
#######################################################
#                                                     #
#                        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_3_4-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_3_4-D1.T0382_D1.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    -       -      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          3.365
LGA    P     103      Q      12          2.664
LGA    Q     104      D      13          4.052
LGA    A     105      L      14          0.551
LGA    -       -      V      15           -
LGA    G     106      A      16          4.166
LGA    D     107      L      17          2.209
LGA    A     108      F      18          1.255
LGA    G     109      A      19          4.170
LGA    M     110      K      20          2.381
LGA    C     111      V      21          5.336
LGA    L     112      T      22          1.399
LGA    -       -      V      23           -
LGA    D     113      E      24          0.952
LGA    L     114      Q      25          4.311
LGA    L     115      D      26          2.098
LGA    D     116      D      27          2.623
LGA    -       -      A      28           -
LGA    D     117      L      29          3.118
LGA    G     118      L      30          2.117
LGA    T     119      G      31          2.204
LGA    -       -      N      32           -
LGA    F     120      Q      33          2.346
LGA    K     121      I      34          3.094
LGA    P     122      S      35          2.431
LGA    -       -      R      36           -
LGA    -       -      F      37           -
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     21    2.95     4.76     10.757     0.688

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.933166 * X  +   0.236638 * Y  +   0.270561 * Z  + -85.126991
  Y_new =   0.196193 * X  +  -0.966025 * Y  +   0.168236 * Z  +  42.837246
  Z_new =   0.301179 * X  +  -0.103910 * Y  +  -0.947889 * Z  + -48.423420 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.032406    0.109187  [ DEG:  -173.7441      6.2559 ]
  Theta =  -0.305929   -2.835664  [ DEG:   -17.5284   -162.4716 ]
  Phi   =   0.207226   -2.934367  [ DEG:    11.8732   -168.1268 ]
 
# 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-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_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   21   2.95    4.76  10.757
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A       
ATOM    795  N   PHE   102     -18.209  38.537 -13.039  1.00  0.00             
ATOM    796  CA  PHE   102     -17.209  37.532 -12.694  1.00  0.00             
ATOM    797  C   PHE   102     -17.202  37.254 -11.195  1.00  0.00             
ATOM    798  O   PHE   102     -16.366  37.772 -10.456  1.00  0.00             
ATOM    799  CB  PHE   102     -17.460  36.237 -13.469  1.00  0.00             
ATOM    800  CG  PHE   102     -16.317  35.830 -14.355  1.00  0.00             
ATOM    801  CD1 PHE   102     -15.167  36.596 -14.421  1.00  0.00             
ATOM    802  CD2 PHE   102     -16.392  34.680 -15.120  1.00  0.00             
ATOM    803  CE1 PHE   102     -14.115  36.221 -15.235  1.00  0.00             
ATOM    804  CE2 PHE   102     -15.340  34.305 -15.934  1.00  0.00             
ATOM    805  CZ  PHE   102     -14.205  35.069 -15.994  1.00  0.00             
ATOM    806  N   PRO   103     -18.144  36.421 -10.729  1.00  0.00             
ATOM    807  CA  PRO   103     -18.252  36.066  -9.310  1.00  0.00             
ATOM    808  C   PRO   103     -17.864  37.229  -8.404  1.00  0.00             
ATOM    809  O   PRO   103     -17.428  37.028  -7.271  1.00  0.00             
