
#######################################################
#                                                     #
#                        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 (  179),  selected   24 , name T0347TS671_3-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS671_3-D2.T0347_D2.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    D     134      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    P     135      L     174          2.850
LGA    F     136      S     175          1.782
LGA    R     137      D     176          3.277
LGA    S     138      S     177          3.221
LGA    L     139      F     178          3.571
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    A     140      A     181          1.301
LGA    G     141      L     182          1.525
LGA    A     142      A     183          1.966
LGA    L     143      E     184          0.901
LGA    R     144      A     185          0.142
LGA    M     145      M     186          1.290
LGA    A     146      K     187          0.682
LGA    G     147      L     188          0.929
LGA    G     148      A     189          1.785
LGA    Y     149      K     190          1.573
LGA    A     150      S     191          1.967
LGA    K     151      -       -           -
LGA    V     152      R     192          2.206
LGA    I     153      E     193           -
LGA    I     154      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    P     155      V     203           #
LGA    F     156      E     204           -
LGA    S     157      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   71    5.0     17    2.05    23.53     21.477     0.792

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.529341 * X  +   0.571932 * Y  +   0.626651 * Z  +  14.823616
  Y_new =   0.817707 * X  +  -0.540831 * Y  +  -0.197123 * Z  +  44.994904
  Z_new =   0.226172 * X  +   0.616762 * Y  +  -0.753957 * Z  +  35.140797 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.455952   -0.685640  [ DEG:   140.7157    -39.2843 ]
  Theta =  -0.228146   -2.913447  [ DEG:   -13.0718   -166.9282 ]
  Phi   =   0.996287   -2.145305  [ DEG:    57.0830   -122.9169 ]
 
# 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: T0347TS671_3-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS671_3-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   71   5.0   17   2.05   23.53  21.477
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS671_3-D2
PFRMAT TS
TARGET T0347
MODEL  3  REFINED
PARENT 1VZ0_A 1R71_B 1ZX4_A
ATOM    870  N   ASP   134       8.837  62.453  -3.218  1.00  0.00
ATOM    871  CA  ASP   134       9.442  63.444  -2.416  1.00  0.00
ATOM    872  C   ASP   134      10.049  64.504  -3.437  1.00  0.00
ATOM    873  O   ASP   134       9.659  65.657  -3.342  1.00  0.00
ATOM    874  CB  ASP   134      10.470  62.819  -1.514  1.00  0.00
ATOM    875  CG  ASP   134      11.191  63.584  -0.454  1.00  0.00
ATOM    876  OD1 ASP   134      11.603  64.738  -0.694  1.00  0.00
ATOM    877  OD2 ASP   134      11.352  63.005   0.669  1.00  0.00
ATOM    878  N   PRO   135      10.863  64.099  -4.519  1.00  0.00
ATOM    879  CA  PRO   135      11.241  65.135  -5.503  1.00  0.00
ATOM    880  C   PRO   135       9.973  65.786  -6.086  1.00  0.00
ATOM    881  O   PRO   135      10.103  66.950  -6.542  1.00  0.00
ATOM    882  CB  PRO   135      11.980  64.531  -6.667  1.00  0.00
ATOM    883  CG  PRO   135      11.501  63.039  -6.614  1.00  0.00
ATOM    884  CD  PRO   135      10.994  62.768  -5.191  1.00  0.00
ATOM    885  N   PHE   136       8.960  65.024  -6.500  1.00  0.00
ATOM    886  CA  PHE   136       7.750  65.592  -7.010  1.00  0.00
