
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0304AL333_4
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304AL333_4.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D      16           -
LGA    S       2      R      17           -
LGA    D       3      P      18           -
LGA    -       -      W      19           -
LGA    T       4      W      20           #
LGA    L       5      G      21          5.533
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    P       6      V      26          1.524
LGA    G       7      T      27          1.974
LGA    -       -      P      28           -
LGA    T       8      C      29          1.216
LGA    T       9      F      30          2.864
LGA    L      10      G      31          1.355
LGA    P      11      A      32          1.810
LGA    D      12      R      33          1.490
LGA    D      13      L      34          1.901
LGA    N      14      V      35          4.236
LGA    H      15      Q      36          4.206
LGA    D      16      -       -           -
LGA    R      17      -       -           -
LGA    P      18      E      37           #
LGA    W      19      G      38           #
LGA    W      20      N      39           #
LGA    G      21      R      40          5.115
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    L      22      L      77          1.778
LGA    P      23      T      78          3.500
LGA    C      24      S      79          2.587
LGA    T      25      G      80          3.210
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    V      26      N      83          2.216
LGA    T      27      P      84          4.183
LGA    P      28      R      85           -
LGA    C      29      H      86           -
LGA    F      30      Q      87           -
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      -       -           -
LGA    V      35      -       -           -
LGA    Q      36      H      88           #
LGA    E      37      T      89          1.254
LGA    G      38      -       -           -
LGA    N      39      V      90          3.529
LGA    R      40      T      91          1.632
LGA    L      41      L      92           #
LGA    H      42      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    Y      43      T      98          4.338
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    L      44      Y     115           #
LGA    A      45      P     116           -
LGA    D      46      -       -           -
LGA    R      47      T     117          2.156
LGA    A      48      P     118          2.671
LGA    G      49      E     119          3.324
LGA    I      50      M     120           #
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50  107    5.0     25    3.05     4.00     14.864     0.794

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.694496 * X  +  -0.000994 * Y  +   0.719496 * Z  +   1.128559
  Y_new =  -0.207136 * X  +   0.957386 * Y  +   0.201261 * Z  +  41.007927
  Z_new =  -0.689036 * X  +  -0.288808 * Y  +   0.664695 * Z  +  83.869904 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.409887    2.731705  [ DEG:   -23.4848    156.5152 ]
  Theta =   0.760158    2.381435  [ DEG:    43.5538    136.4462 ]
  Phi   =  -0.289854    2.851739  [ DEG:   -16.6074    163.3926 ]
 
# 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: T0304AL333_4                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL333_4.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50  107   5.0   25   3.05    4.00  14.864
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL333_4
REMARK Aligment from pdb entry: 1glq_A
ATOM      1  N   MET     1      47.689  21.895  32.932  1.00  0.00              
ATOM      2  CA  MET     1      47.094  21.282  34.101  1.00  0.00              
ATOM      3  C   MET     1      48.092  20.202  34.519  1.00  0.00              
ATOM      4  O   MET     1      49.081  20.034  33.777  1.00  0.00              
