
#######################################################
#                                                     #
#                        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   21 (  153),  selected   21 , name T0382TS009_2_4-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_2_4-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    F     102      M       9          4.756
LGA    P     103      T      10          1.580
LGA    Q     104      T      11          0.821
LGA    A     105      Q      12           #
LGA    G     106      D      13          3.346
LGA    D     107      L      14          2.695
LGA    A     108      V      15          3.578
LGA    -       -      A      16           -
LGA    G     109      L      17          2.711
LGA    M     110      F      18          3.686
LGA    C     111      A      19          0.289
LGA    L     112      K      20          4.213
LGA    D     113      V      21          2.182
LGA    L     114      T      22          3.623
LGA    L     115      V      23          3.228
LGA    D     116      E      24          1.666
LGA    -       -      Q      25           -
LGA    D     117      D      26          2.103
LGA    G     118      D      27          2.507
LGA    T     119      A      28          2.048
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    F     120      Q      33          1.814
LGA    K     121      I      34          3.149
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    P     122      F      37          1.695
LGA    -       -      N      38           -
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  119    5.0     20    2.81     5.00     10.394     0.687

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.682048 * X  +   0.652320 * Y  +   0.330590 * Z  +  55.571945
  Y_new =  -0.392525 * X  +  -0.707962 * Y  +   0.587124 * Z  +  78.847275
  Z_new =   0.617037 * X  +   0.270682 * Y  +   0.738916 * Z  + -30.307671 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.351141   -2.790451  [ DEG:    20.1189   -159.8811 ]
  Theta =  -0.664972   -2.476620  [ DEG:   -38.1001   -141.8999 ]
  Phi   =  -2.619375    0.522217  [ DEG:  -150.0791     29.9208 ]
 
# 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-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_4-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  119   5.0   20   2.81    5.00  10.394
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    795  N   PHE   102     -15.205  39.529 -16.398  1.00  0.00             
ATOM    796  CA  PHE   102     -14.633  38.272 -15.929  1.00  0.00             
ATOM    797  C   PHE   102     -14.956  38.035 -14.458  1.00  0.00             
ATOM    798  O   PHE   102     -14.151  38.332 -13.574  1.00  0.00             
ATOM    799  CB  PHE   102     -15.142  37.102 -16.775  1.00  0.00             
ATOM    800  CG  PHE   102     -14.052  36.343 -17.477  1.00  0.00             
ATOM    801  CD1 PHE   102     -12.727  36.714 -17.333  1.00  0.00             
ATOM    802  CD2 PHE   102     -14.353  35.257 -18.280  1.00  0.00             
ATOM    803  CE1 PHE   102     -11.724  36.015 -17.979  1.00  0.00             
ATOM    804  CE2 PHE   102     -13.351  34.558 -18.926  1.00  0.00             
ATOM    805  CZ  PHE   102     -12.041  34.933 -18.778  1.00  0.00             
ATOM    806  N   PRO   103     -16.149  37.491 -14.178  1.00  0.00             
ATOM    807  CA  PRO   103     -16.588  37.210 -12.808  1.00  0.00             
ATOM    808  C   PRO   103     -16.125  38.287 -11.833  1.00  0.00             
ATOM    809  O   PRO   103     -15.908  38.015 -10.652  1.00  0.00             