ATOM    810  CB  PRO   103     -19.740  35.746  -9.147  1.00  0.00             
ATOM    811  CG  PRO   103     -20.436  36.778  -9.970  1.00  0.00             
ATOM    812  CD  PRO   103     -19.175  35.764 -11.552  1.00  0.00             
ATOM    813  N   GLN   104     -18.025  38.447  -8.911  1.00  0.00             
ATOM    814  CA  GLN   104     -17.693  39.644  -8.149  1.00  0.00             
ATOM    815  C   GLN   104     -16.498  39.402  -7.233  1.00  0.00             
ATOM    816  O   GLN   104     -16.614  39.483  -6.011  1.00  0.00             
ATOM    817  CB  GLN   104     -17.405  40.816  -9.090  1.00  0.00             
ATOM    818  CG  GLN   104     -18.329  42.008  -8.898  1.00  0.00             
ATOM    819  CD  GLN   104     -18.014  43.147  -9.847  1.00  0.00             
ATOM    820  OE1 GLN   104     -18.671  44.188  -9.822  1.00  0.00             
ATOM    821  NE2 GLN   104     -17.005  42.953 -10.688  1.00  0.00             
ATOM    822  N   ALA   105     -15.351  39.101  -7.833  1.00  0.00             
ATOM    823  CA  ALA   105     -14.133  38.846  -7.074  1.00  0.00             
ATOM    824  C   ALA   105     -14.211  37.513  -6.338  1.00  0.00             
ATOM    825  O   ALA   105     -13.720  37.381  -5.217  1.00  0.00             
ATOM    826  CB  ALA   105     -12.920  38.867  -7.992  1.00  0.00             
ATOM    827  N   GLY   106     -14.833  36.525  -6.977  1.00  0.00             
ATOM    828  CA  GLY   106     -14.962  35.217  -6.364  1.00  0.00             
ATOM    829  C   GLY   106     -15.230  35.296  -4.874  1.00  0.00             
ATOM    830  O   GLY   106     -14.388  34.915  -4.061  1.00  0.00             
ATOM    831  N   ASP   107     -16.407  35.795  -4.511  1.00  0.00             
ATOM    832  CA  ASP   107     -16.785  35.925  -3.109  1.00  0.00             
ATOM    833  C   ASP   107     -15.973  37.015  -2.417  1.00  0.00             
ATOM    834  O   ASP   107     -15.974  37.119  -1.191  1.00  0.00             
ATOM    835  CB  ASP   107     -18.280  36.222  -2.982  1.00  0.00             
ATOM    836  CG  ASP   107     -19.020  35.162  -2.189  1.00  0.00             
ATOM    837  OD1 ASP   107     -19.907  35.528  -1.391  1.00  0.00             
ATOM    838  OD2 ASP   107     -18.711  33.965  -2.366  1.00  0.00             
ATOM    839  N   ALA   108     -15.281  37.825  -3.212  1.00  0.00             
ATOM    840  CA  ALA   108     -14.465  38.909  -2.679  1.00  0.00             
ATOM    841  C   ALA   108     -14.164  38.695  -1.200  1.00  0.00             
ATOM    842  O   ALA   108     -14.601  39.472  -0.349  1.00  0.00             
ATOM    843  CB  ALA   108     -13.169  39.031  -3.465  1.00  0.00             
ATOM    844  N   GLY   109     -13.417  37.639  -0.899  1.00  0.00             
ATOM    845  CA  GLY   109     -13.072  37.345   0.480  1.00  0.00             
ATOM    846  C   GLY   109     -14.290  37.041   1.330  1.00  0.00             
ATOM    847  O   GLY   109     -14.201  36.967   2.555  1.00  0.00             
ATOM    848  N   MET   110     -15.436  36.864   0.679  1.00  0.00             
ATOM    849  CA  MET   110     -16.677  36.567   1.382  1.00  0.00             
ATOM    850  C   MET   110     -16.534  36.802   2.881  1.00  0.00             
ATOM    851  O   MET   110     -16.534  35.858   3.672  1.00  0.00             
ATOM    852  CB  MET   110     -17.825  37.412   0.824  1.00  0.00             
ATOM    853  CG  MET   110     -18.973  36.598   0.250  1.00  0.00             
ATOM    854  SD  MET   110     -20.302  37.632  -0.395  1.00  0.00             
ATOM    855  CE  MET   110     -21.450  36.384  -0.975  1.00  0.00             