ATOM      5  N   SER     2      47.979  19.480  35.633  1.00  0.00              
ATOM      6  CA  SER     2      46.963  19.676  36.680  1.00  0.00              
ATOM      7  C   SER     2      47.081  20.993  37.475  1.00  0.00              
ATOM      8  O   SER     2      48.161  21.596  37.454  1.00  0.00              
ATOM      9  N   ASP     3      46.014  21.508  38.100  1.00  0.00              
ATOM     10  CA  ASP     3      46.025  22.758  38.833  1.00  0.00              
ATOM     11  C   ASP     3      45.899  22.464  40.307  1.00  0.00              
ATOM     12  O   ASP     3      45.124  21.573  40.692  1.00  0.00              
ATOM     13  N   THR     4      46.675  23.193  41.112  1.00  0.00              
ATOM     14  CA  THR     4      46.614  23.118  42.564  1.00  0.00              
ATOM     15  C   THR     4      46.606  24.553  43.099  1.00  0.00              
ATOM     16  O   THR     4      47.440  25.365  42.689  1.00  0.00              
ATOM     17  N   LEU     5      45.692  24.914  44.006  1.00  0.00              
ATOM     18  CA  LEU     5      45.706  26.214  44.649  1.00  0.00              
ATOM     19  C   LEU     5      46.136  25.968  46.091  1.00  0.00              
ATOM     20  O   LEU     5      45.625  25.072  46.763  1.00  0.00              
ATOM     21  N   PRO     6      35.171  27.413  33.404  1.00  0.00              
ATOM     22  CA  PRO     6      35.783  26.854  32.218  1.00  0.00              
ATOM     23  C   PRO     6      35.831  25.342  32.253  1.00  0.00              
ATOM     24  O   PRO     6      36.597  24.730  31.504  1.00  0.00              
ATOM     25  N   GLY     7      35.049  24.722  33.138  1.00  0.00              
ATOM     26  CA  GLY     7      34.961  23.274  33.240  1.00  0.00              
ATOM     27  C   GLY     7      36.257  22.607  33.693  1.00  0.00              
ATOM     28  O   GLY     7      36.524  21.450  33.354  1.00  0.00              
ATOM     29  N   THR     8      37.108  23.300  34.447  1.00  0.00              
ATOM     30  CA  THR     8      38.380  22.738  34.859  1.00  0.00              
ATOM     31  C   THR     8      38.224  22.209  36.270  1.00  0.00              
ATOM     32  O   THR     8      37.369  22.702  37.022  1.00  0.00              
ATOM     33  N   THR     9      38.990  21.192  36.649  1.00  0.00              
ATOM     34  CA  THR     9      39.030  20.837  38.051  1.00  0.00              
ATOM     35  C   THR     9      40.407  21.239  38.578  1.00  0.00              
ATOM     36  O   THR     9      41.330  21.449  37.777  1.00  0.00              
ATOM     37  N   LEU    10      40.563  21.365  39.905  1.00  0.00              
ATOM     38  CA  LEU    10      41.810  21.716  40.563  1.00  0.00              
ATOM     39  C   LEU    10      41.871  21.049  41.935  1.00  0.00              
ATOM     40  O   LEU    10      40.843  20.622  42.463  1.00  0.00              
ATOM     41  N   PRO    11      43.048  20.931  42.521  1.00  0.00              
ATOM     42  CA  PRO    11      43.248  20.386  43.843  1.00  0.00              
ATOM     43  C   PRO    11      43.363  21.610  44.761  1.00  0.00              
ATOM     44  O   PRO    11      43.931  22.643  44.390  1.00  0.00              
ATOM     45  N   ASP    12      42.871  21.548  45.991  1.00  0.00              
ATOM     46  CA  ASP    12      42.879  22.688  46.887  1.00  0.00              
ATOM     47  C   ASP    12      43.757  22.225  48.025  1.00  0.00              
ATOM     48  O   ASP    12      43.516  21.142  48.576  1.00  0.00              
ATOM     49  N   ASP    13      44.802  22.975  48.339  1.00  0.00              
ATOM     50  CA  ASP    13      45.744  22.608  49.371  1.00  0.00              
ATOM     51  C   ASP    13      45.543  23.710  50.415  1.00  0.00              
ATOM     52  O   ASP    13      45.950  24.857  50.254  1.00  0.00              
ATOM     53  N   ASN    14      44.825  23.402  51.495  1.00  0.00              
