
#######################################################
#                                                     #
#                        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   24 (  186),  selected   24 , name T0382TS009_1_3
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS009_1_3.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    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    K     100      V      23           #
LGA    W     101      E      24           -
LGA    F     102      -       -           -
LGA    P     103      -       -           -
LGA    Q     104      -       -           -
LGA    A     105      Q      25           #
LGA    G     106      D      26          2.637
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    D     107      L      29          1.267
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    A     108      Q      33           #
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    G     109      F      37          1.183
LGA    -       -      N      38           -
LGA    M     110      R      39          2.821
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    C     111      G      42          3.221
LGA    L     112      V      43          1.742
LGA    D     113      M      44          3.119
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    L     114      I      47          1.243
LGA    L     115      A      48          3.629
LGA    -       -      D      49           -
LGA    D     116      E      50          2.499
LGA    D     117      L      51          4.088
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    G     118      D      57          3.742
LGA    T     119      Q      58          1.634
LGA    -       -      R      59           -
LGA    F     120      T      60          3.334
LGA    K     121      A      61          1.444
LGA    P     122      L      62          1.336
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    K     123      L      65          1.258
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)   24  121    5.0     17    2.57     0.00      9.703     0.638

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.712271 * X  +   0.698584 * Y  +  -0.068198 * Z  +  20.892685
  Y_new =   0.696000 * X  +   0.690360 * Y  +  -0.197450 * Z  +  75.127083
  Z_new =  -0.090854 * X  +  -0.188103 * Y  +  -0.977938 * Z  +   7.255073 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.951567    0.190026  [ DEG:  -169.1123     10.8877 ]
  Theta =   0.090979    3.050613  [ DEG:     5.2127    174.7873 ]
  Phi   =   2.367748   -0.773845  [ DEG:   135.6619    -44.3381 ]
 
# 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_1_3                                
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_1_3.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  121   5.0   17   2.57    0.00   9.703
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_1_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A
ATOM    772  N   LYS   100     -16.407  42.477  17.408  1.00  0.00              
ATOM    773  CA  LYS   100     -17.544  41.599  17.158  1.00  0.00              
ATOM    774  C   LYS   100     -18.827  42.178  17.742  1.00  0.00              
ATOM    775  O   LYS   100     -19.791  42.431  17.019  1.00  0.00              
ATOM    776  CB  LYS   100     -17.713  41.353  15.657  1.00  0.00              
ATOM    777  CG  LYS   100     -17.188  40.007  15.186  1.00  0.00              
ATOM    778  CD  LYS   100     -16.743  40.066  13.733  1.00  0.00              
ATOM    779  CE  LYS   100     -16.487  38.675  13.177  1.00  0.00              
