
#######################################################
#                                                     #
#                        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   55 (  220),  selected   55 , name T0316TS307_2u-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS307_2u-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      -       -           -
LGA    R     221      -       -           -
LGA    M     222      G     220           #
LGA    M     223      R     221          3.544
LGA    T     224      M     222          2.700
LGA    V     225      M     223          4.862
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    D     226      M     230          1.868
LGA    G     227      G     231          0.492
LGA    R     228      E     232          2.323
LGA    D     229      H     233          2.313
LGA    M     230      A     234          2.680
LGA    E     232      G     235          1.360
LGA    H     233      L     236          1.332
LGA    A     234      M     237          2.992
LGA    G     235      Y     238          2.664
LGA    L     236      Y     239          4.150
LGA    M     237      T     240          4.090
LGA    Y     238      I     241          4.615
LGA    -       -      G     242           -
LGA    Y     239      Q     243          4.957
LGA    T     240      R     244          2.301
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    I     241      W     260          2.392
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    G     242      G     275          4.124
LGA    Q     243      Q     276           #
LGA    R     244      G     277          3.166
LGA    G     245      F     278          3.954
LGA    G     246      Y     279          1.337
LGA    L     247      H     280          1.233
LGA    G     248      D     281          2.894
LGA    I     249      -       -           -
LGA    G     250      -       -           -
LGA    G     251      -       -           -
LGA    Q     252      -       -           -
LGA    A     258      -       -           -
LGA    P     259      -       -           -
LGA    W     260      -       -           -
LGA    F     261      -       -           -
LGA    V     262      -       -           -
LGA    D     266      -       -           -
LGA    L     267      -       -           -
LGA    S     268      -       -           -
LGA    K     269      -       -           -
LGA    N     270      -       -           -
LGA    I     271      -       -           -
LGA    L     272      -       -           -
LGA    Y     273      -       -           -
LGA    V     274      S     282           #
LGA    G     275      L     283          2.443
LGA    Q     276      -       -           -
LGA    G     277      -       -           -
LGA    F     278      -       -           -
LGA    Y     279      -       -           -
LGA    H     280      -       -           -
LGA    D     281      -       -           -
LGA    S     282      -       -           -
LGA    L     283      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   55   60    5.0     25    3.07     8.00     25.266     0.788

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.248530 * X  +   0.944150 * Y  +  -0.216366 * Z  + -14.464446
  Y_new =  -0.340336 * X  +   0.294249 * Y  +   0.893078 * Z  + -60.756374
  Z_new =   0.906865 * X  +  -0.148320 * Y  +   0.394458 * Z  + -16.493612 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.359655    2.781938  [ DEG:   -20.6067    159.3933 ]
  Theta =  -1.135784   -2.005808  [ DEG:   -65.0756   -114.9244 ]
  Phi   =  -0.940056    2.201536  [ DEG:   -53.8613    126.1387 ]
 
# 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: T0316TS307_2u-D2                              
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS307_2u-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   55   60   5.0   25   3.07    8.00  25.266
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS307_2u-D2
PFRMAT   TS
TARGET   T0316
MODEL    2  UNREFINED
PARENT   1kor_A
ATOM     1   N   GLY   220      46.256  11.523 -19.746  1.00                    
ATOM     1   CA  GLY   220      45.236  10.859 -18.961  1.00                    
ATOM     1   C   GLY   220      44.192  11.802 -18.382  1.00                    
ATOM     1   O   GLY   220      43.137  11.359 -17.941  1.00                    