ATOM     54  CA  ASN    14      44.441  24.421  52.467  1.00  0.00              
ATOM     55  C   ASN    14      45.500  24.540  53.544  1.00  0.00              
ATOM     56  O   ASN    14      45.939  23.539  54.116  1.00  0.00              
ATOM     57  N   HIS    15      45.926  25.755  53.852  1.00  0.00              
ATOM     58  CA  HIS    15      46.954  25.969  54.859  1.00  0.00              
ATOM     59  C   HIS    15      46.270  26.648  56.040  1.00  0.00              
ATOM     60  O   HIS    15      45.733  27.755  55.906  1.00  0.00              
ATOM     61  N   ASP    16      46.213  25.991  57.199  1.00  0.00              
ATOM     62  CA  ASP    16      45.611  26.619  58.364  1.00  0.00              
ATOM     63  C   ASP    16      46.613  27.631  58.931  1.00  0.00              
ATOM     64  O   ASP    16      47.828  27.546  58.695  1.00  0.00              
ATOM     65  N   ARG    17      46.163  28.566  59.763  1.00  0.00              
ATOM     66  CA  ARG    17      47.040  29.564  60.378  1.00  0.00              
ATOM     67  C   ARG    17      48.051  28.879  61.303  1.00  0.00              
ATOM     68  O   ARG    17      49.188  29.303  61.387  1.00  0.00              
ATOM     69  N   PRO    18      47.702  27.772  61.959  1.00  0.00              
ATOM     70  CA  PRO    18      48.610  27.033  62.824  1.00  0.00              
ATOM     71  C   PRO    18      49.781  26.536  62.009  1.00  0.00              
ATOM     72  O   PRO    18      50.935  26.779  62.361  1.00  0.00              
ATOM     73  N   TRP    19      49.519  25.854  60.873  1.00  0.00              
ATOM     74  CA  TRP    19      50.573  25.432  59.967  1.00  0.00              
ATOM     75  C   TRP    19      51.369  26.637  59.496  1.00  0.00              
ATOM     76  O   TRP    19      52.594  26.580  59.627  1.00  0.00              
ATOM     77  N   TRP    20      50.737  27.733  59.025  1.00  0.00              
ATOM     78  CA  TRP    20      51.471  28.878  58.529  1.00  0.00              
ATOM     79  C   TRP    20      52.412  29.395  59.599  1.00  0.00              
ATOM     80  O   TRP    20      53.602  29.626  59.315  1.00  0.00              
ATOM     81  N   GLY    21      59.646  29.234  51.728  1.00  0.00              
ATOM     82  CA  GLY    21      59.776  28.665  50.398  1.00  0.00              
ATOM     83  C   GLY    21      58.929  29.436  49.386  1.00  0.00              
ATOM     84  O   GLY    21      59.023  29.207  48.169  1.00  0.00              
ATOM     85  N   LEU    22      58.040  30.310  49.861  1.00  0.00              
ATOM     86  CA  LEU    22      57.201  31.132  49.010  1.00  0.00              
ATOM     87  C   LEU    22      58.043  32.279  48.494  1.00  0.00              
ATOM     88  O   LEU    22      58.712  32.931  49.299  1.00  0.00              
ATOM     89  N   PRO    23      58.022  32.564  47.185  1.00  0.00              
ATOM     90  CA  PRO    23      58.891  33.593  46.595  1.00  0.00              
ATOM     91  C   PRO    23      58.865  34.930  47.329  1.00  0.00              
ATOM     92  O   PRO    23      59.897  35.491  47.687  1.00  0.00              
ATOM     93  N   CYS    24      57.666  35.466  47.521  1.00  0.00              
ATOM     94  CA  CYS    24      57.528  36.724  48.238  1.00  0.00              
ATOM     95  C   CYS    24      57.069  36.501  49.698  1.00  0.00              
ATOM     96  O   CYS    24      56.475  37.420  50.283  1.00  0.00              
ATOM     97  N   THR    25      57.205  35.290  50.262  1.00  0.00              
ATOM     98  CA  THR    25      56.753  34.920  51.613  1.00  0.00              
ATOM     99  C   THR    25      55.240  34.929  51.804  1.00  0.00              
ATOM    100  O   THR    25      54.759  34.994  52.933  1.00  0.00              
ATOM    101  N   VAL    26      54.411  34.844  50.759  1.00  0.00              
ATOM    102  CA  VAL    26      52.963  34.960  50.923  1.00  0.00              
