
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_3_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    S      71      L      20          1.705
LGA    A      72      A      21          0.484
LGA    F      73      R      22          3.294
LGA    -       -      G      23           -
LGA    -       -      L      24           -
LGA    W      74      A      25          0.405
LGA    -       -      V      26           -
LGA    -       -      I      27           -
LGA    L      75      R      28          1.312
LGA    T      76      C      29          0.390
LGA    P      77      F      30          0.646
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    -       -      R      55           -
LGA    -       -      F      56           -
LGA    -       -      L      57           -
LGA    -       -      L      58           -
LGA    -       -      T      59           -
LGA    -       -      L      60           -
LGA    -       -      V      61           -
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    1.53    14.29     10.900     0.429

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.948316 * X  +   0.316504 * Y  +   0.022831 * Z  +   0.311122
  Y_new =   0.171184 * X  +  -0.570831 * Y  +   0.803025 * Z  +  69.526649
  Z_new =   0.267194 * X  +  -0.757613 * Y  +  -0.595508 * Z  + -27.053682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.236962    0.904630  [ DEG:  -128.1685     51.8315 ]
  Theta =  -0.270480   -2.871113  [ DEG:   -15.4973   -164.5027 ]
  Phi   =   0.178590   -2.963002  [ DEG:    10.2325   -169.7675 ]
 
# 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_3_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_3_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   1.53   14.29  10.900
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_C
ATOM    549  N   SER    71      11.340  57.591  30.395  1.00  0.00
ATOM    550  CA  SER    71      10.433  56.752  31.211  1.00  0.00
ATOM    551  C   SER    71      10.000  55.563  30.423  1.00  0.00
ATOM    552  O   SER    71      10.819  54.876  29.816  1.00  0.00
ATOM    553  CB  SER    71       9.194  57.548  31.623  1.00  0.00
ATOM    554  OG  SER    71       8.417  57.905  30.492  1.00  0.00
ATOM    555  N   ALA    72       8.683  55.287  30.420  1.00  0.00
ATOM    556  CA  ALA    72       8.207  54.162  29.677  1.00  0.00
ATOM    557  C   ALA    72       8.445  54.471  28.241  1.00  0.00
ATOM    558  O   ALA    72       8.342  55.620  27.815  1.00  0.00
ATOM    559  CB  ALA    72       6.725  53.943  29.937  1.00  0.00
ATOM    560  N   PHE    73       8.796  53.439  27.453  1.00  0.00
ATOM    561  CA  PHE    73       9.053  53.675  26.068  1.00  0.00
ATOM    562  C   PHE    73       8.112  52.808  25.301  1.00  0.00
ATOM    563  O   PHE    73       7.890  51.649  25.649  1.00  0.00
ATOM    564  CB  PHE    73      10.501  53.321  25.724  1.00  0.00
ATOM    565  CG  PHE    73      10.830  53.465  24.265  1.00  0.00
ATOM    566  CD1 PHE    73      11.078  54.711  23.716  1.00  0.00
ATOM    567  CD2 PHE    73      10.892  52.354  23.442  1.00  0.00
ATOM    568  CE1 PHE    73      11.381  54.844  22.375  1.00  0.00
ATOM    569  CE2 PHE    73      11.195  52.487  22.100  1.00  0.00
ATOM    570  CZ  PHE    73      11.438  53.725  21.566  1.00  0.00
ATOM    571  N   TRP    74       7.514  53.368  24.234  1.00  0.00
ATOM    572  CA  TRP    74       6.600  52.610  23.434  1.00  0.00
ATOM    573  C   TRP    74       7.384  52.168  22.248  1.00  0.00
ATOM    574  O   TRP    74       8.194  52.927  21.718  1.00  0.00
ATOM    575  CB  TRP    74       5.411  53.475  23.012  1.00  0.00
ATOM    576  CG  TRP    74       4.538  53.893  24.156  1.00  0.00
ATOM    577  CD1 TRP    74       4.601  55.066  24.851  1.00  0.00
ATOM    578  CD2 TRP    74       3.468  53.136  24.740  1.00  0.00
ATOM    579  NE1 TRP    74       3.638  55.090  25.831  1.00  0.00
ATOM    580  CE2 TRP    74       2.929  53.916  25.783  1.00  0.00
ATOM    581  CE3 TRP    74       2.915  51.880  24.483  1.00  0.00
ATOM    582  CZ2 TRP    74       1.864  53.477  26.567  1.00  0.00
ATOM    583  CZ3 TRP    74       1.859  51.450  25.263  1.00  0.00
ATOM    584  CH2 TRP    74       1.342  52.243  26.293  1.00  0.00
ATOM    585  N   LEU    75       7.190  50.912  21.807  1.00  0.00
ATOM    586  CA  LEU    75       7.961  50.496  20.677  1.00  0.00
ATOM    587  C   LEU    75       7.020  50.435  19.521  1.00  0.00
ATOM    588  O   LEU    75       6.137  49.581  19.467  1.00  0.00
ATOM    589  CB  LEU    75       8.584  49.122  20.931  1.00  0.00
ATOM    590  CG  LEU    75       9.413  48.531  19.789  1.00  0.00
ATOM    591  CD1 LEU    75      10.614  49.413  19.482  1.00  0.00
ATOM    592  CD2 LEU    75       9.921  47.145  20.153  1.00  0.00
ATOM    593  N   THR    76       7.184  51.365  18.562  1.00  0.00
ATOM    594  CA  THR    76       6.359  51.346  17.394  1.00  0.00
ATOM    595  C   THR    76       7.294  51.327  16.234  1.00  0.00
ATOM    596  O   THR    76       8.345  51.964  16.261  1.00  0.00
ATOM    597  CB  THR    76       5.449  52.587  17.326  1.00  0.00
ATOM    598  OG1 THR    76       4.608  52.630  18.485  1.00  0.00
ATOM    599  CG2 THR    76       4.573  52.539  16.084  1.00  0.00
ATOM    600  N   PRO    77       6.955  50.585  15.222  1.00  0.00
ATOM    601  CA  PRO    77       7.848  50.529  14.103  1.00  0.00
ATOM    602  C   PRO    77       7.866  51.807  13.337  1.00  0.00
ATOM    603  O   PRO    77       6.813  52.417  13.156  1.00  0.00
ATOM    604  CB  PRO    77       7.300  49.384  13.249  1.00  0.00
ATOM    605  CG  PRO    77       5.852  49.314  13.604  1.00  0.00
ATOM    606  CD  PRO    77       5.759  49.703  15.052  1.00  0.00
TER
END