ATOM    887  C   PHE   136       7.345  66.788  -6.131  1.00  0.00
ATOM    888  O   PHE   136       6.929  67.805  -6.724  1.00  0.00
ATOM    889  CB  PHE   136       6.706  64.485  -7.119  1.00  0.00
ATOM    890  CG  PHE   136       5.693  64.622  -8.228  1.00  0.00
ATOM    891  CD1 PHE   136       6.121  64.994  -9.503  1.00  0.00
ATOM    892  CD2 PHE   136       4.341  64.398  -7.979  1.00  0.00
ATOM    893  CE1 PHE   136       5.210  65.149 -10.547  1.00  0.00
ATOM    894  CE2 PHE   136       3.415  64.538  -9.007  1.00  0.00
ATOM    895  CZ  PHE   136       3.856  64.914 -10.278  1.00  0.00
ATOM    896  N   ARG   137       7.240  66.596  -4.795  1.00  0.00
ATOM    897  CA  ARG   137       6.956  67.738  -3.973  1.00  0.00
ATOM    898  C   ARG   137       8.009  68.778  -4.349  1.00  0.00
ATOM    899  O   ARG   137       7.684  69.837  -4.908  1.00  0.00
ATOM    900  CB  ARG   137       6.886  67.484  -2.495  1.00  0.00
ATOM    901  CG  ARG   137       6.005  66.390  -2.033  1.00  0.00
ATOM    902  CD  ARG   137       4.757  66.935  -1.363  1.00  0.00
ATOM    903  NE  ARG   137       4.032  65.905  -0.612  1.00  0.00
ATOM    904  CZ  ARG   137       3.610  64.746  -1.119  1.00  0.00
ATOM    905  NH1 ARG   137       2.958  63.886  -0.344  1.00  0.00
ATOM    906  NH2 ARG   137       3.841  64.436  -2.393  1.00  0.00
ATOM    907  N   SER   138       9.292  68.406  -4.095  1.00  0.00
ATOM    908  CA  SER   138      10.409  69.207  -4.478  1.00  0.00
ATOM    909  C   SER   138      11.766  68.413  -4.310  1.00  0.00
ATOM    910  O   SER   138      12.191  68.079  -3.180  1.00  0.00
ATOM    911  CB  SER   138      10.441  70.501  -3.620  1.00  0.00
ATOM    912  OG  SER   138      10.220  70.327  -2.222  1.00  0.00
ATOM    913  N   LEU   139      12.537  68.504  -5.411  1.00  0.00
ATOM    914  CA  LEU   139      13.954  68.041  -5.556  1.00  0.00
ATOM    915  C   LEU   139      14.289  66.576  -5.045  1.00  0.00
ATOM    916  O   LEU   139      14.167  65.693  -5.865  1.00  0.00
ATOM    917  CB  LEU   139      14.808  69.155  -4.950  1.00  0.00
ATOM    918  CG  LEU   139      14.719  70.593  -5.406  1.00  0.00
ATOM    919  CD1 LEU   139      15.617  71.472  -4.557  1.00  0.00
ATOM    920  CD2 LEU   139      15.120  70.725  -6.867  1.00  0.00
ATOM    921  N   ALA   140      15.364  66.525  -4.197  1.00  0.00
ATOM    922  CA  ALA   140      15.943  65.396  -3.396  1.00  0.00
ATOM    923  C   ALA   140      16.739  64.168  -4.004  1.00  0.00
ATOM    924  O   ALA   140      16.092  63.167  -4.366  1.00  0.00
ATOM    925  CB  ALA   140      14.758  64.835  -2.581  1.00  0.00
ATOM    926  N   GLY   141      18.074  64.234  -4.260  1.00  0.00
ATOM    927  CA  GLY   141      18.851  63.006  -4.625  1.00  0.00
ATOM    928  C   GLY   141      20.039  62.739  -3.638  1.00  0.00
ATOM    929  O   GLY   141      19.952  61.831  -2.800  1.00  0.00
ATOM    930  N   ALA   142      20.765  63.856  -3.419  1.00  0.00
ATOM    931  CA  ALA   142      21.994  63.964  -2.629  1.00  0.00
ATOM    932  C   ALA   142      21.676  64.526  -1.212  1.00  0.00
ATOM    933  O   ALA   142      22.617  64.549  -0.429  1.00  0.00
ATOM    934  CB  ALA   142      23.008  64.832  -3.393  1.00  0.00
ATOM    935  N   LEU   143      20.600  65.310  -1.010  1.00  0.00
ATOM    936  CA  LEU   143      20.236  65.796   0.311  1.00  0.00
ATOM    937  C   LEU   143      20.070  64.562   1.288  1.00  0.00
ATOM    938  O   LEU   143      20.404  64.695   2.466  1.00  0.00
ATOM    939  CB  LEU   143      19.075  66.834   0.326  1.00  0.00
ATOM    940  CG  LEU   143      18.408  67.325   1.648  1.00  0.00