ATOM    103  C   VAL    26      52.264  33.973  50.034  1.00  0.00              
ATOM    104  O   VAL    26      52.905  33.398  49.142  1.00  0.00              
ATOM    105  N   THR    27      50.965  33.774  50.287  1.00  0.00              
ATOM    106  CA  THR    27      50.091  32.932  49.498  1.00  0.00              
ATOM    107  C   THR    27      49.074  33.823  48.769  1.00  0.00              
ATOM    108  O   THR    27      48.826  34.912  49.290  1.00  0.00              
ATOM    109  N   PRO    28      48.401  33.493  47.649  1.00  0.00              
ATOM    110  CA  PRO    28      48.389  32.141  47.043  1.00  0.00              
ATOM    111  C   PRO    28      49.631  31.601  46.338  1.00  0.00              
ATOM    112  O   PRO    28      50.496  32.349  45.884  1.00  0.00              
ATOM    113  N   CYS    29      49.748  30.285  46.322  1.00  0.00              
ATOM    114  CA  CYS    29      50.767  29.616  45.544  1.00  0.00              
ATOM    115  C   CYS    29      49.937  28.796  44.557  1.00  0.00              
ATOM    116  O   CYS    29      48.886  28.250  44.933  1.00  0.00              
ATOM    117  N   PHE    30      50.322  28.698  43.280  1.00  0.00              
ATOM    118  CA  PHE    30      49.525  27.991  42.283  1.00  0.00              
ATOM    119  C   PHE    30      50.442  27.073  41.475  1.00  0.00              
ATOM    120  O   PHE    30      51.545  27.491  41.114  1.00  0.00              
ATOM    121  N   GLY    31      53.988  21.822  35.705  1.00  0.00              
ATOM    122  CA  GLY    31      55.395  22.140  35.916  1.00  0.00              
ATOM    123  C   GLY    31      55.684  23.547  36.465  1.00  0.00              
ATOM    124  O   GLY    31      56.761  23.816  37.001  1.00  0.00              
ATOM    125  N   ALA    32      54.747  24.466  36.250  1.00  0.00              
ATOM    126  CA  ALA    32      54.898  25.870  36.597  1.00  0.00              
ATOM    127  C   ALA    32      54.299  26.226  37.965  1.00  0.00              
ATOM    128  O   ALA    32      53.110  26.015  38.227  1.00  0.00              
ATOM    129  N   ARG    33      55.130  26.804  38.820  1.00  0.00              
ATOM    130  CA  ARG    33      54.698  27.259  40.123  1.00  0.00              
ATOM    131  C   ARG    33      54.679  28.768  40.017  1.00  0.00              
ATOM    132  O   ARG    33      55.653  29.397  39.597  1.00  0.00              
ATOM    133  N   LEU    34      53.543  29.351  40.345  1.00  0.00              
ATOM    134  CA  LEU    34      53.374  30.785  40.296  1.00  0.00              
ATOM    135  C   LEU    34      52.967  31.308  41.662  1.00  0.00              
ATOM    136  O   LEU    34      52.421  30.568  42.504  1.00  0.00              
ATOM    137  N   VAL    35      53.341  32.563  41.894  1.00  0.00              
ATOM    138  CA  VAL    35      52.890  33.334  43.053  1.00  0.00              
ATOM    139  C   VAL    35      52.261  34.566  42.429  1.00  0.00              
ATOM    140  O   VAL    35      52.448  34.815  41.228  1.00  0.00              
ATOM    141  N   GLN    36      51.582  35.361  43.273  1.00  0.00              
ATOM    142  CA  GLN    36      50.874  36.598  42.939  1.00  0.00              
ATOM    143  C   GLN    36      49.525  36.326  42.280  1.00  0.00              
ATOM    144  O   GLN    36      49.449  35.952  41.092  1.00  0.00              
ATOM    145  N   GLU    37      48.401  36.572  43.000  1.00  0.00              
ATOM    146  CA  GLU    37      47.072  36.258  42.511  1.00  0.00              
ATOM    147  C   GLU    37      46.726  36.852  41.152  1.00  0.00              
ATOM    148  O   GLU    37      46.100  36.177  40.326  1.00  0.00              
ATOM    149  N   GLY    38      47.148  38.071  40.824  1.00  0.00              
ATOM    150  CA  GLY    38      46.794  38.607  39.513  1.00  0.00              
ATOM    151  C   GLY    38      47.673  38.038  38.412  1.00  0.00              