ATOM    810  CB  PRO   103     -18.114  37.228 -12.925  1.00  0.00             
ATOM    811  CG  PRO   103     -18.405  38.362 -13.849  1.00  0.00             
ATOM    812  CD  PRO   103     -17.160  37.112 -15.181  1.00  0.00             
ATOM    813  N   GLN   104     -15.974  39.508 -12.335  1.00  0.00             
ATOM    814  CA  GLN   104     -15.535  40.626 -11.509  1.00  0.00             
ATOM    815  C   GLN   104     -14.507  40.179 -10.476  1.00  0.00             
ATOM    816  O   GLN   104     -14.762  40.223  -9.273  1.00  0.00             
ATOM    817  CB  GLN   104     -14.955  41.741 -12.381  1.00  0.00             
ATOM    818  CG  GLN   104     -15.686  43.069 -12.260  1.00  0.00             
ATOM    819  CD  GLN   104     -15.083  44.147 -13.138  1.00  0.00             
ATOM    820  OE1 GLN   104     -15.558  45.283 -13.156  1.00  0.00             
ATOM    821  NE2 GLN   104     -14.032  43.796 -13.869  1.00  0.00             
ATOM    822  N   ALA   105     -13.343  39.751 -10.953  1.00  0.00             
ATOM    823  CA  ALA   105     -12.274  39.296 -10.073  1.00  0.00             
ATOM    824  C   ALA   105     -12.589  37.923  -9.487  1.00  0.00             
ATOM    825  O   ALA   105     -12.318  37.661  -8.316  1.00  0.00             
ATOM    826  CB  ALA   105     -10.951  39.255 -10.823  1.00  0.00             
ATOM    827  N   GLY   106     -13.162  37.051 -10.311  1.00  0.00             
ATOM    828  CA  GLY   106     -13.503  35.718  -9.852  1.00  0.00             
ATOM    829  C   GLY   106     -14.088  35.716  -8.454  1.00  0.00             
ATOM    830  O   GLY   106     -13.451  35.261  -7.504  1.00  0.00             
ATOM    831  N   ASP   107     -15.308  36.227  -8.323  1.00  0.00             
ATOM    832  CA  ASP   107     -15.980  36.284  -7.031  1.00  0.00             
ATOM    833  C   ASP   107     -15.364  37.353  -6.135  1.00  0.00             
ATOM    834  O   ASP   107     -15.591  37.369  -4.925  1.00  0.00             
ATOM    835  CB  ASP   107     -17.475  36.550  -7.216  1.00  0.00             
ATOM    836  CG  ASP   107     -18.340  35.443  -6.647  1.00  0.00             
ATOM    837  OD1 ASP   107     -19.388  35.756  -6.044  1.00  0.00             
ATOM    838  OD2 ASP   107     -17.969  34.260  -6.805  1.00  0.00             
ATOM    839  N   ALA   108     -14.585  38.245  -6.738  1.00  0.00             
ATOM    840  CA  ALA   108     -13.934  39.319  -5.995  1.00  0.00             
ATOM    841  C   ALA   108     -13.833  38.982  -4.511  1.00  0.00             
ATOM    842  O   ALA   108     -14.481  39.613  -3.676  1.00  0.00             
ATOM    843  CB  ALA   108     -12.552  39.596  -6.565  1.00  0.00             
ATOM    844  N   GLY   109     -13.016  37.985  -4.191  1.00  0.00             
ATOM    845  CA  GLY   109     -12.847  37.583  -2.807  1.00  0.00             
ATOM    846  C   GLY   109     -14.114  37.000  -2.213  1.00  0.00             
ATOM    847  O   GLY   109     -14.225  36.842  -0.997  1.00  0.00             
ATOM    848  N   MET   110     -15.076  36.680  -3.072  1.00  0.00             
ATOM    849  CA  MET   110     -16.343  36.112  -2.627  1.00  0.00             
ATOM    850  C   MET   110     -16.536  36.304  -1.125  1.00  0.00             
ATOM    851  O   MET   110     -16.495  35.344  -0.357  1.00  0.00             
ATOM    852  CB  MET   110     -17.510  36.739  -3.392  1.00  0.00             
ATOM    853  CG  MET   110     -18.339  35.741  -4.185  1.00  0.00             
ATOM    854  SD  MET   110     -19.703  36.520  -5.071  1.00  0.00             
ATOM    855  CE  MET   110     -20.443  35.098  -5.869  1.00  0.00             
