
#######################################################
#                                                     #
#                        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   22 (  163),  selected   22 , name T0382TS009_2_4
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS009_2_4.T0382.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    F     102      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    P     103      M       9           #
LGA    Q     104      T      10          3.743
LGA    A     105      T      11          2.892
LGA    G     106      Q      12          4.246
LGA    D     107      D      13          2.102
LGA    A     108      L      14          1.123
LGA    G     109      V      15          4.061
LGA    M     110      A      16          1.012
LGA    -       -      L      17           -
LGA    C     111      F      18          3.403
LGA    L     112      A      19          3.435
LGA    D     113      K      20          1.443
LGA    -       -      V      21           -
LGA    L     114      T      22          3.199
LGA    L     115      V      23          4.103
LGA    D     116      E      24          1.624
LGA    D     117      Q      25          3.704
LGA    G     118      D      26          3.108
LGA    -       -      D      27           -
LGA    T     119      A      28          1.641
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    F     120      Q      33          2.408
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    K     121      R      36          1.016
LGA    P     122      F      37          3.558
LGA    K     123      N      38          0.903
LGA    -       -      R      39           -
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  121    5.0     20    2.87     5.00     10.370     0.673

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.650027 * X  +   0.477428 * Y  +   0.591208 * Z  +  57.130959
  Y_new =  -0.144072 * X  +  -0.841313 * Y  +   0.520994 * Z  +  56.022377
  Z_new =   0.746129 * X  +   0.253484 * Y  +   0.615660 * Z  + -45.501854 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.390575   -2.751018  [ DEG:    22.3783   -157.6217 ]
  Theta =  -0.842229   -2.299364  [ DEG:   -48.2561   -131.7439 ]
  Phi   =  -2.923479    0.218114  [ DEG:  -167.5030     12.4970 ]
 
# 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: T0382TS009_2_4                                
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_4.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  121   5.0   20   2.87    5.00  10.370
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_4
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    795  N   PHE   102     -18.219  39.001 -17.548  1.00  0.00             
ATOM    796  CA  PHE   102     -17.930  37.670 -17.026  1.00  0.00             
ATOM    797  C   PHE   102     -18.057  37.634 -15.508  1.00  0.00             
ATOM    798  O   PHE   102     -17.068  37.754 -14.784  1.00  0.00             
ATOM    799  CB  PHE   102     -18.862  36.633 -17.658  1.00  0.00             
ATOM    800  CG  PHE   102     -18.143  35.555 -18.417  1.00  0.00             
ATOM    801  CD1 PHE   102     -16.762  35.551 -18.502  1.00  0.00             
ATOM    802  CD2 PHE   102     -18.849  34.543 -19.045  1.00  0.00             
ATOM    803  CE1 PHE   102     -16.101  34.558 -19.201  1.00  0.00             
ATOM    804  CE2 PHE   102     -18.188  33.551 -19.743  1.00  0.00             
ATOM    805  CZ  PHE   102     -16.820  33.555 -19.823  1.00  0.00             
ATOM    806  N   PRO   103     -19.289  37.464 -15.005  1.00  0.00             
ATOM    807  CA  PRO   103     -19.554  37.410 -13.565  1.00  0.00             
ATOM    808  C   PRO   103     -18.668  38.379 -12.789  1.00  0.00             
ATOM    809  O   PRO   103     -18.339  38.140 -11.627  1.00  0.00             
ATOM    810  CB  PRO   103     -21.018  37.844 -13.467  1.00  0.00             
