
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_3_2-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
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    I      34      R      39          0.624
LGA    S      35      L      40          1.064
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    R      36      V      43          0.426
LGA    F      37      M      44          0.821
LGA    N      38      A      45          0.760
LGA    R      39      E      46          2.717
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    L      40      D      49          2.501
LGA    F      41      E      50          2.918
LGA    G      42      L      51          2.160
LGA    V      43      K      52          1.362
LGA    M      44      A      53          3.219
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    A      45      G      56          2.129
LGA    E      46      D      57          2.927
LGA    I      47      Q      58          2.253
LGA    A      48      R      59          1.799
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    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  119    5.0     15    2.06     0.00     10.501     0.696

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.992522 * X  +   0.093474 * Y  +   0.078504 * Z  +  17.016815
  Y_new =  -0.121314 * X  +  -0.826662 * Y  +  -0.549466 * Z  +  32.153484
  Z_new =   0.013536 * X  +  -0.554881 * Y  +   0.831819 * Z  +  -1.484746 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.588281    2.553311  [ DEG:   -33.7060    146.2940 ]
  Theta =  -0.013536   -3.128057  [ DEG:    -0.7756   -179.2244 ]
  Phi   =  -3.019968    0.121625  [ DEG:  -173.0314      6.9686 ]
 
# 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_3_2-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_2-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  119   5.0   15   2.06    0.00  10.501
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                       
ATOM    256  N   ILE    34      -2.686  37.362   4.134  1.00  0.00             
ATOM    257  CA  ILE    34      -3.692  36.318   4.480  1.00  0.00             
ATOM    258  C   ILE    34      -5.114  36.850   4.328  1.00  0.00             
ATOM    259  O   ILE    34      -5.557  37.696   5.105  1.00  0.00             
ATOM    260  CB  ILE    34      -3.529  35.062   3.604  1.00  0.00             
ATOM    261  CG2 ILE    34      -2.405  34.186   4.135  1.00  0.00             
ATOM    262  CG1 ILE    34      -3.265  35.457   2.150  1.00  0.00             
ATOM    263  CD1 ILE    34      -2.367  34.492   1.407  1.00  0.00             
ATOM    264  N   SER    35      -5.823  36.349   3.321  1.00  0.00             
ATOM    265  CA  SER    35      -7.194  36.773   3.066  1.00  0.00             
ATOM    266  C   SER    35      -7.300  37.529   1.745  1.00  0.00             
ATOM    267  O   SER    35      -8.256  38.273   1.520  1.00  0.00             
ATOM    268  CB  SER    35      -8.136  35.566   3.058  1.00  0.00             
ATOM    269  OG  SER    35      -8.680  35.337   4.346  1.00  0.00             
ATOM    270  N   ARG    36      -6.315  37.333   0.876  1.00  0.00             
ATOM    271  CA  ARG    36      -6.296  37.995  -0.423  1.00  0.00             
ATOM    272  C   ARG    36      -7.224  39.205  -0.439  1.00  0.00             
ATOM    273  O   ARG    36      -7.328  39.906  -1.445  1.00  0.00             
ATOM    274  CB  ARG    36      -4.871  38.419  -0.788  1.00  0.00             
ATOM    275  CG  ARG    36      -4.387  37.882  -2.125  1.00  0.00             
ATOM    276  CD  ARG    36      -3.205  38.683  -2.646  1.00  0.00             
ATOM    277  NE  ARG    36      -2.537  38.013  -3.757  1.00  0.00             
ATOM    278  CZ  ARG    36      -2.655  38.380  -5.029  1.00  0.00             
ATOM    279  NH1 ARG    36      -3.416  39.415  -5.354  1.00  0.00             
