATOM    146  C   ILE    30      47.582  29.656  66.646  1.00  9.99
ATOM    147  O   ILE    30      46.826  30.616  66.789  1.00  9.99
ATOM    148  CB  ILE    30      48.688  27.899  68.090  1.00  9.99
ATOM    149  N   ASP    31      48.524  29.617  65.725  1.00  9.99
ATOM    150  CA  ASP    31      48.892  30.732  64.879  1.00  9.99
ATOM    151  C   ASP    31      47.860  31.044  63.803  1.00  9.99
ATOM    152  O   ASP    31      47.609  32.232  63.563  1.00  9.99
ATOM    153  CB  ASP    31      50.258  30.476  64.211  1.00  9.99
ATOM    154  N   PRO    32      47.188  30.048  63.250  1.00  9.99
ATOM    155  CA  PRO    32      46.227  30.311  62.173  1.00  9.99
ATOM    156  C   PRO    32      44.789  29.972  62.522  1.00  9.99
ATOM    157  O   PRO    32      44.441  28.806  62.742  1.00  9.99
ATOM    158  CB  PRO    32      46.709  29.539  60.933  1.00  9.99
ATOM    159  N   GLN    33      43.949  30.992  62.613  1.00  9.99
ATOM    160  CA  GLN    33      42.522  30.820  62.937  1.00  9.99
ATOM    161  C   GLN    33      41.632  31.034  61.731  1.00  9.99
ATOM    162  O   GLN    33      40.390  31.122  61.783  1.00  9.99
ATOM    163  CB  GLN    33      42.208  31.827  64.052  1.00  9.99
ATOM    164  N   GLY    34      42.206  30.993  60.507  1.00  9.99
ATOM    165  CA  GLY    34      41.469  31.238  59.285  1.00  9.99
ATOM    166  C   GLY    34      40.336  30.293  58.932  1.00  9.99
ATOM    167  O   GLY    34      39.394  30.738  58.267  1.00  9.99
ATOM    168  N   ASN    35      40.320  29.043  59.424  1.00  9.99
ATOM    169  CA  ASN    35      39.179  28.157  59.168  1.00  9.99
ATOM    170  C   ASN    35      37.861  28.721  59.713  1.00  9.99
ATOM    171  O   ASN    35      36.772  28.282  59.283  1.00  9.99
ATOM    172  CB  ASN    35      39.449  26.791  59.856  1.00  9.99
ATOM    173  N   PRO    36      37.885  29.686  60.657  1.00  9.99
ATOM    174  CA  PRO    36      36.668  30.233  61.210  1.00  9.99
ATOM    175  C   PRO    36      36.040  31.381  60.407  1.00  9.99
ATOM    176  O   PRO    36      34.985  31.884  60.770  1.00  9.99
ATOM    177  CB  PRO    36      36.870  30.674  62.680  1.00  9.99
ATOM    178  N   ASP    37      36.652  31.777  59.292  1.00  9.99
ATOM    179  CA  ASP    37      36.055  32.866  58.467  1.00  9.99
ATOM    180  C   ASP    37      34.649  32.499  58.038  1.00  9.99
ATOM    181  O   ASP    37      34.447  31.373  57.573  1.00  9.99
ATOM    182  CB  ASP    37      36.963  33.153  57.270  1.00  9.99
ATOM    183  N   GLY    38      33.690  33.401  58.217  1.00  9.99
ATOM    184  CA  GLY    38      32.292  33.242  57.923  1.00  9.99
ATOM    185  C   GLY    38      31.581  32.069  58.631  1.00  9.99
ATOM    186  O   GLY    38      30.577  31.570  58.096  1.00  9.99
ATOM    187  N   GLN    39      32.057  31.662  59.801  1.00  9.99
ATOM    188  CA  GLN    39      31.416  30.567  60.542  1.00  9.99
ATOM    189  C   GLN    39      30.725  31.074  61.797  1.00  9.99
ATOM    190  O   GLN    39      31.167  32.062  62.360  1.00  9.99
ATOM    191  CB  GLN    39      32.491  29.559  61.033  1.00  9.99
TER
END