ATOM    780  NZ  LYS   100     -15.641  38.713  11.952  1.00  0.00              
ATOM    781  N   TRP   101     -18.832  42.387  19.055  1.00  0.00              
ATOM    782  CA  TRP   101     -19.997  42.938  19.738  1.00  0.00              
ATOM    783  C   TRP   101     -19.845  44.438  19.965  1.00  0.00              
ATOM    784  O   TRP   101     -20.031  45.237  19.047  1.00  0.00              
ATOM    785  CB  TRP   101     -21.271  42.653  18.940  1.00  0.00              
ATOM    786  CG  TRP   101     -22.182  41.661  19.598  1.00  0.00              
ATOM    787  CD1 TRP   101     -23.408  41.256  19.158  1.00  0.00              
ATOM    788  CD2 TRP   101     -21.937  40.948  20.817  1.00  0.00              
ATOM    789  NE1 TRP   101     -23.945  40.336  20.025  1.00  0.00              
ATOM    790  CE2 TRP   101     -23.059  40.130  21.053  1.00  0.00              
ATOM    791  CE3 TRP   101     -20.878  40.923  21.730  1.00  0.00              
ATOM    792  CZ2 TRP   101     -23.153  39.294  22.165  1.00  0.00              
ATOM    793  CZ3 TRP   101     -20.974  40.094  22.831  1.00  0.00              
ATOM    794  CH2 TRP   101     -22.103  39.289  23.042  1.00  0.00              
ATOM    795  N   PHE   102     -19.507  44.814  21.194  1.00  0.00              
ATOM    796  CA  PHE   102     -19.329  46.218  21.543  1.00  0.00              
ATOM    797  C   PHE   102     -18.680  46.994  20.402  1.00  0.00              
ATOM    798  O   PHE   102     -19.059  48.127  20.105  1.00  0.00              
ATOM    799  CB  PHE   102     -20.672  46.853  21.913  1.00  0.00              
ATOM    800  CG  PHE   102     -20.840  47.105  23.384  1.00  0.00              
ATOM    801  CD1 PHE   102     -20.188  46.314  24.315  1.00  0.00              
ATOM    802  CD2 PHE   102     -21.647  48.134  23.837  1.00  0.00              
ATOM    803  CE1 PHE   102     -20.343  46.547  25.669  1.00  0.00              
ATOM    804  CE2 PHE   102     -21.801  48.366  25.190  1.00  0.00              
ATOM    805  CZ  PHE   102     -21.153  47.578  26.105  1.00  0.00              
ATOM    806  N   PRO   103     -17.683  46.384  19.745  1.00  0.00              
ATOM    807  CA  PRO   103     -16.972  47.013  18.627  1.00  0.00              
ATOM    808  C   PRO   103     -17.206  46.270  17.316  1.00  0.00              
ATOM    809  O   PRO   103     -18.348  46.044  16.916  1.00  0.00              
ATOM    810  CB  PRO   103     -17.598  48.406  18.563  1.00  0.00              
ATOM    811  CG  PRO   103     -19.056  48.153  18.373  1.00  0.00              
ATOM    812  CD  PRO   103     -17.177  45.033  20.043  1.00  0.00              
ATOM    813  N   GLN   104     -16.119  45.894  16.653  1.00  0.00              
ATOM    814  CA  GLN   104     -16.204  45.177  15.386  1.00  0.00              
ATOM    815  C   GLN   104     -14.961  44.327  15.149  1.00  0.00              
ATOM    816  O   GLN   104     -13.901  44.586  15.718  1.00  0.00              
ATOM    817  CB  GLN   104     -17.457  44.300  15.350  1.00  0.00              
ATOM    818  CG  GLN   104     -18.318  44.496  14.113  1.00  0.00              
ATOM    819  CD  GLN   104     -19.431  43.472  14.008  1.00  0.00              
ATOM    820  OE1 GLN   104     -20.027  43.297  12.946  1.00  0.00              
ATOM    821  NE2 GLN   104     -19.714  42.794  15.114  1.00  0.00              
ATOM    822  N   ALA   105     -15.098  43.308  14.305  1.00  0.00              
ATOM    823  CA  ALA   105     -13.988  42.418  13.991  1.00  0.00              