ATOM     1   N   ARG   221      44.475  13.102 -18.387  1.00                    
ATOM     1   CA  ARG   221      43.531  14.079 -17.842  1.00                    
ATOM     1   C   ARG   221      43.067  15.097 -18.876  1.00                    
ATOM     1   O   ARG   221      43.834  15.480 -19.760  1.00                    
ATOM     1   N   MET   222      41.801  15.548 -18.777  1.00                    
ATOM     1   CA  MET   222      41.256  16.536 -19.718  1.00                    
ATOM     1   C   MET   222      41.860  17.901 -19.388  1.00                    
ATOM     1   O   MET   222      41.860  18.320 -18.230  1.00                    
ATOM     1   N   MET   223      42.388  18.586 -20.398  1.00                    
ATOM     1   CA  MET   223      43.023  19.879 -20.173  1.00                    
ATOM     1   C   MET   223      42.425  21.060 -20.923  1.00                    
ATOM     1   O   MET   223      42.789  22.198 -20.655  1.00                    
ATOM     1   N   THR   224      41.520  20.795 -21.858  1.00                    
ATOM     1   CA  THR   224      40.904  21.863 -22.634  1.00                    
ATOM     1   C   THR   224      39.518  21.487 -23.136  1.00                    
ATOM     1   O   THR   224      39.213  20.312 -23.327  1.00                    
ATOM     1   N   VAL   225      38.682  22.503 -23.341  1.00                    
ATOM     1   CA  VAL   225      37.331  22.310 -23.851  1.00                    
ATOM     1   C   VAL   225      37.139  23.323 -24.976  1.00                    
ATOM     1   O   VAL   225      37.286  24.525 -24.772  1.00                    
ATOM     1   N   ASP   226      36.825  22.823 -26.163  1.00                    
ATOM     1   CA  ASP   226      36.634  23.668 -27.336  1.00                    
ATOM     1   C   ASP   226      37.855  24.536 -27.592  1.00                    
ATOM     1   O   ASP   226      37.734  25.695 -27.975  1.00                    
ATOM     1   N   GLY   227      39.035  23.969 -27.369  1.00                    
ATOM     1   CA  GLY   227      40.261  24.707 -27.599  1.00                    
ATOM     1   C   GLY   227      40.695  25.630 -26.473  1.00                    
ATOM     1   O   GLY   227      41.771  26.222 -26.537  1.00                    
ATOM     1   N   ARG   228      39.876  25.773 -25.438  1.00                    
ATOM     1   CA  ARG   228      40.255  26.642 -24.330  1.00                    
ATOM     1   C   ARG   228      40.850  25.839 -23.174  1.00                    
ATOM     1   O   ARG   228      40.198  24.939 -22.632  1.00                    
ATOM     1   N   ASP   229      42.091  26.144 -22.808  1.00                    
ATOM     1   CA  ASP   229      42.716  25.443 -21.696  1.00                    
ATOM     1   C   ASP   229      42.031  25.868 -20.394  1.00                    
ATOM     1   O   ASP   229      41.831  27.055 -20.143  1.00                    
ATOM     1   N   MET   230      41.655  24.885 -19.579  1.00                    
ATOM     1   CA  MET   230      40.960  25.145 -18.317  1.00                    
ATOM     1   C   MET   230      41.491  24.308 -17.154  1.00                    
ATOM     1   O   MET   230      41.830  23.137 -17.328  1.00                    
ATOM     1   N   GLU   232      41.546  24.914 -15.969  1.00                    
ATOM     1   CA  GLU   232      42.007  24.217 -14.774  1.00                    
ATOM     1   C   GLU   232      40.998  23.106 -14.485  1.00                    
ATOM     1   O   GLU   232      39.854  23.161 -14.948  1.00                    
ATOM     1   N   HIS   233      41.412  22.083 -13.719  1.00                    
ATOM     1   CA  HIS   233      40.534  20.962 -13.378  1.00                    
ATOM     1   C   HIS   233      39.106  21.349 -12.985  1.00                    
ATOM     1   O   HIS   233      38.150  20.906 -13.621  1.00                    
ATOM     1   N   ALA   234      38.957  22.174 -11.952  1.00                    
ATOM     1   CA  ALA   234      37.621  22.571 -11.507  1.00                    
ATOM     1   C   ALA   234      36.885  23.409 -12.549  1.00                    
ATOM     1   O   ALA   234      35.687  23.250 -12.742  1.00                    
ATOM     1   N   GLY   235      37.603  24.300 -13.218  1.00                    
ATOM     1   CA  GLY   235      36.986  25.140 -14.233  1.00                    