ATOM    811  CG  PRO   103     -21.148  38.949 -14.462  1.00  0.00             
ATOM    812  CD  PRO   103     -20.515  37.313 -15.808  1.00  0.00             
ATOM    813  N   GLN   104     -18.285  39.473 -13.440  1.00  0.00             
ATOM    814  CA  GLN   104     -17.436  40.479 -12.812  1.00  0.00             
ATOM    815  C   GLN   104     -16.406  39.835 -11.890  1.00  0.00             
ATOM    816  O   GLN   104     -16.439  40.030 -10.675  1.00  0.00             
ATOM    817  CB  GLN   104     -16.734  41.326 -13.875  1.00  0.00             
ATOM    818  CG  GLN   104     -17.058  42.809 -13.801  1.00  0.00             
ATOM    819  CD  GLN   104     -16.345  43.615 -14.869  1.00  0.00             
ATOM    820  OE1 GLN   104     -16.499  44.834 -14.946  1.00  0.00             
ATOM    821  NE2 GLN   104     -15.559  42.936 -15.696  1.00  0.00             
ATOM    822  N   ALA   105     -15.493  39.068 -12.476  1.00  0.00             
ATOM    823  CA  ALA   105     -14.452  38.395 -11.708  1.00  0.00             
ATOM    824  C   ALA   105     -15.017  37.207 -10.935  1.00  0.00             
ATOM    825  O   ALA   105     -14.636  36.961  -9.792  1.00  0.00             
ATOM    826  CB  ALA   105     -13.330  37.936 -12.627  1.00  0.00             
ATOM    827  N   GLY   106     -15.928  36.475 -11.569  1.00  0.00             
ATOM    828  CA  GLY   106     -16.529  35.324 -10.922  1.00  0.00             
ATOM    829  C   GLY   106     -16.854  35.581  -9.465  1.00  0.00             
ATOM    830  O   GLY   106     -16.213  35.032  -8.569  1.00  0.00             
ATOM    831  N   ASP   107     -17.857  36.418  -9.222  1.00  0.00             
ATOM    832  CA  ASP   107     -18.268  36.748  -7.862  1.00  0.00             
ATOM    833  C   ASP   107     -17.252  37.663  -7.185  1.00  0.00             
ATOM    834  O   ASP   107     -17.264  37.823  -5.965  1.00  0.00             
ATOM    835  CB  ASP   107     -19.648  37.407  -7.864  1.00  0.00             
ATOM    836  CG  ASP   107     -20.669  36.626  -7.061  1.00  0.00             
ATOM    837  OD1 ASP   107     -21.482  37.259  -6.356  1.00  0.00             
ATOM    838  OD2 ASP   107     -20.656  35.379  -7.138  1.00  0.00             
ATOM    839  N   ALA   108     -16.375  38.259  -7.987  1.00  0.00             
ATOM    840  CA  ALA   108     -15.351  39.158  -7.466  1.00  0.00             
ATOM    841  C   ALA   108     -15.099  38.908  -5.983  1.00  0.00             
ATOM    842  O   ALA   108     -15.410  39.750  -5.140  1.00  0.00             
ATOM    843  CB  ALA   108     -14.058  39.000  -8.252  1.00  0.00             
ATOM    844  N   GLY   109     -14.533  37.747  -5.672  1.00  0.00             
ATOM    845  CA  GLY   109     -14.250  37.410  -4.289  1.00  0.00             
ATOM    846  C   GLY   109     -15.510  37.245  -3.462  1.00  0.00             
ATOM    847  O   GLY   109     -15.457  37.207  -2.233  1.00  0.00             
ATOM    848  N   MET   110     -16.651  37.147  -4.137  1.00  0.00             
ATOM    849  CA  MET   110     -17.931  36.986  -3.459  1.00  0.00             
ATOM    850  C   MET   110     -17.816  37.327  -1.976  1.00  0.00             
ATOM    851  O   MET   110     -17.905  36.447  -1.120  1.00  0.00             
ATOM    852  CB  MET   110     -19.001  37.859  -4.119  1.00  0.00             
ATOM    853  CG  MET   110     -20.183  37.079  -4.671  1.00  0.00             
ATOM    854  SD  MET   110     -21.420  38.144  -5.439  1.00  0.00             
ATOM    855  CE  MET   110     -22.630  36.934  -5.963  1.00  0.00             
ATOM    856  N   CYS   111     -17.619  38.608  -1.682  1.00  0.00             
ATOM    857  CA  CYS   111     -17.492  39.066  -0.305  1.00  0.00             
ATOM    858  C   CYS   111     -16.186  38.585   0.318  1.00  0.00             
ATOM    859  O   CYS   111     -16.095  38.406   1.533  1.00  0.00             