ATOM    824  C   ALA   105     -14.486  41.095  13.419  1.00  0.00              
ATOM    825  O   ALA   105     -15.562  41.030  12.823  1.00  0.00              
ATOM    826  CB  ALA   105     -13.033  43.085  13.013  1.00  0.00              
ATOM    827  N   GLY   106     -13.698  40.041  13.606  1.00  0.00              
ATOM    828  CA  GLY   106     -14.079  38.734  13.102  1.00  0.00              
ATOM    829  C   GLY   106     -12.880  37.865  12.780  1.00  0.00              
ATOM    830  O   GLY   106     -12.744  37.368  11.662  1.00  0.00              
ATOM    831  N   ASP   107     -12.006  37.677  13.763  1.00  0.00              
ATOM    832  CA  ASP   107     -10.813  36.860  13.580  1.00  0.00              
ATOM    833  C   ASP   107      -9.708  37.646  12.881  1.00  0.00              
ATOM    834  O   ASP   107      -9.530  38.838  13.128  1.00  0.00              
ATOM    835  CB  ASP   107     -10.311  36.334  14.927  1.00  0.00              
ATOM    836  CG  ASP   107     -10.331  34.820  15.005  1.00  0.00              
ATOM    837  OD1 ASP   107      -9.747  34.267  15.960  1.00  0.00              
ATOM    838  OD2 ASP   107     -10.930  34.187  14.111  1.00  0.00              
ATOM    839  N   ALA   108      -8.970  36.969  12.006  1.00  0.00              
ATOM    840  CA  ALA   108      -7.884  37.603  11.269  1.00  0.00              
ATOM    841  C   ALA   108      -7.596  36.865   9.967  1.00  0.00              
ATOM    842  O   ALA   108      -8.284  35.903   9.622  1.00  0.00              
ATOM    843  CB  ALA   108      -8.214  39.061  10.985  1.00  0.00              
ATOM    844  N   GLY   109      -6.578  37.321   9.245  1.00  0.00              
ATOM    845  CA  GLY   109      -6.222  36.690   7.988  1.00  0.00              
ATOM    846  C   GLY   109      -5.911  37.698   6.900  1.00  0.00              
ATOM    847  O   GLY   109      -5.952  38.908   7.131  1.00  0.00              
ATOM    848  N   MET   110      -5.599  37.204   5.707  1.00  0.00              
ATOM    849  CA  MET   110      -5.279  38.069   4.578  1.00  0.00              
ATOM    850  C   MET   110      -4.616  37.284   3.451  1.00  0.00              
ATOM    851  O   MET   110      -4.115  36.179   3.662  1.00  0.00              
ATOM    852  CB  MET   110      -6.541  38.764   4.062  1.00  0.00              
ATOM    853  CG  MET   110      -6.451  40.281   4.047  1.00  0.00              
ATOM    854  SD  MET   110      -8.065  41.073   3.901  1.00  0.00              
ATOM    855  CE  MET   110      -7.606  42.801   4.014  1.00  0.00              
ATOM    856  N   CYS   111      -4.619  37.860   2.254  1.00  0.00              
ATOM    857  CA  CYS   111      -4.018  37.216   1.091  1.00  0.00              
ATOM    858  C   CYS   111      -4.813  37.512  -0.176  1.00  0.00              
ATOM    859  O   CYS   111      -5.612  36.690  -0.625  1.00  0.00              
ATOM    860  CB  CYS   111      -2.566  37.668   0.920  1.00  0.00              
ATOM    861  SG  CYS   111      -1.330  36.373   1.255  1.00  0.00              
ATOM    862  N   LEU   112      -4.590  38.690  -0.747  1.00  0.00              
ATOM    863  CA  LEU   112      -5.284  39.096  -1.963  1.00  0.00              
ATOM    864  C   LEU   112      -6.128  40.344  -1.725  1.00  0.00              
ATOM    865  O   LEU   112      -6.044  40.970  -0.669  1.00  0.00              
ATOM    866  CB  LEU   112      -4.284  39.345  -3.094  1.00  0.00              
ATOM    867  CG  LEU   112      -4.409  38.439  -4.321  1.00  0.00              
ATOM    868  CD1 LEU   112      -4.289  39.250  -5.602  1.00  0.00              
