
#######################################################
#                                                     #
#                        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_3_4
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS009_3_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    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    F     102      T      11          3.357
LGA    P     103      Q      12          2.944
LGA    Q     104      D      13          3.982
LGA    A     105      L      14          0.871
LGA    -       -      V      15           -
LGA    G     106      A      16          4.424
LGA    D     107      L      17          1.989
LGA    A     108      F      18          1.412
LGA    G     109      A      19          3.950
LGA    M     110      K      20          1.959
LGA    C     111      V      21          5.326
LGA    L     112      T      22          1.058
LGA    -       -      V      23           -
LGA    D     113      E      24          0.838
LGA    L     114      Q      25          4.371
LGA    L     115      D      26          1.811
LGA    D     116      D      27          3.114
LGA    -       -      A      28           -
LGA    D     117      L      29          3.041
LGA    G     118      L      30          2.428
LGA    -       -      G      31           -
LGA    T     119      N      32          2.548
LGA    F     120      Q      33          2.946
LGA    K     121      I      34          1.563
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    P     122      N      38          2.626
LGA    K     123      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     21    2.96     4.76     10.345     0.687

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.869853 * X  +   0.438092 * Y  +   0.226784 * Z  + -84.896156
  Y_new =   0.377141 * X  +  -0.886913 * Y  +   0.266738 * Z  +  29.924622
  Z_new =   0.317994 * X  +  -0.146493 * Y  +  -0.936707 * Z  + -48.787006 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.986458    0.155135  [ DEG:  -171.1114      8.8886 ]
  Theta =  -0.323613   -2.817980  [ DEG:   -18.5416   -161.4584 ]
  Phi   =   0.409106   -2.732487  [ DEG:    23.4400   -156.5600 ]
 
# 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_3_4                                
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_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   21   2.96    4.76  10.345
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_4
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A       
ATOM    795  N   PHE   102     -18.559  38.398 -13.063  1.00  0.00             
ATOM    796  CA  PHE   102     -17.367  37.616 -12.756  1.00  0.00             
ATOM    797  C   PHE   102     -17.298  37.275 -11.272  1.00  0.00             
ATOM    798  O   PHE   102     -16.591  37.926 -10.502  1.00  0.00             
ATOM    799  CB  PHE   102     -17.336  36.336 -13.593  1.00  0.00             
ATOM    800  CG  PHE   102     -16.133  36.225 -14.486  1.00  0.00             
ATOM    801  CD1 PHE   102     -15.174  37.222 -14.507  1.00  0.00             
ATOM    802  CD2 PHE   102     -15.961  35.123 -15.305  1.00  0.00             
ATOM    803  CE1 PHE   102     -14.067  37.119 -15.328  1.00  0.00             
ATOM    804  CE2 PHE   102     -14.854  35.020 -16.126  1.00  0.00             
ATOM    805  CZ  PHE   102     -13.910  36.012 -16.140  1.00  0.00             
ATOM    806  N   PRO   103     -18.039  36.239 -10.853  1.00  0.00             
ATOM    807  CA  PRO   103     -18.066  35.803  -9.453  1.00  0.00             
ATOM    808  C   PRO   103     -17.936  36.978  -8.491  1.00  0.00             
ATOM    809  O   PRO   103     -17.465  36.822  -7.364  1.00  0.00             
ATOM    810  CB  PRO   103     -19.451  35.164  -9.318  1.00  0.00             
ATOM    811  CG  PRO   103     -20.353  36.061 -10.098  1.00  0.00             