ATOM    941  CD1 LEU   143      18.760  68.786   1.921  1.00  0.00
ATOM    942  CD2 LEU   143      16.924  67.098   1.611  1.00  0.00
ATOM    943  N   ARG   144      19.552  63.423   0.831  1.00  0.00
ATOM    944  CA  ARG   144      19.426  62.202   1.546  1.00  0.00
ATOM    945  C   ARG   144      20.841  61.630   1.845  1.00  0.00
ATOM    946  O   ARG   144      21.044  61.198   2.977  1.00  0.00
ATOM    947  CB  ARG   144      18.510  61.171   0.837  1.00  0.00
ATOM    948  CG  ARG   144      17.105  61.651   0.680  1.00  0.00
ATOM    949  CD  ARG   144      16.372  61.884   2.016  1.00  0.00
ATOM    950  NE  ARG   144      16.783  63.101   2.733  1.00  0.00
ATOM    951  CZ  ARG   144      17.177  63.148   4.014  1.00  0.00
ATOM    952  NH1 ARG   144      17.242  62.047   4.760  1.00  0.00
ATOM    953  NH2 ARG   144      17.471  64.323   4.568  1.00  0.00
ATOM    954  N   MET   145      21.707  61.403   0.830  1.00  0.00
ATOM    955  CA  MET   145      23.087  60.960   0.986  1.00  0.00
ATOM    956  C   MET   145      23.874  61.866   1.990  1.00  0.00
ATOM    957  O   MET   145      24.773  61.338   2.628  1.00  0.00
ATOM    958  CB  MET   145      23.716  60.961  -0.409  1.00  0.00
ATOM    959  CG  MET   145      24.856  59.973  -0.612  1.00  0.00
ATOM    960  SD  MET   145      24.366  58.260  -0.282  1.00  0.00
ATOM    961  CE  MET   145      25.867  57.529  -0.872  1.00  0.00
ATOM    962  N   ALA   146      23.770  63.205   1.897  1.00  0.00
ATOM    963  CA  ALA   146      24.392  64.135   2.833  1.00  0.00
ATOM    964  C   ALA   146      23.940  63.854   4.275  1.00  0.00
ATOM    965  O   ALA   146      24.836  63.784   5.141  1.00  0.00
ATOM    966  CB  ALA   146      24.139  65.564   2.350  1.00  0.00
ATOM    967  N   GLY   147      22.665  63.964   4.638  1.00  0.00
ATOM    968  CA  GLY   147      22.179  63.610   5.985  1.00  0.00
ATOM    969  C   GLY   147      22.639  62.179   6.456  1.00  0.00
ATOM    970  O   GLY   147      23.187  62.071   7.564  1.00  0.00
ATOM    971  N   GLY   148      22.270  61.139   5.729  1.00  0.00
ATOM    972  CA  GLY   148      22.562  59.741   6.109  1.00  0.00
ATOM    973  C   GLY   148      24.077  59.383   6.136  1.00  0.00
ATOM    974  O   GLY   148      24.497  58.760   7.103  1.00  0.00
ATOM    975  N   TYR   149      24.775  59.540   5.016  1.00  0.00
ATOM    976  CA  TYR   149      26.213  59.192   4.925  1.00  0.00
ATOM    977  C   TYR   149      27.114  60.038   5.860  1.00  0.00
ATOM    978  O   TYR   149      28.226  59.577   6.118  1.00  0.00
ATOM    979  CB  TYR   149      26.654  59.303   3.466  1.00  0.00
ATOM    980  CG  TYR   149      28.111  59.061   3.240  1.00  0.00
ATOM    981  CD1 TYR   149      28.618  57.767   3.270  1.00  0.00
ATOM    982  CD2 TYR   149      29.004  60.088   2.953  1.00  0.00
ATOM    983  CE1 TYR   149      29.967  57.506   3.012  1.00  0.00
ATOM    984  CE2 TYR   149      30.360  59.871   2.703  1.00  0.00
ATOM    985  CZ  TYR   149      30.830  58.554   2.710  1.00  0.00
ATOM    986  OH  TYR   149      32.150  58.329   2.460  1.00  0.00
ATOM    987  N   ALA   150      26.721  61.228   6.318  1.00  0.00
ATOM    988  CA  ALA   150      27.590  61.986   7.185  1.00  0.00
ATOM    989  C   ALA   150      27.386  61.489   8.605  1.00  0.00
ATOM    990  O   ALA   150      26.299  61.792   9.217  1.00  0.00
ATOM    991  CB  ALA   150      27.273  63.497   7.030  1.00  0.00
ATOM    992  N   LYS   151      28.270  60.632   9.124  1.00  0.00
ATOM    993  CA  LYS   151      28.085  60.116  10.494  1.00  0.00
ATOM    994  C   LYS   151      27.939  61.259  11.495  1.00  0.00