ATOM     1   C   GLY   235      36.504  24.286 -15.404  1.00                    
ATOM     1   O   GLY   235      35.449  24.545 -15.970  1.00                    
ATOM     1   N   LEU   236      37.272  23.255 -15.751  1.00                    
ATOM     1   CA  LEU   236      36.911  22.378 -16.863  1.00                    
ATOM     1   C   LEU   236      35.660  21.540 -16.578  1.00                    
ATOM     1   O   LEU   236      34.802  21.389 -17.446  1.00                    
ATOM     1   N   MET   237      35.553  20.994 -15.368  1.00                    
ATOM     1   CA  MET   237      34.382  20.191 -15.017  1.00                    
ATOM     1   C   MET   237      33.153  21.101 -15.026  1.00                    
ATOM     1   O   MET   237      32.074  20.718 -15.477  1.00                    
ATOM     1   N   TYR   238      33.334  22.312 -14.510  1.00                    
ATOM     1   CA  TYR   238      32.256  23.295 -14.447  1.00                    
ATOM     1   C   TYR   238      31.730  23.608 -15.846  1.00                    
ATOM     1   O   TYR   238      30.519  23.617 -16.087  1.00                    
ATOM     1   N   TYR   239      32.651  23.860 -16.767  1.00                    
ATOM     1   CA  TYR   239      32.287  24.174 -18.141  1.00                    
ATOM     1   C   TYR   239      31.500  23.030 -18.783  1.00                    
ATOM     1   O   TYR   239      30.480  23.253 -19.436  1.00                    
ATOM     1   N   THR   240      28.029  22.868 -17.533  1.00                    
ATOM     1   CA  THR   240      27.187  23.873 -18.183  1.00                    
ATOM     1   C   THR   240      26.732  23.373 -19.544  1.00                    
ATOM     1   O   THR   240      25.546  23.431 -19.878  1.00                    
ATOM     1   N   ILE   241      27.689  22.880 -20.328  1.00                    
ATOM     1   CA  ILE   241      27.419  22.376 -21.667  1.00                    
ATOM     1   C   ILE   241      26.563  21.104 -21.652  1.00                    
ATOM     1   O   ILE   241      25.583  20.998 -22.386  1.00                    
ATOM     1   N   GLY   242      26.935  20.133 -20.826  1.00                    
ATOM     1   CA  GLY   242      26.146  18.914 -20.745  1.00                    
ATOM     1   C   GLY   242      24.790  19.189 -20.111  1.00                    
ATOM     1   O   GLY   242      23.754  18.680 -20.559  1.00                    
ATOM     1   N   GLN   243      24.794  20.011 -19.068  1.00                    
ATOM     1   CA  GLN   243      23.557  20.339 -18.381  1.00                    
ATOM     1   C   GLN   243      22.478  20.913 -19.283  1.00                    
ATOM     1   O   GLN   243      21.338  20.459 -19.247  1.00                    
ATOM     1   N   ARG   244      22.837  21.904 -20.099  1.00                    
ATOM     1   CA  ARG   244      21.874  22.545 -20.997  1.00                    
ATOM     1   C   ARG   244      21.139  21.516 -21.851  1.00                    
ATOM     1   O   ARG   244      19.981  21.721 -22.210  1.00                    
ATOM     1   N   GLY   245      21.804  20.401 -22.161  1.00                    
ATOM     1   CA  GLY   245      21.182  19.368 -22.984  1.00                    
ATOM     1   C   GLY   245      20.568  18.187 -22.233  1.00                    
ATOM     1   O   GLY   245      20.053  17.258 -22.858  1.00                    
ATOM     1   N   GLY   246      20.619  18.222 -20.905  1.00                    
ATOM     1   CA  GLY   246      20.035  17.151 -20.111  1.00                    
ATOM     1   C   GLY   246      20.818  15.851 -20.058  1.00                    
ATOM     1   O   GLY   246      20.268  14.798 -19.742  1.00                    
ATOM     1   N   LEU   247      22.107  15.926 -20.358  1.00                    
ATOM     1   CA  LEU   247      22.979  14.754 -20.352  1.00                    
ATOM     1   C   LEU   247      23.355  14.259 -18.952  1.00                    
ATOM     1   O   LEU   247      23.402  15.039 -18.009  1.00                    
ATOM     1   N   GLY   248      23.623  12.956 -18.840  1.00                    
ATOM     1   CA  GLY   248      24.084  12.379 -17.588  1.00                    
ATOM     1   C   GLY   248      23.113  11.934 -16.511  1.00                    
ATOM     1   O   GLY   248      23.471  11.923 -15.333  1.00                    