ATOM    856  N   CYS   111     -16.747  37.551  -0.716  1.00  0.00             
ATOM    857  CA  CYS   111     -16.947  37.871   0.692  1.00  0.00             
ATOM    858  C   CYS   111     -15.659  37.687   1.487  1.00  0.00             
ATOM    859  O   CYS   111     -15.693  37.405   2.685  1.00  0.00             
ATOM    860  CB  CYS   111     -17.461  39.303   0.848  1.00  0.00             
ATOM    861  SG  CYS   111     -19.084  39.436   1.664  1.00  0.00             
ATOM    862  N   LEU   112     -14.525  37.847   0.814  1.00  0.00             
ATOM    863  CA  LEU   112     -13.224  37.699   1.457  1.00  0.00             
ATOM    864  C   LEU   112     -13.300  36.742   2.641  1.00  0.00             
ATOM    865  O   LEU   112     -12.914  37.088   3.758  1.00  0.00             
ATOM    866  CB  LEU   112     -12.182  37.208   0.449  1.00  0.00             
ATOM    867  CG  LEU   112     -10.978  38.124   0.220  1.00  0.00             
ATOM    868  CD1 LEU   112      -9.747  37.310  -0.150  1.00  0.00             
ATOM    869  CD2 LEU   112     -10.711  38.980   1.449  1.00  0.00             
ATOM    870  N   ASP   113     -13.801  35.536   2.390  1.00  0.00             
ATOM    871  CA  ASP   113     -13.929  34.527   3.435  1.00  0.00             
ATOM    872  C   ASP   113     -14.738  35.054   4.615  1.00  0.00             
ATOM    873  O   ASP   113     -14.416  34.783   5.771  1.00  0.00             
ATOM    874  CB  ASP   113     -14.577  33.258   2.877  1.00  0.00             
ATOM    875  CG  ASP   113     -13.683  32.041   3.010  1.00  0.00             
ATOM    876  OD1 ASP   113     -14.205  30.953   3.334  1.00  0.00             
ATOM    877  OD2 ASP   113     -12.461  32.175   2.791  1.00  0.00             
ATOM    878  N   LEU   114     -15.790  35.809   4.315  1.00  0.00             
ATOM    879  CA  LEU   114     -16.647  36.376   5.349  1.00  0.00             
ATOM    880  C   LEU   114     -15.828  36.848   6.546  1.00  0.00             
ATOM    881  O   LEU   114     -16.098  36.468   7.685  1.00  0.00             
ATOM    882  CB  LEU   114     -17.473  37.534   4.787  1.00  0.00             
ATOM    883  CG  LEU   114     -18.993  37.377   4.852  1.00  0.00             
ATOM    884  CD1 LEU   114     -19.668  38.734   4.984  1.00  0.00             
ATOM    885  CD2 LEU   114     -19.390  36.462   6.001  1.00  0.00             
ATOM    886  N   LEU   115     -14.825  37.679   6.279  1.00  0.00             
ATOM    887  CA  LEU   115     -13.965  38.205   7.333  1.00  0.00             
ATOM    888  C   LEU   115     -13.413  37.083   8.205  1.00  0.00             
ATOM    889  O   LEU   115     -13.313  37.223   9.424  1.00  0.00             
ATOM    890  CB  LEU   115     -12.818  39.018   6.731  1.00  0.00             
ATOM    891  CG  LEU   115     -12.736  40.488   7.149  1.00  0.00             
ATOM    892  CD1 LEU   115     -11.294  40.971   7.138  1.00  0.00             
ATOM    893  CD2 LEU   115     -13.366  40.694   8.518  1.00  0.00             
ATOM    894  N   ASP   116     -13.055  35.970   7.573  1.00  0.00             
ATOM    895  CA  ASP   116     -12.513  34.823   8.289  1.00  0.00             
ATOM    896  C   ASP   116     -13.253  34.592   9.602  1.00  0.00             
ATOM    897  O   ASP   116     -13.042  33.583  10.276  1.00  0.00             
ATOM    898  CB  ASP   116     -12.580  33.566   7.419  1.00  0.00             
ATOM    899  CG  ASP   116     -11.215  32.961   7.163  1.00  0.00             
ATOM    900  OD1 ASP   116     -11.103  31.717   7.183  1.00  0.00             
ATOM    901  OD2 ASP   116     -10.256  33.729   6.942  1.00  0.00             