ATOM    812  CD  PRO   103     -18.906  35.417 -11.714  1.00  0.00             
ATOM    813  N   GLN   104     -18.355  38.156  -8.942  1.00  0.00             
ATOM    814  CA  GLN   104     -18.285  39.359  -8.122  1.00  0.00             
ATOM    815  C   GLN   104     -17.065  39.335  -7.208  1.00  0.00             
ATOM    816  O   GLN   104     -17.194  39.332  -5.985  1.00  0.00             
ATOM    817  CB  GLN   104     -18.257  40.608  -9.006  1.00  0.00             
ATOM    818  CG  GLN   104     -19.415  41.564  -8.767  1.00  0.00             
ATOM    819  CD  GLN   104     -19.352  42.787  -9.659  1.00  0.00             
ATOM    820  OE1 GLN   104     -20.218  43.661  -9.592  1.00  0.00             
ATOM    821  NE2 GLN   104     -18.327  42.855 -10.500  1.00  0.00             
ATOM    822  N   ALA   105     -15.881  39.316  -7.812  1.00  0.00             
ATOM    823  CA  ALA   105     -14.635  39.292  -7.055  1.00  0.00             
ATOM    824  C   ALA   105     -14.425  37.940  -6.382  1.00  0.00             
ATOM    825  O   ALA   105     -13.915  37.864  -5.264  1.00  0.00             
ATOM    826  CB  ALA   105     -13.457  39.616  -7.961  1.00  0.00             
ATOM    827  N   GLY   106     -14.821  36.874  -7.071  1.00  0.00             
ATOM    828  CA  GLY   106     -14.666  35.540  -6.521  1.00  0.00             
ATOM    829  C   GLY   106     -14.943  35.490  -5.032  1.00  0.00             
ATOM    830  O   GLY   106     -14.037  35.260  -4.230  1.00  0.00             
ATOM    831  N   ASP   107     -16.199  35.707  -4.656  1.00  0.00             
ATOM    832  CA  ASP   107     -16.594  35.688  -3.253  1.00  0.00             
ATOM    833  C   ASP   107     -16.034  36.893  -2.504  1.00  0.00             
ATOM    834  O   ASP   107     -16.055  36.936  -1.274  1.00  0.00             
ATOM    835  CB  ASP   107     -18.118  35.651  -3.125  1.00  0.00             
ATOM    836  CG  ASP   107     -18.611  34.421  -2.389  1.00  0.00             
ATOM    837  OD1 ASP   107     -19.556  34.551  -1.582  1.00  0.00             
ATOM    838  OD2 ASP   107     -18.053  33.327  -2.618  1.00  0.00             
ATOM    839  N   ALA   108     -15.533  37.868  -3.255  1.00  0.00             
ATOM    840  CA  ALA   108     -14.967  39.075  -2.665  1.00  0.00             
ATOM    841  C   ALA   108     -14.625  38.861  -1.195  1.00  0.00             
ATOM    842  O   ALA   108     -15.217  39.486  -0.313  1.00  0.00             
ATOM    843  CB  ALA   108     -13.728  39.510  -3.433  1.00  0.00             
ATOM    844  N   GLY   109     -13.668  37.977  -0.936  1.00  0.00             
ATOM    845  CA  GLY   109     -13.267  37.699   0.430  1.00  0.00             
ATOM    846  C   GLY   109     -14.390  37.102   1.254  1.00  0.00             
ATOM    847  O   GLY   109     -14.285  36.991   2.476  1.00  0.00             
ATOM    848  N   MET   110     -15.472  36.714   0.586  1.00  0.00             
ATOM    849  CA  MET   110     -16.620  36.125   1.264  1.00  0.00             
ATOM    850  C   MET   110     -16.527  36.315   2.774  1.00  0.00             
ATOM    851  O   MET   110     -16.324  35.356   3.519  1.00  0.00             
ATOM    852  CB  MET   110     -17.922  36.730   0.736  1.00  0.00             
ATOM    853  CG  MET   110     -18.870  35.717   0.115  1.00  0.00             
ATOM    854  SD  MET   110     -20.391  36.471  -0.493  1.00  0.00             
ATOM    855  CE  MET   110     -21.245  35.036  -1.140  1.00  0.00             
ATOM    856  N   CYS   111     -16.677  37.559   3.219  1.00  0.00             
ATOM    857  CA  CYS   111     -16.610  37.877   4.641  1.00  0.00             
ATOM    858  C   CYS   111     -15.191  37.715   5.175  1.00  0.00             
ATOM    859  O   CYS   111     -14.992  37.433   6.357  1.00  0.00             
ATOM    860  CB  CYS   111     -17.109  39.301   4.895  1.00  0.00             