ATOM    995  O   LYS   151      28.525  62.340  11.284  1.00  0.00
ATOM    996  CB  LYS   151      29.170  59.125  10.926  1.00  0.00
ATOM    997  CG  LYS   151      29.771  58.257   9.874  1.00  0.00
ATOM    998  CD  LYS   151      29.409  56.904   9.439  1.00  0.00
ATOM    999  CE  LYS   151      28.120  56.539   9.152  1.00  0.00
ATOM   1000  NZ  LYS   151      27.888  55.312   8.320  1.00  0.00
ATOM   1001  N   VAL   152      26.894  61.119  12.292  1.00  0.00
ATOM   1002  CA  VAL   152      26.658  62.154  13.306  1.00  0.00
ATOM   1003  C   VAL   152      28.004  62.622  13.966  1.00  0.00
ATOM   1004  O   VAL   152      28.340  63.801  13.889  1.00  0.00
ATOM   1005  CB  VAL   152      25.637  61.631  14.322  1.00  0.00
ATOM   1006  CG1 VAL   152      25.503  62.538  15.571  1.00  0.00
ATOM   1007  CG2 VAL   152      24.261  61.486  13.712  1.00  0.00
ATOM   1008  N   ILE   153      28.819  61.731  14.570  1.00  0.00
ATOM   1009  CA  ILE   153      30.121  62.101  15.108  1.00  0.00
ATOM   1010  C   ILE   153      31.054  62.668  13.990  1.00  0.00
ATOM   1011  O   ILE   153      31.714  63.668  14.272  1.00  0.00
ATOM   1012  CB  ILE   153      30.796  60.868  15.802  1.00  0.00
ATOM   1013  CG1 ILE   153      29.976  60.542  17.090  1.00  0.00
ATOM   1014  CG2 ILE   153      32.303  61.072  16.196  1.00  0.00
ATOM   1015  CD1 ILE   153      30.348  59.288  17.929  1.00  0.00
ATOM   1016  N   ILE   154      31.082  62.088  12.752  1.00  0.00
ATOM   1017  CA  ILE   154      32.031  62.634  11.755  1.00  0.00
ATOM   1018  C   ILE   154      31.700  64.074  11.378  1.00  0.00
ATOM   1019  O   ILE   154      32.224  64.926  12.060  1.00  0.00
ATOM   1020  CB  ILE   154      32.306  61.688  10.584  1.00  0.00
ATOM   1021  CG1 ILE   154      32.739  60.292  11.136  1.00  0.00
ATOM   1022  CG2 ILE   154      33.346  62.217   9.550  1.00  0.00
ATOM   1023  CD1 ILE   154      32.527  59.172  10.084  1.00  0.00
ATOM   1024  N   PRO   155      30.981  64.516  10.313  1.00  0.00
ATOM   1025  CA  PRO   155      30.610  65.977  10.186  1.00  0.00
ATOM   1026  C   PRO   155      29.949  66.670  11.513  1.00  0.00
ATOM   1027  O   PRO   155      30.333  67.844  11.756  1.00  0.00
ATOM   1028  CB  PRO   155      29.829  66.313   8.802  1.00  0.00
ATOM   1029  CG  PRO   155      30.362  64.993   8.081  1.00  0.00
ATOM   1030  CD  PRO   155      30.362  63.860   9.155  1.00  0.00
ATOM   1031  N   PHE   156      28.960  66.132  12.285  1.00  0.00
ATOM   1032  CA  PHE   156      28.393  66.985  13.363  1.00  0.00
ATOM   1033  C   PHE   156      29.436  67.557  14.338  1.00  0.00
ATOM   1034  O   PHE   156      29.274  68.714  14.748  1.00  0.00
ATOM   1035  CB  PHE   156      27.241  66.309  14.126  1.00  0.00
ATOM   1036  CG  PHE   156      25.935  66.171  13.479  1.00  0.00
ATOM   1037  CD1 PHE   156      25.039  67.243  13.570  1.00  0.00
ATOM   1038  CD2 PHE   156      25.567  64.996  12.817  1.00  0.00
ATOM   1039  CE1 PHE   156      23.773  67.136  12.998  1.00  0.00
ATOM   1040  CE2 PHE   156      24.300  64.902  12.250  1.00  0.00
ATOM   1041  CZ  PHE   156      23.405  65.966  12.339  1.00  0.00
ATOM   1042  N   SER   157      30.295  66.691  14.887  1.00  0.00
ATOM   1043  CA  SER   157      31.398  67.039  15.778  1.00  0.00
ATOM   1044  C   SER   157      32.620  67.408  14.914  1.00  0.00
ATOM   1045  O   SER   157      33.269  68.439  15.128  1.00  0.00
ATOM   1046  CB  SER   157      31.665  65.827  16.710  1.00  0.00
ATOM   1047  OG  SER   157      30.949  65.909  17.978  1.00  0.00
ATOM   1048  OXT SER   157      32.859  66.658  13.951  1.00  0.00
TER
END