ATOM    902  N   ASP   117     -14.120  35.533   9.960  1.00  0.00             
ATOM    903  CA  ASP   117     -14.894  35.434  11.193  1.00  0.00             
ATOM    904  C   ASP   117     -14.279  34.417  12.149  1.00  0.00             
ATOM    905  O   ASP   117     -14.374  33.210  11.931  1.00  0.00             
ATOM    906  CB  ASP   117     -14.996  36.801  11.873  1.00  0.00             
ATOM    907  CG  ASP   117     -16.430  37.268  12.028  1.00  0.00             
ATOM    908  OD1 ASP   117     -16.756  37.841  13.088  1.00  0.00             
ATOM    909  OD2 ASP   117     -17.227  37.061  11.089  1.00  0.00             
ATOM    910  N   GLY   118     -13.649  34.915  13.208  1.00  0.00             
ATOM    911  CA  GLY   118     -13.029  34.034  14.180  1.00  0.00             
ATOM    912  C   GLY   118     -12.149  32.983  13.532  1.00  0.00             
ATOM    913  O   GLY   118     -12.644  32.030  12.930  1.00  0.00             
ATOM    914  N   THR   119     -10.837  33.154  13.654  1.00  0.00             
ATOM    915  CA  THR   119      -9.863  32.193  13.063  1.00  0.00             
ATOM    916  C   THR   119      -8.465  32.798  12.989  1.00  0.00             
ATOM    917  O   THR   119      -7.811  32.748  11.947  1.00  0.00             
ATOM    918  CB  THR   119      -9.802  30.882  13.871  1.00  0.00             
ATOM    919  OG1 THR   119     -10.198  31.134  15.225  1.00  0.00             
ATOM    920  CG2 THR   119     -10.726  29.839  13.262  1.00  0.00             
ATOM    921  N   PHE   120      -8.014  33.370  14.100  1.00  0.00             
ATOM    922  CA  PHE   120      -6.694  33.986  14.164  1.00  0.00             
ATOM    923  C   PHE   120      -5.891  33.700  12.899  1.00  0.00             
ATOM    924  O   PHE   120      -5.369  32.600  12.719  1.00  0.00             
ATOM    925  CB  PHE   120      -6.818  35.496  14.378  1.00  0.00             
ATOM    926  CG  PHE   120      -6.159  35.985  15.637  1.00  0.00             
ATOM    927  CD1 PHE   120      -5.516  35.102  16.487  1.00  0.00             
ATOM    928  CD2 PHE   120      -6.185  37.327  15.972  1.00  0.00             
ATOM    929  CE1 PHE   120      -4.912  35.552  17.645  1.00  0.00             
ATOM    930  CE2 PHE   120      -5.580  37.777  17.130  1.00  0.00             
ATOM    931  CZ  PHE   120      -4.946  36.895  17.966  1.00  0.00             
ATOM    932  N   LYS   121      -5.796  34.697  12.026  1.00  0.00             
ATOM    933  CA  LYS   121      -5.056  34.555  10.777  1.00  0.00             
ATOM    934  C   LYS   121      -5.479  35.613   9.763  1.00  0.00             
ATOM    935  O   LYS   121      -6.504  35.479   9.094  1.00  0.00             
ATOM    936  CB  LYS   121      -3.551  34.643  11.033  1.00  0.00             
ATOM    937  CG  LYS   121      -2.778  33.401  10.619  1.00  0.00             
ATOM    938  CD  LYS   121      -1.292  33.557  10.901  1.00  0.00             
ATOM    939  CE  LYS   121      -0.519  32.314  10.488  1.00  0.00             
ATOM    940  NZ  LYS   121       0.938  32.452  10.758  1.00  0.00             
ATOM    941  N   PRO   122      -4.683  36.685   9.637  1.00  0.00             
ATOM    942  CA  PRO   122      -4.969  37.775   8.702  1.00  0.00             
ATOM    943  C   PRO   122      -5.401  39.046   9.427  1.00  0.00             
ATOM    944  O   PRO   122      -6.335  39.727   9.003  1.00  0.00             
ATOM    945  CB  PRO   122      -3.623  37.996   8.008  1.00  0.00             
ATOM    946  CG  PRO   122      -2.615  37.862   9.099  1.00  0.00             
ATOM    947  CD  PRO   122      -3.444  36.911  10.402  1.00  0.00             
TER
END
