
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_2_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    S      71      A      21          1.708
LGA    A      72      R      22          2.949
LGA    -       -      G      23           -
LGA    F      73      L      24          1.348
LGA    W      74      A      25          2.577
LGA    -       -      V      26           -
LGA    -       -      I      27           -
LGA    L      75      R      28          0.486
LGA    -       -      C      29           -
LGA    T      76      F      30          1.803
LGA    P      77      D      31          1.894
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    1.97     0.00     10.490     0.338

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.652305 * X  +  -0.658499 * Y  +   0.375335 * Z  +  -0.032190
  Y_new =  -0.540528 * X  +  -0.057002 * Y  +   0.839393 * Z  +  59.753777
  Z_new =  -0.531345 * X  +  -0.750419 * Y  +  -0.393120 * Z  +  -4.012999 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.053355    1.088238  [ DEG:  -117.6486     62.3514 ]
  Theta =   0.560187    2.581406  [ DEG:    32.0964    147.9036 ]
  Phi   =  -0.691964    2.449629  [ DEG:   -39.6466    140.3534 ]
 
# 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_2_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_2_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   1.97    0.00  10.490
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_D
ATOM    549  N   SER    71       9.031  56.552  29.722  1.00  0.00
ATOM    550  CA  SER    71       8.484  55.259  30.191  1.00  0.00
ATOM    551  C   SER    71       8.394  54.278  29.074  1.00  0.00
ATOM    552  O   SER    71       9.336  53.536  28.800  1.00  0.00
ATOM    553  CB  SER    71       7.081  55.449  30.771  1.00  0.00
ATOM    554  OG  SER    71       7.112  56.275  31.921  1.00  0.00
ATOM    555  N   ALA    72       7.237  54.257  28.391  1.00  0.00
ATOM    556  CA  ALA    72       7.050  53.319  27.331  1.00  0.00
ATOM    557  C   ALA    72       7.969  53.690  26.222  1.00  0.00
ATOM    558  O   ALA    72       8.230  54.865  25.974  1.00  0.00
ATOM    559  CB  ALA    72       5.611  53.355  26.840  1.00  0.00
ATOM    560  N   PHE    73       8.512  52.665  25.542  1.00  0.00
ATOM    561  CA  PHE    73       9.371  52.908  24.428  1.00  0.00
ATOM    562  C   PHE    73       8.590  52.475  23.237  1.00  0.00
ATOM    563  O   PHE    73       8.111  51.343  23.182  1.00  0.00
ATOM    564  CB  PHE    73      10.665  52.103  24.563  1.00  0.00
ATOM    565  CG  PHE    73      11.539  52.547  25.701  1.00  0.00
ATOM    566  CD1 PHE    73      11.410  51.978  26.956  1.00  0.00
ATOM    567  CD2 PHE    73      12.490  53.536  25.517  1.00  0.00
ATOM    568  CE1 PHE    73      12.215  52.387  28.002  1.00  0.00
ATOM    569  CE2 PHE    73      13.294  53.945  26.563  1.00  0.00
ATOM    570  CZ  PHE    73      13.160  53.375  27.802  1.00  0.00
ATOM    571  N   TRP    74       8.427  53.368  22.245  1.00  0.00
ATOM    572  CA  TRP    74       7.660  52.930  21.123  1.00  0.00
ATOM    573  C   TRP    74       8.503  51.937  20.403  1.00  0.00
ATOM    574  O   TRP    74       9.658  52.205  20.072  1.00  0.00
ATOM    575  CB  TRP    74       7.323  54.112  20.211  1.00  0.00
ATOM    576  CG  TRP    74       6.347  55.075  20.815  1.00  0.00
ATOM    577  CD1 TRP    74       6.624  56.311  21.322  1.00  0.00
ATOM    578  CD2 TRP    74       4.937  54.882  20.971  1.00  0.00
ATOM    579  NE1 TRP    74       5.473  56.902  21.787  1.00  0.00
ATOM    580  CE2 TRP    74       4.423  56.043  21.583  1.00  0.00
ATOM    581  CE3 TRP    74       4.056  53.842  20.655  1.00  0.00
ATOM    582  CZ2 TRP    74       3.070  56.192  21.885  1.00  0.00
ATOM    583  CZ3 TRP    74       2.717  53.995  20.956  1.00  0.00
ATOM    584  CH2 TRP    74       2.233  55.158  21.564  1.00  0.00
ATOM    585  N   LEU    75       7.939  50.739  20.165  1.00  0.00
ATOM    586  CA  LEU    75       8.678  49.702  19.512  1.00  0.00
ATOM    587  C   LEU    75       8.513  49.938  18.048  1.00  0.00
ATOM    588  O   LEU    75       7.431  50.320  17.610  1.00  0.00
ATOM    589  CB  LEU    75       8.131  48.327  19.903  1.00  0.00
ATOM    590  CG  LEU    75       8.209  47.964  21.387  1.00  0.00
ATOM    591  CD1 LEU    75       7.562  46.612  21.644  1.00  0.00
ATOM    592  CD2 LEU    75       9.656  47.897  21.851  1.00  0.00
ATOM    593  N   THR    76       9.586  49.744  17.250  1.00  0.00
ATOM    594  CA  THR    76       9.425  49.976  15.843  1.00  0.00
ATOM    595  C   THR    76       8.647  48.838  15.296  1.00  0.00
ATOM    596  O   THR    76       8.997  47.672  15.468  1.00  0.00
ATOM    597  CB  THR    76      10.786  50.063  15.127  1.00  0.00
ATOM    598  OG1 THR    76      11.557  51.133  15.689  1.00  0.00
ATOM    599  CG2 THR    76      10.589  50.327  13.642  1.00  0.00
ATOM    600  N   PRO    77       7.607  49.194  14.600  1.00  0.00
ATOM    601  CA  PRO    77       6.702  48.215  14.077  1.00  0.00
ATOM    602  C   PRO    77       7.368  47.350  13.070  1.00  0.00
ATOM    603  O   PRO    77       8.406  47.739  12.534  1.00  0.00
ATOM    604  CB  PRO    77       5.584  49.045  13.446  1.00  0.00
ATOM    605  CG  PRO    77       5.665  50.368  14.133  1.00  0.00
ATOM    606  CD  PRO    77       7.123  50.603  14.411  1.00  0.00
TER
END