ATOM    856  N   CYS   111     -16.410  38.068   3.267  1.00  0.00             
ATOM    857  CA  CYS   111     -16.263  38.430   4.673  1.00  0.00             
ATOM    858  C   CYS   111     -14.908  37.993   5.216  1.00  0.00             
ATOM    859  O   CYS   111     -14.763  37.730   6.410  1.00  0.00             
ATOM    860  CB  CYS   111     -16.444  39.938   4.858  1.00  0.00             
ATOM    861  SG  CYS   111     -17.818  40.401   5.962  1.00  0.00             
ATOM    862  N   LEU   112     -13.918  37.917   4.333  1.00  0.00             
ATOM    863  CA  LEU   112     -12.572  37.512   4.724  1.00  0.00             
ATOM    864  C   LEU   112     -12.604  36.597   5.943  1.00  0.00             
ATOM    865  O   LEU   112     -11.946  36.864   6.949  1.00  0.00             
ATOM    866  CB  LEU   112     -11.864  36.815   3.560  1.00  0.00             
ATOM    867  CG  LEU   112     -10.571  37.466   3.065  1.00  0.00             
ATOM    868  CD1 LEU   112      -9.622  36.418   2.505  1.00  0.00             
ATOM    869  CD2 LEU   112      -9.907  38.258   4.181  1.00  0.00             
ATOM    870  N   ASP   113     -13.372  35.516   5.846  1.00  0.00             
ATOM    871  CA  ASP   113     -13.489  34.560   6.939  1.00  0.00             
ATOM    872  C   ASP   113     -13.934  35.247   8.227  1.00  0.00             
ATOM    873  O   ASP   113     -13.452  34.922   9.312  1.00  0.00             
ATOM    874  CB  ASP   113     -14.472  33.445   6.573  1.00  0.00             
ATOM    875  CG  ASP   113     -13.827  32.073   6.588  1.00  0.00             
ATOM    876  OD1 ASP   113     -14.481  31.115   7.053  1.00  0.00             
ATOM    877  OD2 ASP   113     -12.669  31.956   6.135  1.00  0.00             
ATOM    878  N   LEU   114     -14.854  36.197   8.098  1.00  0.00             
ATOM    879  CA  LEU   114     -15.363  36.930   9.251  1.00  0.00             
ATOM    880  C   LEU   114     -14.249  37.235  10.247  1.00  0.00             
ATOM    881  O   LEU   114     -14.363  36.923  11.433  1.00  0.00             
ATOM    882  CB  LEU   114     -16.038  38.229   8.803  1.00  0.00             
ATOM    883  CG  LEU   114     -17.517  38.384   9.163  1.00  0.00             
ATOM    884  CD1 LEU   114     -17.871  39.850   9.360  1.00  0.00             
ATOM    885  CD2 LEU   114     -17.855  37.575  10.406  1.00  0.00             
ATOM    886  N   LEU   115     -13.175  37.844   9.759  1.00  0.00             
ATOM    887  CA  LEU   115     -12.039  38.191  10.605  1.00  0.00             
ATOM    888  C   LEU   115     -11.560  36.985  11.406  1.00  0.00             
ATOM    889  O   LEU   115     -11.198  37.110  12.576  1.00  0.00             
ATOM    890  CB  LEU   115     -10.893  38.752   9.761  1.00  0.00             
ATOM    891  CG  LEU   115     -10.443  40.177  10.089  1.00  0.00             
ATOM    892  CD1 LEU   115      -8.964  40.358   9.783  1.00  0.00             
ATOM    893  CD2 LEU   115     -10.740  40.513  11.542  1.00  0.00             
ATOM    894  N   ASP   116     -11.560  35.820  10.768  1.00  0.00             
ATOM    895  CA  ASP   116     -11.124  34.590  11.420  1.00  0.00             
ATOM    896  C   ASP   116     -11.626  34.521  12.857  1.00  0.00             
ATOM    897  O   ASP   116     -11.491  33.494  13.524  1.00  0.00             
ATOM    898  CB  ASP   116     -11.608  33.368  10.635  1.00  0.00             
ATOM    899  CG  ASP   116     -10.465  32.497  10.151  1.00  0.00             
ATOM    900  OD1 ASP   116     -10.600  31.257  10.206  1.00  0.00             
ATOM    901  OD2 ASP   116      -9.434  33.055   9.718  1.00  0.00             