ATOM    869  CD2 LEU   112      -5.720  37.669  -4.290  1.00  0.00              
ATOM    870  N   ASP   113      -6.943  40.699  -2.715  1.00  0.00              
ATOM    871  CA  ASP   113      -7.803  41.872  -2.614  1.00  0.00              
ATOM    872  C   ASP   113      -8.282  42.323  -3.990  1.00  0.00              
ATOM    873  O   ASP   113      -8.323  43.517  -4.284  1.00  0.00              
ATOM    874  CB  ASP   113      -9.001  41.581  -1.709  1.00  0.00              
ATOM    875  CG  ASP   113      -9.023  42.457  -0.473  1.00  0.00              
ATOM    876  OD1 ASP   113     -10.093  42.559   0.164  1.00  0.00              
ATOM    877  OD2 ASP   113      -7.971  43.042  -0.140  1.00  0.00              
ATOM    878  N   LEU   114      -8.643  41.359  -4.831  1.00  0.00              
ATOM    879  CA  LEU   114      -9.119  41.655  -6.177  1.00  0.00              
ATOM    880  C   LEU   114      -8.613  43.011  -6.655  1.00  0.00              
ATOM    881  O   LEU   114      -9.020  43.500  -7.709  1.00  0.00              
ATOM    882  CB  LEU   114      -8.687  40.558  -7.152  1.00  0.00              
ATOM    883  CG  LEU   114      -9.666  40.229  -8.280  1.00  0.00              
ATOM    884  CD1 LEU   114      -8.928  40.050  -9.598  1.00  0.00              
ATOM    885  CD2 LEU   114     -10.731  41.308  -8.399  1.00  0.00              
ATOM    886  N   LEU   115      -7.724  43.615  -5.874  1.00  0.00              
ATOM    887  CA  LEU   115      -7.161  44.915  -6.216  1.00  0.00              
ATOM    888  C   LEU   115      -8.163  45.764  -6.991  1.00  0.00              
ATOM    889  O   LEU   115      -8.197  46.986  -6.849  1.00  0.00              
ATOM    890  CB  LEU   115      -6.711  45.653  -4.953  1.00  0.00              
ATOM    891  CG  LEU   115      -5.342  46.335  -5.017  1.00  0.00              
ATOM    892  CD1 LEU   115      -5.456  47.805  -4.643  1.00  0.00              
ATOM    893  CD2 LEU   115      -4.727  46.174  -6.398  1.00  0.00              
ATOM    894  N   ASP   116      -8.978  45.107  -7.810  1.00  0.00              
ATOM    895  CA  ASP   116      -9.982  45.800  -8.609  1.00  0.00              
ATOM    896  C   ASP   116     -11.031  46.461  -7.722  1.00  0.00              
ATOM    897  O   ASP   116     -12.043  46.966  -8.211  1.00  0.00              
ATOM    898  CB  ASP   116      -9.322  46.844  -9.512  1.00  0.00              
ATOM    899  CG  ASP   116      -9.514  46.544 -10.986  1.00  0.00              
ATOM    900  OD1 ASP   116      -9.833  47.482 -11.746  1.00  0.00              
ATOM    901  OD2 ASP   116      -9.346  45.371 -11.379  1.00  0.00              
ATOM    902  N   ASP   117     -10.784  46.457  -6.416  1.00  0.00              
ATOM    903  CA  ASP   117     -11.706  47.057  -5.459  1.00  0.00              
ATOM    904  C   ASP   117     -12.763  47.898  -6.165  1.00  0.00              
ATOM    905  O   ASP   117     -13.963  47.682  -5.989  1.00  0.00              
ATOM    906  CB  ASP   117     -12.376  45.974  -4.611  1.00  0.00              
ATOM    907  CG  ASP   117     -12.701  46.451  -3.209  1.00  0.00              
ATOM    908  OD1 ASP   117     -13.730  46.012  -2.656  1.00  0.00              
ATOM    909  OD2 ASP   117     -11.926  47.266  -2.663  1.00  0.00              
ATOM    910  N   GLY   118     -12.311  48.859  -6.966  1.00  0.00              
ATOM    911  CA  GLY   118     -13.234  49.716  -7.685  1.00  0.00              
ATOM    912  C   GLY   118     -14.294  48.931  -8.431  1.00  0.00              
ATOM    913  O   GLY   118     -15.285  49.494  -8.896  1.00  0.00              
