
#######################################################
#                                                     #
#                        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    7 (   58),  selected    7 , name T0381TS268_1_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_1_2-D1.T0381_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    -       -      V      17           -
LGA    -       -      Q      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      A      21           -
LGA    -       -      R      22           -
LGA    -       -      G      23           -
LGA    -       -      L      24           -
LGA    -       -      A      25           -
LGA    -       -      V      26           -
LGA    -       -      I      27           -
LGA    -       -      R      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      D      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      N      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      R      37           -
LGA    -       -      T      38           -
LGA    -       -      L      39           -
LGA    -       -      S      40           -
LGA    -       -      D      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      T      46           -
LGA    -       -      D      47           -
LGA    -       -      L      48           -
LGA    -       -      T      49           -
LGA    -       -      R      50           -
LGA    S      71      A      51          2.555
LGA    A      72      T      52          2.836
LGA    F      73      A      53          2.446
LGA    W      74      R      54          1.435
LGA    -       -      R      55           -
LGA    -       -      F      56           -
LGA    L      75      L      57          0.728
LGA    T      76      L      58          1.948
LGA    -       -      T      59           -
LGA    -       -      L      60           -
LGA    P      77      V      61          0.648
LGA    -       -      E      62           -
LGA    -       -      L      63           -
LGA    -       -      G      64           -
LGA    -       -      Y      65           -
LGA    -       -      V      66           -
LGA    -       -      A      67           -
LGA    -       -      T      68           -
LGA    -       -      D      69           -
LGA    -       -      G      70           -
LGA    -       -      S      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      W      74           -
LGA    -       -      L      75           -
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   61    5.0      7    1.98    14.29     10.505     0.337

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.157067 * X  +   0.571439 * Y  +   0.805473 * Z  +  60.141602
  Y_new =  -0.882776 * X  +  -0.284415 * Y  +   0.373918 * Z  +  81.364769
  Z_new =   0.442760 * X  +  -0.769783 * Y  +   0.459780 * Z  +  13.141953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.032375    2.109218  [ DEG:   -59.1507    120.8493 ]
  Theta =  -0.458675   -2.682918  [ DEG:   -26.2801   -153.7198 ]
  Phi   =  -1.394715    1.746878  [ DEG:   -79.9113    100.0887 ]
 
# 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: T0381TS268_1_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_1_2-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   61   5.0    7   1.98   14.29  10.505
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_C
ATOM    549  N   SER    71       2.952  68.597  23.696  1.00  0.00
ATOM    550  CA  SER    71       2.028  67.614  23.087  1.00  0.00
ATOM    551  C   SER    71       2.684  66.274  23.070  1.00  0.00
ATOM    552  O   SER    71       3.003  65.715  24.117  1.00  0.00
ATOM    553  CB  SER    71       1.681  68.022  21.654  1.00  0.00
ATOM    554  OG  SER    71       2.827  67.983  20.821  1.00  0.00
ATOM    555  N   ALA    72       2.905  65.718  21.864  1.00  0.00
ATOM    556  CA  ALA    72       3.533  64.437  21.774  1.00  0.00
ATOM    557  C   ALA    72       4.953  64.620  22.183  1.00  0.00
ATOM    558  O   ALA    72       5.526  65.695  22.017  1.00  0.00
ATOM    559  CB  ALA    72       3.458  63.908  20.350  1.00  0.00
ATOM    560  N   PHE    73       5.556  63.563  22.757  1.00  0.00
ATOM    561  CA  PHE    73       6.920  63.668  23.172  1.00  0.00
ATOM    562  C   PHE    73       7.730  63.730  21.922  1.00  0.00
ATOM    563  O   PHE    73       7.483  62.990  20.972  1.00  0.00
ATOM    564  CB  PHE    73       7.319  62.454  24.015  1.00  0.00
ATOM    565  CG  PHE    73       6.705  62.438  25.384  1.00  0.00
ATOM    566  CD1 PHE    73       5.612  61.635  25.660  1.00  0.00
ATOM    567  CD2 PHE    73       7.218  63.228  26.399  1.00  0.00
ATOM    568  CE1 PHE    73       5.047  61.620  26.920  1.00  0.00
ATOM    569  CE2 PHE    73       6.653  63.213  27.659  1.00  0.00
ATOM    570  CZ  PHE    73       5.571  62.414  27.923  1.00  0.00
ATOM    571  N   TRP    74       8.716  64.645  21.883  1.00  0.00
ATOM    572  CA  TRP    74       9.517  64.776  20.704  1.00  0.00
ATOM    573  C   TRP    74      10.505  63.661  20.712  1.00  0.00
ATOM    574  O   TRP    74      11.058  63.315  21.752  1.00  0.00
ATOM    575  CB  TRP    74      10.245  66.122  20.698  1.00  0.00
ATOM    576  CG  TRP    74       9.333  67.296  20.511  1.00  0.00
ATOM    577  CD1 TRP    74       8.892  68.152  21.478  1.00  0.00
ATOM    578  CD2 TRP    74       8.751  67.743  19.281  1.00  0.00
ATOM    579  NE1 TRP    74       8.070  69.106  20.927  1.00  0.00
ATOM    580  CE2 TRP    74       7.968  68.875  19.577  1.00  0.00
ATOM    581  CE3 TRP    74       8.814  67.297  17.957  1.00  0.00
ATOM    582  CZ2 TRP    74       7.254  69.568  18.601  1.00  0.00
ATOM    583  CZ3 TRP    74       8.105  67.986  16.992  1.00  0.00
ATOM    584  CH2 TRP    74       7.336  69.109  17.315  1.00  0.00
ATOM    585  N   LEU    75      10.742  63.054  19.535  1.00  0.00
ATOM    586  CA  LEU    75      11.695  61.988  19.480  1.00  0.00
ATOM    587  C   LEU    75      12.906  62.553  18.817  1.00  0.00
ATOM    588  O   LEU    75      12.811  63.196  17.773  1.00  0.00
ATOM    589  CB  LEU    75      11.137  60.812  18.675  1.00  0.00
ATOM    590  CG  LEU    75       9.852  60.175  19.209  1.00  0.00
ATOM    591  CD1 LEU    75       9.365  59.081  18.271  1.00  0.00
ATOM    592  CD2 LEU    75      10.087  59.557  20.578  1.00  0.00
ATOM    593  N   THR    76      14.086  62.343  19.430  1.00  0.00
ATOM    594  CA  THR    76      15.285  62.856  18.841  1.00  0.00
ATOM    595  C   THR    76      16.227  61.713  18.673  1.00  0.00
ATOM    596  O   THR    76      16.238  60.764  19.456  1.00  0.00
ATOM    597  CB  THR    76      15.936  63.931  19.732  1.00  0.00
ATOM    598  OG1 THR    76      16.290  63.358  20.996  1.00  0.00
ATOM    599  CG2 THR    76      14.972  65.084  19.966  1.00  0.00
ATOM    600  N   PRO    77      16.996  61.783  17.627  1.00  0.00
ATOM    601  CA  PRO    77      17.977  60.767  17.374  1.00  0.00
ATOM    602  C   PRO    77      19.169  61.005  18.238  1.00  0.00
ATOM    603  O   PRO    77      19.345  62.125  18.717  1.00  0.00
ATOM    604  CB  PRO    77      18.301  60.927  15.888  1.00  0.00
ATOM    605  CG  PRO    77      18.107  62.382  15.616  1.00  0.00
ATOM    606  CD  PRO    77      16.934  62.808  16.453  1.00  0.00
TER
END