ATOM    861  SG  CYS   111     -18.549  39.406   6.007  1.00  0.00             
ATOM    862  N   LEU   112     -14.209  37.895   4.299  1.00  0.00             
ATOM    863  CA  LEU   112     -12.807  37.770   4.681  1.00  0.00             
ATOM    864  C   LEU   112     -12.640  36.812   5.856  1.00  0.00             
ATOM    865  O   LEU   112     -12.054  37.166   6.879  1.00  0.00             
ATOM    866  CB  LEU   112     -11.968  37.296   3.493  1.00  0.00             
ATOM    867  CG  LEU   112     -10.845  38.232   3.040  1.00  0.00             
ATOM    868  CD1 LEU   112      -9.695  37.439   2.440  1.00  0.00             
ATOM    869  CD2 LEU   112     -10.365  39.093   4.197  1.00  0.00             
ATOM    870  N   ASP   113     -13.159  35.598   5.703  1.00  0.00             
ATOM    871  CA  ASP   113     -13.067  34.589   6.750  1.00  0.00             
ATOM    872  C   ASP   113     -13.646  35.103   8.064  1.00  0.00             
ATOM    873  O   ASP   113     -13.104  34.838   9.137  1.00  0.00             
ATOM    874  CB  ASP   113     -13.788  33.308   6.324  1.00  0.00             
ATOM    875  CG  ASP   113     -12.865  32.107   6.281  1.00  0.00             
ATOM    876  OD1 ASP   113     -13.297  31.009   6.696  1.00  0.00             
ATOM    877  OD2 ASP   113     -11.709  32.261   5.833  1.00  0.00             
ATOM    878  N   LEU   114     -14.749  35.839   7.971  1.00  0.00             
ATOM    879  CA  LEU   114     -15.402  36.391   9.152  1.00  0.00             
ATOM    880  C   LEU   114     -14.378  36.880  10.171  1.00  0.00             
ATOM    881  O   LEU   114     -14.420  36.495  11.340  1.00  0.00             
ATOM    882  CB  LEU   114     -16.340  37.535   8.760  1.00  0.00             
ATOM    883  CG  LEU   114     -17.817  37.352   9.113  1.00  0.00             
ATOM    884  CD1 LEU   114     -18.477  38.697   9.375  1.00  0.00             
ATOM    885  CD2 LEU   114     -17.972  36.431  10.315  1.00  0.00             
ATOM    886  N   LEU   115     -13.460  37.728   9.721  1.00  0.00             
ATOM    887  CA  LEU   115     -12.423  38.269  10.592  1.00  0.00             
ATOM    888  C   LEU   115     -11.696  37.158  11.341  1.00  0.00             
ATOM    889  O   LEU   115     -11.367  37.301  12.518  1.00  0.00             
ATOM    890  CB  LEU   115     -11.426  39.102   9.785  1.00  0.00             
ATOM    891  CG  LEU   115     -11.291  40.573  10.182  1.00  0.00             
ATOM    892  CD1 LEU   115      -9.886  41.081   9.898  1.00  0.00             
ATOM    893  CD2 LEU   115     -11.651  40.769  11.647  1.00  0.00             
ATOM    894  N   ASP   116     -11.447  36.051  10.649  1.00  0.00             
ATOM    895  CA  ASP   116     -10.757  34.913  11.247  1.00  0.00             
ATOM    896  C   ASP   116     -11.230  34.671  12.676  1.00  0.00             
ATOM    897  O   ASP   116     -10.877  33.667  13.295  1.00  0.00             
ATOM    898  CB  ASP   116     -10.968  33.655  10.402  1.00  0.00             
ATOM    899  CG  ASP   116      -9.666  33.073   9.889  1.00  0.00             
ATOM    900  OD1 ASP   116      -9.532  31.831   9.884  1.00  0.00             
ATOM    901  OD2 ASP   116      -8.779  33.858   9.491  1.00  0.00             
ATOM    902  N   ASP   117     -12.029  35.598  13.195  1.00  0.00             
ATOM    903  CA  ASP   117     -12.552  35.486  14.552  1.00  0.00             
ATOM    904  C   ASP   117     -11.748  34.482  15.371  1.00  0.00             
ATOM    905  O   ASP   117     -11.862  33.272  15.172  1.00  0.00             
ATOM    906  CB  ASP   117     -12.546  36.851  15.241  1.00  0.00             
ATOM    907  CG  ASP   117     -13.931  37.295  15.668  1.00  0.00             
ATOM    908  OD1 ASP   117     -14.060  37.863  16.773  1.00  0.00             