ATOM    280  NH2 ARG    36      -2.008  37.709  -5.974  1.00  0.00             
ATOM    281  N   PHE    37      -7.896  39.444   0.682  1.00  0.00             
ATOM    282  CA  PHE    37      -8.815  40.569   0.799  1.00  0.00             
ATOM    283  C   PHE    37      -8.310  41.778   0.020  1.00  0.00             
ATOM    284  O   PHE    37      -8.987  42.276  -0.880  1.00  0.00             
ATOM    285  CB  PHE    37     -10.210  40.174   0.310  1.00  0.00             
ATOM    286  CG  PHE    37     -11.324  40.688   1.177  1.00  0.00             
ATOM    287  CD1 PHE    37     -11.062  41.202   2.435  1.00  0.00             
ATOM    288  CD2 PHE    37     -12.635  40.657   0.735  1.00  0.00             
ATOM    289  CE1 PHE    37     -12.086  41.675   3.232  1.00  0.00             
ATOM    290  CE2 PHE    37     -13.661  41.130   1.531  1.00  0.00             
ATOM    291  CZ  PHE    37     -13.391  41.638   2.775  1.00  0.00             
ATOM    292  N   ASN    38      -7.117  42.246   0.370  1.00  0.00             
ATOM    293  CA  ASN    38      -6.518  43.397  -0.295  1.00  0.00             
ATOM    294  C   ASN    38      -6.800  43.374  -1.795  1.00  0.00             
ATOM    295  O   ASN    38      -6.005  43.871  -2.592  1.00  0.00             
ATOM    296  CB  ASN    38      -7.036  44.699   0.318  1.00  0.00             
ATOM    297  CG  ASN    38      -6.084  45.276   1.348  1.00  0.00             
ATOM    298  OD1 ASN    38      -6.259  46.406   1.804  1.00  0.00             
ATOM    299  ND2 ASN    38      -5.074  44.499   1.719  1.00  0.00             
ATOM    300  N   ARG    39      -7.936  42.796  -2.169  1.00  0.00             
ATOM    301  CA  ARG    39      -8.324  42.708  -3.572  1.00  0.00             
ATOM    302  C   ARG    39      -7.130  42.941  -4.491  1.00  0.00             
ATOM    303  O   ARG    39      -6.028  42.461  -4.226  1.00  0.00             
ATOM    304  CB  ARG    39      -8.958  41.347  -3.868  1.00  0.00             
ATOM    305  CG  ARG    39     -10.477  41.370  -3.933  1.00  0.00             
ATOM    306  CD  ARG    39     -11.055  39.967  -3.852  1.00  0.00             
ATOM    307  NE  ARG    39     -12.512  39.971  -3.929  1.00  0.00             
ATOM    308  CZ  ARG    39     -13.200  40.023  -5.066  1.00  0.00             
ATOM    309  NH1 ARG    39     -12.560  40.077  -6.226  1.00  0.00             
ATOM    310  NH2 ARG    39     -14.526  40.021  -5.039  1.00  0.00             
ATOM    311  N   LEU    40      -7.357  43.682  -5.571  1.00  0.00             
ATOM    312  CA  LEU    40      -6.301  43.980  -6.531  1.00  0.00             
ATOM    313  C   LEU    40      -6.489  45.362  -7.146  1.00  0.00             
ATOM    314  O   LEU    40      -6.351  46.379  -6.466  1.00  0.00             
ATOM    315  CB  LEU    40      -4.928  43.884  -5.863  1.00  0.00             
ATOM    316  CG  LEU    40      -4.213  42.536  -5.972  1.00  0.00             
ATOM    317  CD1 LEU    40      -2.716  42.701  -5.759  1.00  0.00             
ATOM    318  CD2 LEU    40      -4.499  41.883  -7.317  1.00  0.00             
ATOM    319  N   PHE    41      -6.804  45.392  -8.437  1.00  0.00             
ATOM    320  CA  PHE    41      -7.013  46.649  -9.146  1.00  0.00             
ATOM    321  C   PHE    41      -8.432  46.744  -9.696  1.00  0.00             
ATOM    322  O   PHE    41      -9.006  47.830  -9.776  1.00  0.00             
ATOM    323  CB  PHE    41      -6.725  47.837  -8.226  1.00  0.00             
ATOM    324  CG  PHE    41      -5.600  48.712  -8.701  1.00  0.00             
ATOM    325  CD1 PHE    41      -5.239  48.737 -10.037  1.00  0.00             
ATOM    326  CD2 PHE    41      -4.901  49.511  -7.812  1.00  0.00             
ATOM    327  CE1 PHE    41      -4.205  49.543 -10.474  1.00  0.00             