ATOM    860  CB  CYS   111     -17.577  40.592  -0.238  1.00  0.00             
ATOM    861  SG  CYS   111     -18.950  41.227   0.778  1.00  0.00             
ATOM    862  N   LEU   112     -15.177  38.377  -0.521  1.00  0.00             
ATOM    863  CA  LEU   112     -13.875  37.918  -0.054  1.00  0.00             
ATOM    864  C   LEU   112     -14.004  37.102   1.228  1.00  0.00             
ATOM    865  O   LEU   112     -13.362  37.403   2.234  1.00  0.00             
ATOM    866  CB  LEU   112     -13.180  37.088  -1.137  1.00  0.00             
ATOM    867  CG  LEU   112     -11.832  37.615  -1.632  1.00  0.00             
ATOM    868  CD1 LEU   112     -10.938  36.467  -2.079  1.00  0.00             
ATOM    869  CD2 LEU   112     -11.149  38.444  -0.556  1.00  0.00             
ATOM    870  N   ASP   113     -14.840  36.069   1.185  1.00  0.00             
ATOM    871  CA  ASP   113     -15.056  35.209   2.343  1.00  0.00             
ATOM    872  C   ASP   113     -15.491  36.021   3.558  1.00  0.00             
ATOM    873  O   ASP   113     -15.065  35.750   4.681  1.00  0.00             
ATOM    874  CB  ASP   113     -16.099  34.137   2.025  1.00  0.00             
ATOM    875  CG  ASP   113     -15.549  32.731   2.166  1.00  0.00             
ATOM    876  OD1 ASP   113     -16.280  31.856   2.678  1.00  0.00             
ATOM    877  OD2 ASP   113     -14.389  32.504   1.765  1.00  0.00             
ATOM    878  N   LEU   114     -16.340  37.016   3.327  1.00  0.00             
ATOM    879  CA  LEU   114     -16.834  37.868   4.402  1.00  0.00             
ATOM    880  C   LEU   114     -15.734  38.174   5.412  1.00  0.00             
ATOM    881  O   LEU   114     -15.903  37.963   6.613  1.00  0.00             
ATOM    882  CB  LEU   114     -17.406  39.169   3.836  1.00  0.00             
ATOM    883  CG  LEU   114     -18.881  39.447   4.130  1.00  0.00             
ATOM    884  CD1 LEU   114     -19.142  40.943   4.204  1.00  0.00             
ATOM    885  CD2 LEU   114     -19.310  38.759   5.417  1.00  0.00             
ATOM    886  N   LEU   115     -14.606  38.674   4.917  1.00  0.00             
ATOM    887  CA  LEU   115     -13.475  39.010   5.775  1.00  0.00             
ATOM    888  C   LEU   115     -13.103  37.841   6.680  1.00  0.00             
ATOM    889  O   LEU   115     -12.770  38.030   7.850  1.00  0.00             
ATOM    890  CB  LEU   115     -12.269  39.429   4.932  1.00  0.00             
ATOM    891  CG  LEU   115     -11.734  40.843   5.169  1.00  0.00             
ATOM    892  CD1 LEU   115     -10.238  40.903   4.903  1.00  0.00             
ATOM    893  CD2 LEU   115     -12.053  41.309   6.582  1.00  0.00             
ATOM    894  N   ASP   116     -13.162  36.632   6.132  1.00  0.00             
ATOM    895  CA  ASP   116     -12.831  35.431   6.888  1.00  0.00             
ATOM    896  C   ASP   116     -13.379  35.505   8.309  1.00  0.00             
ATOM    897  O   ASP   116     -13.334  34.526   9.054  1.00  0.00             
ATOM    898  CB  ASP   116     -13.371  34.186   6.181  1.00  0.00             
ATOM    899  CG  ASP   116     -12.275  33.209   5.805  1.00  0.00             
ATOM    900  OD1 ASP   116     -12.495  31.987   5.946  1.00  0.00             
ATOM    901  OD2 ASP   116     -11.197  33.663   5.368  1.00  0.00             
ATOM    902  N   ASP   117     -13.895  36.673   8.678  1.00  0.00             
ATOM    903  CA  ASP   117     -14.453  36.877  10.010  1.00  0.00             
ATOM    904  C   ASP   117     -13.980  35.797  10.978  1.00  0.00             
ATOM    905  O   ASP   117     -14.425  34.652  10.911  1.00  0.00             
ATOM    906  CB  ASP   117     -14.077  38.262  10.542  1.00  0.00             
ATOM    907  CG  ASP   117     -15.290  39.119  10.844  1.00  0.00             
ATOM    908  OD1 ASP   117     -15.274  39.831  11.869  1.00  0.00             