ATOM    902  N   ASP   117     -12.204  35.620  13.332  1.00  0.00             
ATOM    903  CA  ASP   117     -12.726  35.687  14.691  1.00  0.00             
ATOM    904  C   ASP   117     -12.149  34.572  15.558  1.00  0.00             
ATOM    905  O   ASP   117     -12.522  33.408  15.416  1.00  0.00             
ATOM    906  CB  ASP   117     -12.422  37.049  15.315  1.00  0.00             
ATOM    907  CG  ASP   117     -13.677  37.799  15.719  1.00  0.00             
ATOM    908  OD1 ASP   117     -13.671  38.432  16.795  1.00  0.00             
ATOM    909  OD2 ASP   117     -14.667  37.752  14.959  1.00  0.00             
ATOM    910  N   GLY   118     -11.239  34.938  16.456  1.00  0.00             
ATOM    911  CA  GLY   118     -10.629  33.955  17.330  1.00  0.00             
ATOM    912  C   GLY   118     -10.117  32.744  16.574  1.00  0.00             
ATOM    913  O   GLY   118     -10.898  31.907  16.122  1.00  0.00             
ATOM    914  N   THR   119      -8.798  32.647  16.438  1.00  0.00             
ATOM    915  CA  THR   119      -8.168  31.505  15.717  1.00  0.00             
ATOM    916  C   THR   119      -6.720  31.815  15.351  1.00  0.00             
ATOM    917  O   THR   119      -6.305  31.628  14.208  1.00  0.00             
ATOM    918  CB  THR   119      -8.211  30.214  16.555  1.00  0.00             
ATOM    919  OG1 THR   119      -8.277  30.548  17.947  1.00  0.00             
ATOM    920  CG2 THR   119      -9.423  29.375  16.182  1.00  0.00             
ATOM    921  N   PHE   120      -5.957  32.289  16.330  1.00  0.00             
ATOM    922  CA  PHE   120      -4.555  32.626  16.113  1.00  0.00             
ATOM    923  C   PHE   120      -4.086  32.176  14.734  1.00  0.00             
ATOM    924  O   PHE   120      -3.837  30.992  14.508  1.00  0.00             
ATOM    925  CB  PHE   120      -4.333  34.130  16.280  1.00  0.00             
ATOM    926  CG  PHE   120      -3.360  34.483  17.368  1.00  0.00             
ATOM    927  CD1 PHE   120      -2.750  33.493  18.119  1.00  0.00             
ATOM    928  CD2 PHE   120      -3.054  35.805  17.641  1.00  0.00             
ATOM    929  CE1 PHE   120      -1.855  33.818  19.120  1.00  0.00             
ATOM    930  CE2 PHE   120      -2.158  36.129  18.642  1.00  0.00             
ATOM    931  CZ  PHE   120      -1.559  35.143  19.380  1.00  0.00             
ATOM    932  N   LYS   121      -3.969  33.128  13.815  1.00  0.00             
ATOM    933  CA  LYS   121      -3.529  32.832  12.456  1.00  0.00             
ATOM    934  C   LYS   121      -3.924  33.948  11.494  1.00  0.00             
ATOM    935  O   LYS   121      -5.065  34.022  11.039  1.00  0.00             
ATOM    936  CB  LYS   121      -2.016  32.615  12.418  1.00  0.00             
ATOM    937  CG  LYS   121      -1.599  31.240  11.922  1.00  0.00             
ATOM    938  CD  LYS   121      -0.086  31.093  11.908  1.00  0.00             
ATOM    939  CE  LYS   121       0.331  29.719  11.412  1.00  0.00             
ATOM    940  NZ  LYS   121       1.812  29.559  11.394  1.00  0.00             
ATOM    941  N   PRO   122      -2.972  34.836  11.172  1.00  0.00             
ATOM    942  CA  PRO   122      -3.215  35.957  10.259  1.00  0.00             
ATOM    943  C   PRO   122      -3.237  37.293  10.995  1.00  0.00             
ATOM    944  O   PRO   122      -4.082  38.146  10.726  1.00  0.00             
ATOM    945  CB  PRO   122      -2.013  35.897   9.314  1.00  0.00             
ATOM    946  CG  PRO   122      -0.858  35.568  10.199  1.00  0.00             
ATOM    947  CD  PRO   122      -1.589  34.812  11.676  1.00  0.00             
TER
END