ATOM    152  O   GLY    38      47.222  37.964  37.278  1.00  0.00              
ATOM    153  N   ASN    39      48.903  37.607  38.733  1.00  0.00              
ATOM    154  CA  ASN    39      49.745  36.929  37.747  1.00  0.00              
ATOM    155  C   ASN    39      49.119  35.577  37.401  1.00  0.00              
ATOM    156  O   ASN    39      49.117  35.147  36.253  1.00  0.00              
ATOM    157  N   ARG    40      48.582  34.864  38.398  1.00  0.00              
ATOM    158  CA  ARG    40      47.876  33.605  38.198  1.00  0.00              
ATOM    159  C   ARG    40      46.606  33.844  37.380  1.00  0.00              
ATOM    160  O   ARG    40      46.327  33.073  36.444  1.00  0.00              
ATOM    161  N   LEU    41      45.815  34.889  37.662  1.00  0.00              
ATOM    162  CA  LEU    41      44.658  35.192  36.835  1.00  0.00              
ATOM    163  C   LEU    41      45.019  35.507  35.386  1.00  0.00              
ATOM    164  O   LEU    41      44.345  35.041  34.466  1.00  0.00              
ATOM    165  N   HIS    42      46.057  36.316  35.162  1.00  0.00              
ATOM    166  CA  HIS    42      46.496  36.637  33.806  1.00  0.00              
ATOM    167  C   HIS    42      47.030  35.375  33.126  1.00  0.00              
ATOM    168  O   HIS    42      46.731  35.161  31.961  1.00  0.00              
ATOM    169  N   TYR    43      47.729  34.482  33.818  1.00  0.00              
ATOM    170  CA  TYR    43      48.199  33.232  33.251  1.00  0.00              
ATOM    171  C   TYR    43      47.013  32.392  32.752  1.00  0.00              
ATOM    172  O   TYR    43      47.025  31.852  31.639  1.00  0.00              
ATOM    173  N   LEU    44      45.972  32.244  33.572  1.00  0.00              
ATOM    174  CA  LEU    44      44.802  31.465  33.185  1.00  0.00              
ATOM    175  C   LEU    44      44.054  32.140  32.040  1.00  0.00              
ATOM    176  O   LEU    44      43.551  31.467  31.135  1.00  0.00              
ATOM    177  N   ALA    45      44.033  33.470  31.992  1.00  0.00              
ATOM    178  CA  ALA    45      43.391  34.195  30.901  1.00  0.00              
ATOM    179  C   ALA    45      44.136  33.904  29.612  1.00  0.00              
ATOM    180  O   ALA    45      43.535  33.610  28.585  1.00  0.00              
ATOM    181  N   ASP    46      45.456  33.905  29.651  1.00  0.00              
ATOM    182  CA  ASP    46      46.305  33.664  28.486  1.00  0.00              
ATOM    183  C   ASP    46      46.164  32.215  28.035  1.00  0.00              
ATOM    184  O   ASP    46      45.781  31.945  26.895  1.00  0.00              
ATOM    185  N   ARG    47      46.313  31.257  28.944  1.00  0.00              
ATOM    186  CA  ARG    47      46.294  29.887  28.524  1.00  0.00              
ATOM    187  C   ARG    47      44.930  29.351  28.198  1.00  0.00              
ATOM    188  O   ARG    47      44.857  28.387  27.440  1.00  0.00              
ATOM    189  N   ALA    48      43.827  29.899  28.713  1.00  0.00              
ATOM    190  CA  ALA    48      42.526  29.348  28.419  1.00  0.00              
ATOM    191  C   ALA    48      41.771  30.212  27.424  1.00  0.00              
ATOM    192  O   ALA    48      40.593  29.975  27.153  1.00  0.00              
ATOM    193  N   GLY    49      42.415  31.217  26.833  1.00  0.00              
ATOM    194  CA  GLY    49      41.785  32.031  25.820  1.00  0.00              
ATOM    195  C   GLY    49      40.770  33.033  26.349  1.00  0.00              
ATOM    196  O   GLY    49      39.763  33.342  25.710  1.00  0.00              
ATOM    197  N   ILE    50      41.064  33.636  27.488  1.00  0.00              
ATOM    198  CA  ILE    50      40.202  34.604  28.146  1.00  0.00              
ATOM    199  C   ILE    50      40.880  35.942  28.270  1.00  0.00              
ATOM    200  O   ILE    50      40.725  36.600  29.309  1.00  0.00              
END