ATOM    909  OD2 ASP   117     -14.889  37.073  14.898  1.00  0.00             
ATOM    910  N   GLY   118     -10.936  34.991  16.292  1.00  0.00             
ATOM    911  CA  GLY   118     -10.128  34.122  17.126  1.00  0.00             
ATOM    912  C   GLY   118      -9.369  33.085  16.319  1.00  0.00             
ATOM    913  O   GLY   118      -9.954  32.123  15.821  1.00  0.00             
ATOM    914  N   THR   119      -8.061  33.279  16.190  1.00  0.00             
ATOM    915  CA  THR   119      -7.201  32.334  15.422  1.00  0.00             
ATOM    916  C   THR   119      -5.854  32.964  15.084  1.00  0.00             
ATOM    917  O   THR   119      -5.410  32.924  13.936  1.00  0.00             
ATOM    918  CB  THR   119      -6.965  31.026  16.199  1.00  0.00             
ATOM    919  OG1 THR   119      -7.100  31.272  17.605  1.00  0.00             
ATOM    920  CG2 THR   119      -7.970  29.966  15.777  1.00  0.00             
ATOM    921  N   PHE   120      -5.209  33.544  16.090  1.00  0.00             
ATOM    922  CA  PHE   120      -3.912  34.183  15.901  1.00  0.00             
ATOM    923  C   PHE   120      -3.359  33.910  14.506  1.00  0.00             
ATOM    924  O   PHE   120      -2.863  32.819  14.228  1.00  0.00             
ATOM    925  CB  PHE   120      -4.018  35.691  16.139  1.00  0.00             
ATOM    926  CG  PHE   120      -3.142  36.192  17.251  1.00  0.00             
ATOM    927  CD1 PHE   120      -2.332  35.321  17.960  1.00  0.00             
ATOM    928  CD2 PHE   120      -3.126  37.535  17.587  1.00  0.00             
ATOM    929  CE1 PHE   120      -1.526  35.783  18.983  1.00  0.00             
ATOM    930  CE2 PHE   120      -2.319  37.996  18.610  1.00  0.00             
ATOM    931  CZ  PHE   120      -1.521  37.127  19.307  1.00  0.00             
ATOM    932  N   LYS   121      -3.451  34.907  13.633  1.00  0.00             
ATOM    933  CA  LYS   121      -2.960  34.777  12.266  1.00  0.00             
ATOM    934  C   LYS   121      -3.586  35.826  11.354  1.00  0.00             
ATOM    935  O   LYS   121      -4.717  35.675  10.892  1.00  0.00             
ATOM    936  CB  LYS   121      -1.435  34.891  12.231  1.00  0.00             
ATOM    937  CG  LYS   121      -0.734  33.662  11.675  1.00  0.00             
ATOM    938  CD  LYS   121       0.775  33.843  11.669  1.00  0.00             
ATOM    939  CE  LYS   121       1.477  32.615  11.113  1.00  0.00             
ATOM    940  NZ  LYS   121       2.957  32.778  11.100  1.00  0.00             
ATOM    941  N   PRO   122      -2.847  36.911  11.081  1.00  0.00             
ATOM    942  CA  PRO   122      -3.326  37.997  10.220  1.00  0.00             
ATOM    943  C   PRO   122      -3.633  39.260  11.017  1.00  0.00             
ATOM    944  O   PRO   122      -4.641  39.924  10.780  1.00  0.00             
ATOM    945  CB  PRO   122      -2.141  38.240   9.283  1.00  0.00             
ATOM    946  CG  PRO   122      -0.941  38.125  10.162  1.00  0.00             
ATOM    947  CD  PRO   122      -1.491  37.161  11.596  1.00  0.00             
ATOM    948  N   LYS   123      -2.757  39.586  11.961  1.00  0.00             
ATOM    949  CA  LYS   123      -2.932  40.769  12.794  1.00  0.00             
ATOM    950  C   LYS   123      -3.517  40.404  14.154  1.00  0.00             
ATOM    951  O   LYS   123      -4.208  41.273  14.727  1.00  0.00             
ATOM    952  CB  LYS   123      -1.600  41.500  12.973  1.00  0.00             
ATOM    953  CG  LYS   123      -1.605  42.931  12.458  1.00  0.00             
ATOM    954  CD  LYS   123      -0.254  43.596  12.667  1.00  0.00             
ATOM    955  CE  LYS   123      -0.258  45.027  12.152  1.00  0.00             
ATOM    956  NZ  LYS   123       1.059  45.692  12.350  1.00  0.00             
ATOM    957  OXT LYS   123      -3.260  39.263  14.594  1.00  0.00             
TER
END