ATOM     1   N   ILE   249      21.908  11.542 -16.901  1.00                    
ATOM     1   CA  ILE   249      20.911  11.107 -15.932  1.00                    
ATOM     1   C   ILE   249      20.839   9.591 -15.821  1.00                    
ATOM     1   O   ILE   249      20.652   8.895 -16.824  1.00                    
ATOM     1   N   GLY   250      20.970   9.094 -14.594  1.00                    
ATOM     1   CA  GLY   250      20.915   7.662 -14.315  1.00                    
ATOM     1   C   GLY   250      19.938   7.356 -13.165  1.00                    
ATOM     1   O   GLY   250      19.818   8.134 -12.217  1.00                    
ATOM     1   N   GLY   251      19.244   6.222 -13.265  1.00                    
ATOM     1   CA  GLY   251      18.254   5.792 -12.264  1.00                    
ATOM     1   C   GLY   251      18.547   4.327 -11.933  1.00                    
ATOM     1   O   GLY   251      18.270   3.440 -12.739  1.00                    
ATOM     1   N   GLN   252      19.071   4.066 -10.740  1.00                    
ATOM     1   CA  GLN   252      19.423   2.698 -10.374  1.00                    
ATOM     1   C   GLN   252      19.104   2.246  -8.957  1.00                    
ATOM     1   O   GLN   252      18.893   3.059  -8.065  1.00                    
ATOM     1   N   ALA   258      20.998   0.299  -6.282  1.00                    
ATOM     1   CA  ALA   258      22.366  -0.125  -5.987  1.00                    
ATOM     1   C   ALA   258      22.509  -0.926  -4.698  1.00                    
ATOM     1   O   ALA   258      21.642  -0.886  -3.824  1.00                    
ATOM     1   N   PRO   259      23.625  -1.637  -4.581  1.00                    
ATOM     1   CA  PRO   259      23.912  -2.415  -3.380  1.00                    
ATOM     1   C   PRO   259      24.826  -1.590  -2.482  1.00                    
ATOM     1   O   PRO   259      25.962  -1.294  -2.850  1.00                    
ATOM     1   N   TRP   260      24.340  -1.204  -1.306  1.00                    
ATOM     1   CA  TRP   260      25.178  -0.435  -0.399  1.00                    
ATOM     1   C   TRP   260      26.203  -1.364   0.235  1.00                    
ATOM     1   O   TRP   260      26.024  -2.578   0.236  1.00                    
ATOM     1   N   PHE   261      27.265  -0.784   0.779  1.00                    
ATOM     1   CA  PHE   261      28.319  -1.556   1.414  1.00                    
ATOM     1   C   PHE   261      27.824  -2.249   2.678  1.00                    
ATOM     1   O   PHE   261      28.240  -3.365   2.983  1.00                    
ATOM     1   N   VAL   262      26.927  -1.599   3.412  1.00                    
ATOM     1   CA  VAL   262      26.440  -2.201   4.640  1.00                    
ATOM     1   C   VAL   262      25.323  -3.235   4.487  1.00                    
ATOM     1   O   VAL   262      24.652  -3.569   5.460  1.00                    
ATOM     1   N   ASP   266      25.103  -3.731   3.267  1.00                    
ATOM     1   CA  ASP   266      24.113  -4.784   3.097  1.00                    
ATOM     1   C   ASP   266      22.789  -4.682   2.357  1.00                    
ATOM     1   O   ASP   266      22.314  -5.704   1.863  1.00                    
ATOM     1   N   LEU   267      22.172  -3.506   2.271  1.00                    
ATOM     1   CA  LEU   267      20.881  -3.415   1.583  1.00                    
ATOM     1   C   LEU   267      20.905  -2.667   0.266  1.00                    
ATOM     1   O   LEU   267      21.835  -1.909  -0.011  1.00                    
ATOM     1   N   SER   268      19.877  -2.891  -0.545  1.00                    
ATOM     1   CA  SER   268      19.765  -2.215  -1.828  1.00                    
ATOM     1   C   SER   268      19.091  -0.869  -1.580  1.00                    
ATOM     1   O   SER   268      18.306  -0.724  -0.646  1.00                    
ATOM     1   N   LYS   269      19.410   0.103  -2.423  1.00                    
ATOM     1   CA  LYS   269      18.890   1.458  -2.304  1.00                    
ATOM     1   C   LYS   269      18.639   2.024  -3.707  1.00                    
ATOM     1   O   LYS   269      19.450   1.815  -4.612  1.00                    
ATOM     1   N   ASN   270      17.515   2.720  -3.891  1.00                    
ATOM     1   CA  ASN   270      17.194   3.311  -5.186  1.00                    