ATOM    914  N   THR   119     -14.088  47.624  -8.550  1.00  0.00              
ATOM    915  CA  THR   119     -15.054  46.739  -9.261  1.00  0.00              
ATOM    916  C   THR   119     -16.420  47.403  -9.387  1.00  0.00              
ATOM    917  O   THR   119     -16.518  48.587  -9.712  1.00  0.00              
ATOM    918  CB  THR   119     -14.545  46.361 -10.665  1.00  0.00              
ATOM    919  OG1 THR   119     -13.355  47.102 -10.960  1.00  0.00              
ATOM    920  CG2 THR   119     -14.241  44.872 -10.737  1.00  0.00              
ATOM    921  N   PHE   120     -17.474  46.635  -9.130  1.00  0.00              
ATOM    922  CA  PHE   120     -18.835  47.148  -9.215  1.00  0.00              
ATOM    923  C   PHE   120     -19.677  46.674  -8.036  1.00  0.00              
ATOM    924  O   PHE   120     -20.248  47.483  -7.303  1.00  0.00              
ATOM    925  CB  PHE   120     -18.829  48.676  -9.278  1.00  0.00              
ATOM    926  CG  PHE   120     -18.966  49.226 -10.669  1.00  0.00              
ATOM    927  CD1 PHE   120     -18.928  48.385 -11.768  1.00  0.00              
ATOM    928  CD2 PHE   120     -19.133  50.584 -10.879  1.00  0.00              
ATOM    929  CE1 PHE   120     -19.054  48.892 -13.048  1.00  0.00              
ATOM    930  CE2 PHE   120     -19.259  51.090 -12.159  1.00  0.00              
ATOM    931  CZ  PHE   120     -19.220  50.250 -13.241  1.00  0.00              
ATOM    932  N   LYS   121     -19.750  45.360  -7.856  1.00  0.00              
ATOM    933  CA  LYS   121     -20.522  44.776  -6.765  1.00  0.00              
ATOM    934  C   LYS   121     -20.136  45.395  -5.425  1.00  0.00              
ATOM    935  O   LYS   121     -19.547  46.475  -5.368  1.00  0.00              
ATOM    936  CB  LYS   121     -22.020  44.955  -7.015  1.00  0.00              
ATOM    937  CG  LYS   121     -22.735  43.682  -7.438  1.00  0.00              
ATOM    938  CD  LYS   121     -24.219  43.927  -7.652  1.00  0.00              
ATOM    939  CE  LYS   121     -24.854  42.804  -8.458  1.00  0.00              
ATOM    940  NZ  LYS   121     -26.305  43.042  -8.694  1.00  0.00              
ATOM    941  N   PRO   122     -20.468  44.707  -4.322  1.00  0.00              
ATOM    942  CA  PRO   122     -20.158  45.184  -2.971  1.00  0.00              
ATOM    943  C   PRO   122     -20.913  44.397  -1.905  1.00  0.00              
ATOM    944  O   PRO   122     -20.926  43.167  -1.922  1.00  0.00              
ATOM    945  CB  PRO   122     -18.654  44.925  -2.851  1.00  0.00              
ATOM    946  CG  PRO   122     -18.401  43.770  -3.760  1.00  0.00              
ATOM    947  CD  PRO   122     -21.170  43.413  -4.313  1.00  0.00              
ATOM    948  N   LYS   123     -21.541  45.115  -0.980  1.00  0.00              
ATOM    949  CA  LYS   123     -22.298  44.486   0.095  1.00  0.00              
ATOM    950  C   LYS   123     -23.736  44.209  -0.333  1.00  0.00              
ATOM    951  O   LYS   123     -24.551  43.924   0.570  1.00  0.00              
ATOM    952  CB  LYS   123     -21.621  43.188   0.539  1.00  0.00              
ATOM    953  CG  LYS   123     -20.630  43.361   1.678  1.00  0.00              
ATOM    954  CD  LYS   123     -20.221  42.020   2.263  1.00  0.00              
ATOM    955  CE  LYS   123     -19.284  42.197   3.446  1.00  0.00              
ATOM    956  NZ  LYS   123     -19.375  41.060   4.403  1.00  0.00              
ATOM    957  OXT LYS   123     -23.989  44.288  -1.553  1.00  0.00              
TER
END
