
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_4_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          1.398
LGA    A      72      T      52          2.568
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      R      55           -
LGA    F      73      F      56          1.597
LGA    W      74      L      57          1.755
LGA    -       -      L      58           -
LGA    -       -      T      59           -
LGA    L      75      L      60          1.168
LGA    T      76      V      61          1.529
LGA    P      77      E      62          1.142
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    1.66    28.57     10.598     0.399

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.157166 * X  +   0.866098 * Y  +  -0.474525 * Z  +  -2.856805
  Y_new =  -0.284444 * X  +  -0.420435 * Y  +  -0.861583 * Z  +  60.337639
  Z_new =  -0.945722 * X  +   0.270387 * Y  +   0.180278 * Z  +  60.447903 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.982742   -2.158851  [ DEG:    56.3070   -123.6930 ]
  Theta =   1.239810    1.901783  [ DEG:    71.0359    108.9641 ]
  Phi   =  -1.066008    2.075585  [ DEG:   -61.0777    118.9223 ]
 
# 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_4_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_4_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   1.66   28.57  10.598
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_A
ATOM    549  N   SER    71       5.353  68.166  23.906  1.00  0.00
ATOM    550  CA  SER    71       5.414  67.403  22.636  1.00  0.00
ATOM    551  C   SER    71       5.517  65.945  22.944  1.00  0.00
ATOM    552  O   SER    71       5.031  65.487  23.976  1.00  0.00
ATOM    553  CB  SER    71       6.632  67.829  21.813  1.00  0.00
ATOM    554  OG  SER    71       7.839  67.486  22.472  1.00  0.00
ATOM    555  N   ALA    72       6.150  65.172  22.041  1.00  0.00
ATOM    556  CA  ALA    72       6.322  63.765  22.250  1.00  0.00
ATOM    557  C   ALA    72       7.789  63.537  22.329  1.00  0.00
ATOM    558  O   ALA    72       8.563  64.196  21.637  1.00  0.00
ATOM    559  CB  ALA    72       5.716  62.980  21.097  1.00  0.00
ATOM    560  N   PHE    73       8.226  62.591  23.181  1.00  0.00
ATOM    561  CA  PHE    73       9.640  62.420  23.274  1.00  0.00
ATOM    562  C   PHE    73      10.026  61.162  22.575  1.00  0.00
ATOM    563  O   PHE    73       9.571  60.071  22.917  1.00  0.00
ATOM    564  CB  PHE    73      10.075  62.334  24.738  1.00  0.00
ATOM    565  CG  PHE    73       9.886  63.612  25.503  1.00  0.00
ATOM    566  CD1 PHE    73       8.698  63.870  26.166  1.00  0.00
ATOM    567  CD2 PHE    73      10.895  64.558  25.560  1.00  0.00
ATOM    568  CE1 PHE    73       8.525  65.047  26.869  1.00  0.00
ATOM    569  CE2 PHE    73      10.721  65.734  26.264  1.00  0.00
ATOM    570  CZ  PHE    73       9.542  65.981  26.916  1.00  0.00
ATOM    571  N   TRP    74      10.887  61.306  21.553  1.00  0.00
ATOM    572  CA  TRP    74      11.444  60.184  20.866  1.00  0.00
ATOM    573  C   TRP    74      12.915  60.382  20.852  1.00  0.00
ATOM    574  O   TRP    74      13.415  61.439  21.235  1.00  0.00
ATOM    575  CB  TRP    74      10.902  60.108  19.437  1.00  0.00
ATOM    576  CG  TRP    74      11.205  61.323  18.615  1.00  0.00
ATOM    577  CD1 TRP    74      10.475  62.475  18.555  1.00  0.00
ATOM    578  CD2 TRP    74      12.321  61.507  17.735  1.00  0.00
ATOM    579  NE1 TRP    74      11.066  63.366  17.692  1.00  0.00
ATOM    580  CE2 TRP    74      12.202  62.795  17.175  1.00  0.00
ATOM    581  CE3 TRP    74      13.409  60.710  17.366  1.00  0.00
ATOM    582  CZ2 TRP    74      13.129  63.302  16.267  1.00  0.00
ATOM    583  CZ3 TRP    74      14.325  61.218  16.466  1.00  0.00
ATOM    584  CH2 TRP    74      14.183  62.501  15.924  1.00  0.00
ATOM    585  N   LEU    75      13.654  59.342  20.436  1.00  0.00
ATOM    586  CA  LEU    75      15.081  59.414  20.473  1.00  0.00
ATOM    587  C   LEU    75      15.546  60.333  19.389  1.00  0.00
ATOM    588  O   LEU    75      15.075  60.266  18.254  1.00  0.00
ATOM    589  CB  LEU    75      15.693  58.029  20.258  1.00  0.00
ATOM    590  CG  LEU    75      17.217  57.938  20.362  1.00  0.00
ATOM    591  CD1 LEU    75      17.679  58.244  21.778  1.00  0.00
ATOM    592  CD2 LEU    75      17.699  56.542  19.995  1.00  0.00
ATOM    593  N   THR    76      16.481  61.236  19.746  1.00  0.00
ATOM    594  CA  THR    76      17.126  62.118  18.815  1.00  0.00
ATOM    595  C   THR    76      18.515  62.285  19.344  1.00  0.00
ATOM    596  O   THR    76      18.782  61.926  20.487  1.00  0.00
ATOM    597  CB  THR    76      16.406  63.477  18.732  1.00  0.00
ATOM    598  OG1 THR    76      16.984  64.263  17.682  1.00  0.00
ATOM    599  CG2 THR    76      16.541  64.232  20.045  1.00  0.00
ATOM    600  N   PRO    77      19.422  62.786  18.555  1.00  0.00
ATOM    601  CA  PRO    77      20.738  62.974  19.101  1.00  0.00
ATOM    602  C   PRO    77      20.752  64.153  20.013  1.00  0.00
ATOM    603  O   PRO    77      20.061  65.127  19.725  1.00  0.00
ATOM    604  CB  PRO    77      21.621  63.195  17.871  1.00  0.00
ATOM    605  CG  PRO    77      20.853  62.586  16.746  1.00  0.00
ATOM    606  CD  PRO    77      19.403  62.841  17.046  1.00  0.00
TER
END