ATOM     1   C   ASN   270      17.786   4.714  -5.248  1.00                    
ATOM     1   O   ASN   270      17.457   5.578  -4.429  1.00                    
ATOM     1   N   ILE   271      18.666   4.932  -6.220  1.00                    
ATOM     1   CA  ILE   271      19.298   6.229  -6.377  1.00                    
ATOM     1   C   ILE   271      19.137   6.819  -7.771  1.00                    
ATOM     1   O   ILE   271      19.002   6.091  -8.757  1.00                    
ATOM     1   N   LEU   272      19.133   8.148  -7.842  1.00                    
ATOM     1   CA  LEU   272      19.010   8.876  -9.105  1.00                    
ATOM     1   C   LEU   272      20.165   9.866  -9.144  1.00                    
ATOM     1   O   LEU   272      20.402  10.579  -8.170  1.00                    
ATOM     1   N   TYR   273      20.890   9.910 -10.258  1.00                    
ATOM     1   CA  TYR   273      22.044  10.800 -10.349  1.00                    
ATOM     1   C   TYR   273      22.180  11.547 -11.670  1.00                    
ATOM     1   O   TYR   273      21.918  10.994 -12.730  1.00                    
ATOM     1   N   VAL   274      22.596  12.811 -11.598  1.00                    
ATOM     1   CA  VAL   274      22.833  13.594 -12.805  1.00                    
ATOM     1   C   VAL   274      24.305  14.014 -12.772  1.00                    
ATOM     1   O   VAL   274      24.758  14.680 -11.842  1.00                    
ATOM     1   N   GLY   275      25.050  13.580 -13.788  1.00                    
ATOM     1   CA  GLY   275      26.486  13.854 -13.891  1.00                    
ATOM     1   C   GLY   275      26.779  14.328 -15.315  1.00                    
ATOM     1   O   GLY   275      27.459  13.642 -16.077  1.00                    
ATOM     1   N   GLN   276      26.266  15.510 -15.691  1.00                    
ATOM     1   CA  GLN   276      26.490  16.034 -17.042  1.00                    
ATOM     1   C   GLN   276      27.940  16.076 -17.515  1.00                    
ATOM     1   O   GLN   276      28.280  15.451 -18.519  1.00                    
ATOM     1   N   GLY   277      28.787  16.806 -16.796  1.00                    
ATOM     1   CA  GLY   277      30.185  16.915 -17.182  1.00                    
ATOM     1   C   GLY   277      30.962  15.604 -17.133  1.00                    
ATOM     1   O   GLY   277      31.713  15.284 -18.052  1.00                    
ATOM     1   N   PHE   278      32.779   9.330 -21.914  1.00                    
ATOM     1   CA  PHE   278      32.797   8.957 -23.320  1.00                    
ATOM     1   C   PHE   278      33.930   9.625 -24.100  1.00                    
ATOM     1   O   PHE   278      34.434   9.055 -25.062  1.00                    
ATOM     1   N   TYR   279      34.336  10.824 -23.682  1.00                    
ATOM     1   CA  TYR   279      35.427  11.527 -24.353  1.00                    
ATOM     1   C   TYR   279      36.720  10.751 -24.097  1.00                    
ATOM     1   O   TYR   279      37.519  10.527 -25.008  1.00                    
ATOM     1   N   HIS   280      36.916  10.346 -22.845  1.00                    
ATOM     1   CA  HIS   280      38.098   9.574 -22.477  1.00                    
ATOM     1   C   HIS   280      38.208   8.303 -23.316  1.00                    
ATOM     1   O   HIS   280      39.225   8.067 -23.953  1.00                    
ATOM     1   N   ASP   281      37.160   7.486 -23.303  1.00                    
ATOM     1   CA  ASP   281      37.163   6.244 -24.064  1.00                    
ATOM     1   C   ASP   281      37.401   6.498 -25.556  1.00                    
ATOM     1   O   ASP   281      38.023   5.682 -26.234  1.00                    
ATOM     1   N   SER   282      36.906   7.625 -26.065  1.00                    
ATOM     1   CA  SER   282      37.097   7.951 -27.476  1.00                    
ATOM     1   C   SER   282      38.586   8.136 -27.790  1.00                    
ATOM     1   O   SER   282      39.078   7.618 -28.794  1.00                    
ATOM     1   N   LEU   283      39.296   8.866 -26.931  1.00                    
ATOM     1   CA  LEU   283      40.725   9.091 -27.132  1.00                    
ATOM     1   C   LEU   283      41.482   7.781 -26.877  1.00                    
ATOM     1   O   LEU   283      42.464   7.474 -27.561  1.00                    
TER
END