ATOM    328  CE2 PHE    41      -3.867  50.316  -8.248  1.00  0.00             
ATOM    329  CZ  PHE    41      -3.518  50.334  -9.574  1.00  0.00             
ATOM    330  N   GLY    42      -8.993  45.599 -10.072  1.00  0.00             
ATOM    331  CA  GLY    42     -10.341  45.579 -10.610  1.00  0.00             
ATOM    332  C   GLY    42     -10.909  46.971 -10.804  1.00  0.00             
ATOM    333  O   GLY    42     -11.924  47.149 -11.477  1.00  0.00             
ATOM    334  N   VAL    43     -10.252  47.965 -10.214  1.00  0.00             
ATOM    335  CA  VAL    43     -10.707  49.380 -10.327  1.00  0.00             
ATOM    336  C   VAL    43     -11.165  49.700 -11.746  1.00  0.00             
ATOM    337  O   VAL    43     -12.181  50.368 -11.945  1.00  0.00             
ATOM    338  CB  VAL    43     -11.855  49.685  -9.346  1.00  0.00             
ATOM    339  CG1 VAL    43     -11.375  50.605  -8.234  1.00  0.00             
ATOM    340  CG2 VAL    43     -12.421  48.395  -8.772  1.00  0.00             
ATOM    341  N   MET    44     -10.411  49.220 -12.729  1.00  0.00             
ATOM    342  CA  MET    44     -10.738  49.454 -14.131  1.00  0.00             
ATOM    343  C   MET    44     -12.013  50.279 -14.268  1.00  0.00             
ATOM    344  O   MET    44     -12.029  51.305 -14.950  1.00  0.00             
ATOM    345  CB  MET    44      -9.579  50.154 -14.841  1.00  0.00             
ATOM    346  CG  MET    44      -9.390  49.728 -16.289  1.00  0.00             
ATOM    347  SD  MET    44      -8.439  50.923 -17.247  1.00  0.00             
ATOM    348  CE  MET    44      -8.669  50.286 -18.906  1.00  0.00             
ATOM    349  N   ALA    45     -13.079  49.825 -13.619  1.00  0.00             
ATOM    350  CA  ALA    45     -14.360  50.521 -13.667  1.00  0.00             
ATOM    351  C   ALA    45     -14.963  50.666 -12.274  1.00  0.00             
ATOM    352  O   ALA    45     -14.636  51.598 -11.540  1.00  0.00             
ATOM    353  CB  ALA    45     -14.196  51.889 -14.313  1.00  0.00             
ATOM    354  N   GLU    46     -15.844  49.738 -11.918  1.00  0.00             
ATOM    355  CA  GLU    46     -16.494  49.761 -10.612  1.00  0.00             
ATOM    356  C   GLU    46     -15.580  49.194  -9.531  1.00  0.00             
ATOM    357  O   GLU    46     -15.479  49.749  -8.436  1.00  0.00             
ATOM    358  CB  GLU    46     -16.918  51.186 -10.249  1.00  0.00             
ATOM    359  CG  GLU    46     -18.250  51.270  -9.521  1.00  0.00             
ATOM    360  CD  GLU    46     -18.643  52.696  -9.191  1.00  0.00             
ATOM    361  OE1 GLU    46     -19.228  53.370 -10.066  1.00  0.00             
ATOM    362  OE2 GLU    46     -18.368  53.142  -8.057  1.00  0.00             
ATOM    363  N   ILE    47     -14.916  48.087  -9.845  1.00  0.00             
ATOM    364  CA  ILE    47     -13.989  47.429  -8.880  1.00  0.00             
ATOM    365  C   ILE    47     -14.334  47.802  -7.442  1.00  0.00             
ATOM    366  O   ILE    47     -15.021  47.057  -6.744  1.00  0.00             
ATOM    367  CB  ILE    47     -14.020  45.895  -9.023  1.00  0.00             
ATOM    368  CG2 ILE    47     -12.889  45.422  -9.922  1.00  0.00             
ATOM    369  CG1 ILE    47     -15.374  45.439  -9.571  1.00  0.00             
ATOM    370  CD1 ILE    47     -15.272  44.361 -10.628  1.00  0.00             
ATOM    371  N   ALA    48     -13.852  48.961  -7.006  1.00  0.00             
ATOM    372  CA  ALA    48     -14.108  49.436  -5.651  1.00  0.00             
ATOM    373  C   ALA    48     -15.380  50.273  -5.591  1.00  0.00             
ATOM    374  O   ALA    48     -15.556  51.210  -6.370  1.00  0.00             
ATOM    375  CB  ALA    48     -14.206  48.263  -4.688  1.00  0.00             
TER
END
