
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0382TS009_2_2
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS009_2_2.T0382.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    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    -       -      N      38           -
LGA    -       -      R      39           -
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    I      34      T      81          4.662
LGA    S      35      L      82          1.965
LGA    R      36      A      83          2.254
LGA    -       -      V      84           -
LGA    F      37      A      85          2.579
LGA    N      38      P      86          3.967
LGA    R      39      V      87          2.744
LGA    L      40      K      88           #
LGA    F      41      A      89          2.465
LGA    G      42      R      90          2.745
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    V      43      E      94          3.080
LGA    M      44      A      95          2.476
LGA    A      45      I      96          2.071
LGA    E      46      V      97          2.768
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    I      47      W     101          4.134
LGA    A      48      F     102          2.934
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  121    5.0     14    3.02     0.00      7.637     0.449

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.891505 * X  +   0.315023 * Y  +   0.325545 * Z  + -34.241611
  Y_new =   0.179645 * X  +   0.413860 * Y  +  -0.892439 * Z  +   7.878926
  Z_new =  -0.415869 * X  +   0.854096 * Y  +   0.312366 * Z  +  -4.342934 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.220180   -1.921412  [ DEG:    69.9112   -110.0888 ]
  Theta =   0.428898    2.712695  [ DEG:    24.5740    155.4260 ]
  Phi   =   0.198844   -2.942748  [ DEG:    11.3929   -168.6071 ]
 
# 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: T0382TS009_2_2                                
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_2.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  121   5.0   14   3.02    0.00   7.637
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    256  N   ILE    34     -15.535  51.942   2.164  1.00  0.00             
ATOM    257  CA  ILE    34     -14.826  53.006   2.929  1.00  0.00             
ATOM    258  C   ILE    34     -14.888  54.344   2.201  1.00  0.00             
ATOM    259  O   ILE    34     -13.919  54.762   1.564  1.00  0.00             
ATOM    260  CB  ILE    34     -15.416  53.174   4.342  1.00  0.00             
ATOM    261  CG2 ILE    34     -14.869  52.108   5.277  1.00  0.00             
ATOM    262  CG1 ILE    34     -16.944  53.119   4.290  1.00  0.00             
ATOM    263  CD1 ILE    34     -17.574  52.507   5.523  1.00  0.00             
ATOM    264  N   SER    35     -16.032  55.013   2.297  1.00  0.00             
ATOM    265  CA  SER    35     -16.223  56.304   1.646  1.00  0.00             
ATOM    266  C   SER    35     -16.336  56.148   0.134  1.00  0.00             
ATOM    267  O   SER    35     -17.211  56.742  -0.498  1.00  0.00             
ATOM    268  CB  SER    35     -17.468  57.002   2.198  1.00  0.00             
ATOM    269  OG  SER    35     -17.139  57.846   3.288  1.00  0.00             
ATOM    270  N   ARG    36     -15.445  55.347  -0.441  1.00  0.00             
ATOM    271  CA  ARG    36     -15.442  55.114  -1.880  1.00  0.00             
ATOM    272  C   ARG    36     -16.846  54.801  -2.390  1.00  0.00             
ATOM    273  O   ARG    36     -17.262  55.299  -3.436  1.00  0.00             
ATOM    274  CB  ARG    36     -14.872  56.325  -2.620  1.00  0.00             
ATOM    275  CG  ARG    36     -13.700  56.001  -3.531  1.00  0.00             
ATOM    276  CD  ARG    36     -13.484  57.095  -4.564  1.00  0.00             
ATOM    277  NE  ARG    36     -12.199  56.960  -5.244  1.00  0.00             
