
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_5_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    -       -      A      51           -
LGA    -       -      T      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    S      71      R      55          2.420
LGA    A      72      F      56          1.667
LGA    F      73      L      57          2.430
LGA    W      74      L      58          3.440
LGA    -       -      T      59           -
LGA    -       -      L      60           -
LGA    L      75      V      61          1.472
LGA    -       -      E      62           -
LGA    -       -      L      63           -
LGA    T      76      G      64          2.029
LGA    P      77      Y      65          2.035
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    2.29     0.00      8.879     0.293

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.077011 * X  +   0.979324 * Y  +   0.187068 * Z  +  20.340420
  Y_new =  -0.982860 * X  +  -0.106089 * Y  +   0.150771 * Z  +  93.814934
  Z_new =   0.167499 * X  +  -0.172250 * Y  +   0.970708 * Z  +  35.465603 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.175620    2.965973  [ DEG:   -10.0623    169.9377 ]
  Theta =  -0.168292   -2.973300  [ DEG:    -9.6424   -170.3576 ]
  Phi   =  -1.648991    1.492602  [ DEG:   -94.4802     85.5198 ]
 
# 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_5_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_5_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   2.29    0.00   8.879
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_A
ATOM    549  N   SER    71       8.575  67.140  24.125  1.00  0.00
ATOM    550  CA  SER    71       8.217  65.727  24.371  1.00  0.00
ATOM    551  C   SER    71       9.293  64.826  23.876  1.00  0.00
ATOM    552  O   SER    71      10.477  65.147  23.963  1.00  0.00
ATOM    553  CB  SER    71       6.916  65.370  23.650  1.00  0.00
ATOM    554  OG  SER    71       6.573  64.011  23.859  1.00  0.00
ATOM    555  N   ALA    72       8.903  63.650  23.352  1.00  0.00
ATOM    556  CA  ALA    72       9.894  62.734  22.882  1.00  0.00
ATOM    557  C   ALA    72      10.467  63.254  21.608  1.00  0.00
ATOM    558  O   ALA    72       9.769  63.820  20.768  1.00  0.00
ATOM    559  CB  ALA    72       9.276  61.367  22.634  1.00  0.00
ATOM    560  N   PHE    73      11.792  63.086  21.463  1.00  0.00
ATOM    561  CA  PHE    73      12.497  63.422  20.267  1.00  0.00
ATOM    562  C   PHE    73      13.479  62.313  20.099  1.00  0.00
ATOM    563  O   PHE    73      13.805  61.629  21.066  1.00  0.00
ATOM    564  CB  PHE    73      13.195  64.775  20.419  1.00  0.00
ATOM    565  CG  PHE    73      14.274  64.786  21.465  1.00  0.00
ATOM    566  CD1 PHE    73      15.585  64.495  21.130  1.00  0.00
ATOM    567  CD2 PHE    73      13.978  65.087  22.783  1.00  0.00
ATOM    568  CE1 PHE    73      16.578  64.505  22.092  1.00  0.00
ATOM    569  CE2 PHE    73      14.970  65.098  23.745  1.00  0.00
ATOM    570  CZ  PHE    73      16.265  64.808  23.404  1.00  0.00
ATOM    571  N   TRP    74      13.970  62.074  18.870  1.00  0.00
ATOM    572  CA  TRP    74      14.823  60.930  18.759  1.00  0.00
ATOM    573  C   TRP    74      16.223  61.316  18.437  1.00  0.00
ATOM    574  O   TRP    74      16.491  62.289  17.734  1.00  0.00
ATOM    575  CB  TRP    74      14.329  59.999  17.650  1.00  0.00
ATOM    576  CG  TRP    74      12.972  59.422  17.911  1.00  0.00
ATOM    577  CD1 TRP    74      11.770  59.945  17.530  1.00  0.00
ATOM    578  CD2 TRP    74      12.676  58.207  18.613  1.00  0.00
ATOM    579  NE1 TRP    74      10.744  59.134  17.951  1.00  0.00
ATOM    580  CE2 TRP    74      11.275  58.059  18.619  1.00  0.00
ATOM    581  CE3 TRP    74      13.459  57.232  19.238  1.00  0.00
ATOM    582  CZ2 TRP    74      10.641  56.975  19.224  1.00  0.00
ATOM    583  CZ3 TRP    74      12.825  56.158  19.836  1.00  0.00
ATOM    584  CH2 TRP    74      11.432  56.036  19.827  1.00  0.00
ATOM    585  N   LEU    75      17.154  60.527  19.005  1.00  0.00
ATOM    586  CA  LEU    75      18.559  60.632  18.761  1.00  0.00
ATOM    587  C   LEU    75      18.879  59.356  18.067  1.00  0.00
ATOM    588  O   LEU    75      18.181  58.361  18.258  1.00  0.00
ATOM    589  CB  LEU    75      19.323  60.779  20.078  1.00  0.00
ATOM    590  CG  LEU    75      18.949  61.980  20.949  1.00  0.00
ATOM    591  CD1 LEU    75      19.722  61.956  22.259  1.00  0.00
ATOM    592  CD2 LEU    75      19.267  63.284  20.232  1.00  0.00
ATOM    593  N   THR    76      19.921  59.332  17.221  1.00  0.00
ATOM    594  CA  THR    76      20.161  58.078  16.580  1.00  0.00
ATOM    595  C   THR    76      20.757  57.154  17.585  1.00  0.00
ATOM    596  O   THR    76      21.590  57.520  18.417  1.00  0.00
ATOM    597  CB  THR    76      21.131  58.227  15.392  1.00  0.00
ATOM    598  OG1 THR    76      20.575  59.132  14.430  1.00  0.00
ATOM    599  CG2 THR    76      21.367  56.881  14.725  1.00  0.00
ATOM    600  N   PRO    77      20.321  55.930  17.443  1.00  0.00
ATOM    601  CA  PRO    77      20.639  54.864  18.352  1.00  0.00
ATOM    602  C   PRO    77      22.112  54.789  18.522  1.00  0.00
ATOM    603  O   PRO    77      22.837  55.292  17.664  1.00  0.00
ATOM    604  CB  PRO    77      20.070  53.616  17.673  1.00  0.00
ATOM    605  CG  PRO    77      18.967  54.131  16.810  1.00  0.00
ATOM    606  CD  PRO    77      19.438  55.453  16.274  1.00  0.00
TER
END