ATOM    909  OD2 ASP   117     -16.258  39.078  10.054  1.00  0.00             
ATOM    910  N   GLY   118     -13.075  36.172  11.876  1.00  0.00             
ATOM    911  CA  GLY   118     -12.558  35.221  12.844  1.00  0.00             
ATOM    912  C   GLY   118     -12.107  33.925  12.200  1.00  0.00             
ATOM    913  O   GLY   118     -12.928  33.109  11.782  1.00  0.00             
ATOM    914  N   THR   119     -10.795  33.732  12.117  1.00  0.00             
ATOM    915  CA  THR   119     -10.221  32.499  11.505  1.00  0.00             
ATOM    916  C   THR   119      -8.744  32.686  11.169  1.00  0.00             
ATOM    917  O   THR   119      -8.308  32.385  10.059  1.00  0.00             
ATOM    918  CB  THR   119     -10.375  31.283  12.437  1.00  0.00             
ATOM    919  OG1 THR   119     -10.462  31.726  13.797  1.00  0.00             
ATOM    920  CG2 THR   119     -11.630  30.498  12.083  1.00  0.00             
ATOM    921  N   PHE   120      -7.982  33.184  12.137  1.00  0.00             
ATOM    922  CA  PHE   120      -6.554  33.411  11.946  1.00  0.00             
ATOM    923  C   PHE   120      -6.075  32.827  10.621  1.00  0.00             
ATOM    924  O   PHE   120      -5.899  31.616  10.493  1.00  0.00             
ATOM    925  CB  PHE   120      -6.237  34.906  12.007  1.00  0.00             
ATOM    926  CG  PHE   120      -5.275  35.278  13.099  1.00  0.00             
ATOM    927  CD1 PHE   120      -4.757  34.311  13.943  1.00  0.00             
ATOM    928  CD2 PHE   120      -4.889  36.594  13.283  1.00  0.00             
ATOM    929  CE1 PHE   120      -3.872  34.653  14.948  1.00  0.00             
ATOM    930  CE2 PHE   120      -4.004  36.936  14.289  1.00  0.00             
ATOM    931  CZ  PHE   120      -3.497  35.972  15.120  1.00  0.00             
ATOM    932  N   LYS   121      -5.865  33.697   9.638  1.00  0.00             
ATOM    933  CA  LYS   121      -5.406  33.269   8.321  1.00  0.00             
ATOM    934  C   LYS   121      -5.695  34.331   7.265  1.00  0.00             
ATOM    935  O   LYS   121      -6.815  34.443   6.766  1.00  0.00             
ATOM    936  CB  LYS   121      -3.911  32.952   8.353  1.00  0.00             
ATOM    937  CG  LYS   121      -3.572  31.518   7.975  1.00  0.00             
ATOM    938  CD  LYS   121      -2.073  31.273   8.027  1.00  0.00             
ATOM    939  CE  LYS   121      -1.735  29.840   7.651  1.00  0.00             
ATOM    940  NZ  LYS   121      -0.269  29.585   7.696  1.00  0.00             
ATOM    941  N   PRO   122      -4.677  35.128   6.912  1.00  0.00             
ATOM    942  CA  PRO   122      -4.815  36.188   5.910  1.00  0.00             
ATOM    943  C   PRO   122      -4.770  37.575   6.543  1.00  0.00             
ATOM    944  O   PRO   122      -5.547  38.459   6.181  1.00  0.00             
ATOM    945  CB  PRO   122      -3.592  35.978   5.014  1.00  0.00             
ATOM    946  CG  PRO   122      -2.490  35.643   5.962  1.00  0.00             
ATOM    947  CD  PRO   122      -3.314  35.052   7.465  1.00  0.00             
ATOM    948  N   LYS   123      -3.855  37.758   7.489  1.00  0.00             
ATOM    949  CA  LYS   123      -3.707  39.037   8.174  1.00  0.00             
ATOM    950  C   LYS   123      -4.396  39.017   9.534  1.00  0.00             
ATOM    951  O   LYS   123      -4.825  40.106   9.969  1.00  0.00             
ATOM    952  CB  LYS   123      -2.227  39.388   8.338  1.00  0.00             
ATOM    953  CG  LYS   123      -1.819  40.690   7.667  1.00  0.00             
ATOM    954  CD  LYS   123      -0.341  40.976   7.870  1.00  0.00             
ATOM    955  CE  LYS   123       0.067  42.278   7.198  1.00  0.00             
ATOM    956  NZ  LYS   123       1.515  42.572   7.388  1.00  0.00             
ATOM    957  OXT LYS   123      -4.477  37.912  10.112  1.00  0.00             
TER
END