ATOM    278  CZ  ARG    36     -12.054  56.507  -6.485  1.00  0.00             
ATOM    279  NH1 ARG    36     -13.120  56.145  -7.187  1.00  0.00             
ATOM    280  NH2 ARG    36     -10.846  56.418  -7.023  1.00  0.00             
ATOM    281  N   PHE    37     -17.569  53.972  -1.646  1.00  0.00             
ATOM    282  CA  PHE    37     -18.926  53.591  -2.020  1.00  0.00             
ATOM    283  C   PHE    37     -19.890  54.763  -1.865  1.00  0.00             
ATOM    284  O   PHE    37     -19.833  55.731  -2.623  1.00  0.00             
ATOM    285  CB  PHE    37     -18.958  53.071  -3.459  1.00  0.00             
ATOM    286  CG  PHE    37     -19.823  51.857  -3.645  1.00  0.00             
ATOM    287  CD1 PHE    37     -20.281  51.141  -2.553  1.00  0.00             
ATOM    288  CD2 PHE    37     -20.179  51.431  -4.913  1.00  0.00             
ATOM    289  CE1 PHE    37     -21.076  50.025  -2.725  1.00  0.00             
ATOM    290  CE2 PHE    37     -20.974  50.314  -5.085  1.00  0.00             
ATOM    291  CZ  PHE    37     -21.423  49.611  -3.997  1.00  0.00             
ATOM    292  N   ASN    38     -20.775  54.667  -0.877  1.00  0.00             
ATOM    293  CA  ASN    38     -21.753  55.718  -0.621  1.00  0.00             
ATOM    294  C   ASN    38     -21.231  56.719   0.404  1.00  0.00             
ATOM    295  O   ASN    38     -21.838  56.919   1.456  1.00  0.00             
ATOM    296  CB  ASN    38     -22.119  56.438  -1.920  1.00  0.00             
ATOM    297  CG  ASN    38     -23.402  55.914  -2.535  1.00  0.00             
ATOM    298  OD1 ASN    38     -23.935  56.501  -3.477  1.00  0.00             
ATOM    299  ND2 ASN    38     -23.903  54.807  -2.001  1.00  0.00             
ATOM    300  N   ARG    39     -20.101  57.344   0.091  1.00  0.00             
ATOM    301  CA  ARG    39     -19.494  58.325   0.984  1.00  0.00             
ATOM    302  C   ARG    39     -19.353  57.771   2.397  1.00  0.00             
ATOM    303  O   ARG    39     -19.933  58.303   3.344  1.00  0.00             
ATOM    304  CB  ARG    39     -18.129  58.762   0.451  1.00  0.00             
ATOM    305  CG  ARG    39     -18.139  60.107  -0.258  1.00  0.00             
ATOM    306  CD  ARG    39     -16.875  60.310  -1.077  1.00  0.00             
ATOM    307  NE  ARG    39     -16.863  61.604  -1.752  1.00  0.00             
ATOM    308  CZ  ARG    39     -16.490  62.743  -1.177  1.00  0.00             
ATOM    309  NH1 ARG    39     -16.098  62.748   0.090  1.00  0.00             
ATOM    310  NH2 ARG    39     -16.511  63.873  -1.869  1.00  0.00             
ATOM    311  N   LEU    40     -18.579  56.699   2.533  1.00  0.00             
ATOM    312  CA  LEU    40     -18.361  56.070   3.830  1.00  0.00             
ATOM    313  C   LEU    40     -19.664  55.527   4.407  1.00  0.00             
ATOM    314  O   LEU    40     -19.842  55.476   5.623  1.00  0.00             
ATOM    315  CB  LEU    40     -17.327  54.948   3.715  1.00  0.00             
ATOM    316  CG  LEU    40     -15.876  55.331   4.008  1.00  0.00             
ATOM    317  CD1 LEU    40     -15.058  54.102   4.375  1.00  0.00             
ATOM    318  CD2 LEU    40     -15.807  56.375   5.113  1.00  0.00             
ATOM    319  N   PHE    41     -20.571  55.121   3.524  1.00  0.00             
ATOM    320  CA  PHE    41     -21.858  54.580   3.942  1.00  0.00             
ATOM    321  C   PHE    41     -22.207  55.020   5.361  1.00  0.00             
ATOM    322  O   PHE    41     -22.870  54.294   6.101  1.00  0.00             
ATOM    323  CB  PHE    41     -22.961  55.009   2.973  1.00  0.00             
ATOM    324  CG  PHE    41     -23.639  53.861   2.279  1.00  0.00             
ATOM    325  CD1 PHE    41     -23.628  52.594   2.835  1.00  0.00             
ATOM    326  CD2 PHE    41     -24.288  54.050   1.071  1.00  0.00             
ATOM    327  CE1 PHE    41     -24.251  51.538   2.197  1.00  0.00             
ATOM    328  CE2 PHE    41     -24.911  52.994   0.433  1.00  0.00             
ATOM    329  CZ  PHE    41     -24.894  51.742   0.991  1.00  0.00             
ATOM    330  N   GLY    42     -21.757  56.214   5.731  1.00  0.00             
ATOM    331  CA  GLY    42     -22.032  56.728   7.060  1.00  0.00             
ATOM    332  C   GLY    42     -21.497  55.824   8.154  1.00  0.00             
ATOM    333  O   GLY    42     -22.210  55.493   9.102  1.00  0.00             
ATOM    334  N   VAL    43     -20.237  55.423   8.024  1.00  0.00             
ATOM    335  CA  VAL    43     -19.591  54.533   9.031  1.00  0.00             
ATOM    336  C   VAL    43     -20.630  53.705   9.782  1.00  0.00             
ATOM    337  O   VAL    43     -20.464  52.499   9.964  1.00  0.00             
ATOM    338  CB  VAL    43     -18.571  53.584   8.375  1.00  0.00             
ATOM    339  CG1 VAL    43     -17.154  53.975   8.764  1.00  0.00             
ATOM    340  CG2 VAL    43     -18.737  53.588   6.862  1.00  0.00             
ATOM    341  N   MET    44     -21.700  54.363  10.218  1.00  0.00             
ATOM    342  CA  MET    44     -22.767  53.690  10.949  1.00  0.00             
ATOM    343  C   MET    44     -22.497  52.193  11.067  1.00  0.00             
ATOM    344  O   MET    44     -22.910  51.551  12.031  1.00  0.00             
ATOM    345  CB  MET    44     -22.932  54.305  12.341  1.00  0.00             
ATOM    346  CG  MET    44     -24.369  54.345  12.835  1.00  0.00             
ATOM    347  SD  MET    44     -24.485  54.527  14.625  1.00  0.00             
ATOM    348  CE  MET    44     -26.232  54.233  14.883  1.00  0.00             
ATOM    349  N   ALA    45     -21.800  51.644  10.076  1.00  0.00             
ATOM    350  CA  ALA    45     -21.474  50.223  10.066  1.00  0.00             
ATOM    351  C   ALA    45     -20.704  49.824  11.320  1.00  0.00             
ATOM    352  O   ALA    45     -20.685  48.654  11.703  1.00  0.00             
ATOM    353  CB  ALA    45     -22.741  49.389   9.941  1.00  0.00             
ATOM    354  N   GLU    46     -20.070  50.805  11.956  1.00  0.00             
ATOM    355  CA  GLU    46     -19.298  50.559  13.167  1.00  0.00             
ATOM    356  C   GLU    46     -19.484  49.128  13.659  1.00  0.00             
ATOM    357  O   GLU    46     -18.615  48.574  14.333  1.00  0.00             
ATOM    358  CB  GLU    46     -17.814  50.842  12.924  1.00  0.00             
ATOM    359  CG  GLU    46     -17.103  51.488  14.101  1.00  0.00             
ATOM    360  CD  GLU    46     -15.640  51.766  13.818  1.00  0.00             
ATOM    361  OE1 GLU    46     -15.340  52.823  13.224  1.00  0.00             
ATOM    362  OE2 GLU    46     -14.793  50.926  14.189  1.00  0.00             
ATOM    363  N   ILE    47     -20.624  48.534  13.319  1.00  0.00             
ATOM    364  CA  ILE    47     -20.934  47.136  13.733  1.00  0.00             
ATOM    365  C   ILE    47     -20.270  46.796  15.064  1.00  0.00             
ATOM    366  O   ILE    47     -20.920  46.299  15.984  1.00  0.00             
ATOM    367  CB  ILE    47     -22.451  46.906  13.854  1.00  0.00             
ATOM    368  CG2 ILE    47     -23.001  46.295  12.574  1.00  0.00             
ATOM    369  CG1 ILE    47     -23.166  48.220  14.175  1.00  0.00             
ATOM    370  CD1 ILE    47     -24.445  48.427  13.394  1.00  0.00             
ATOM    371  N   ALA    48     -18.973  47.068  15.160  1.00  0.00             
ATOM    372  CA  ALA    48     -18.220  46.791  16.377  1.00  0.00             
ATOM    373  C   ALA    48     -18.761  47.594  17.555  1.00  0.00             
ATOM    374  O   ALA    48     -19.974  47.692  17.746  1.00  0.00             
ATOM    375  CB  ALA    48     -18.254  45.305  16.696  1.00  0.00             
TER
END
