
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS174_1u-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS174_1u-D1.T0372_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    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    K     290      R      24          4.345
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    Y     291      C      97          1.304
LGA    M     292      S      98          1.431
LGA    A     293      N      99          1.317
LGA    C     294      M     100          0.613
LGA    L     295      R     101          0.311
LGA    K     296      A     102          0.647
LGA    D     297      D     103          0.169
LGA    H     298      L     104          0.646
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    1.69    11.11      6.819     0.503

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.412606 * X  +   0.414675 * Y  +  -0.811049 * Z  +  33.900093
  Y_new =  -0.670037 * X  +   0.465020 * Y  +   0.578625 * Z  +  48.173367
  Z_new =   0.617095 * X  +   0.782178 * Y  +   0.085978 * Z  + -29.922148 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.461315   -1.680278  [ DEG:    83.7272    -96.2728 ]
  Theta =  -0.665046   -2.476547  [ DEG:   -38.1043   -141.8957 ]
  Phi   =  -2.122750    1.018843  [ DEG:  -121.6246     58.3754 ]
 
# 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: T0372TS174_1u-D1                              
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS174_1u-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   1.69   11.11   6.819
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS174_1u-D1
PFRMAT TS
TARGET T0372
MODEL 1  UNREFINED
PARENT 1ew6_A 
ATOM    927  N   LYS   290      27.890  53.512  11.017  1.00  1.00
ATOM    928  CA  LYS   290      27.155  54.571  10.289  1.00  1.00
ATOM    929  C   LYS   290      26.402  53.977   9.093  1.00  1.00
ATOM    930  O   LYS   290      25.308  54.440   8.738  1.00  1.00
ATOM    931  CB  LYS   290      28.121  55.680   9.848  1.00  1.00
ATOM    932  CG  LYS   290      28.606  56.353  10.967  1.00  1.00
ATOM    933  CD  LYS   290      29.559  57.477  10.563  1.00  1.00
ATOM    934  CE  LYS   290      28.803  58.596   9.844  1.00  1.00
ATOM    935  NZ  LYS   290      29.727  59.687   9.441  1.00  1.00
ATOM    936  N   TYR   291      26.728  52.740   8.799  1.00  1.00
ATOM    937  CA  TYR   291      26.447  52.093   7.497  1.00  1.00
ATOM    938  C   TYR   291      25.034  52.445   7.017  1.00  1.00
ATOM    939  O   TYR   291      24.809  52.671   5.818  1.00  1.00
ATOM    940  CB  TYR   291      26.640  50.573   7.607  1.00  1.00
ATOM    941  CG  TYR   291      26.446  49.822   6.305  1.00  1.00
ATOM    942  CD1 TYR   291      27.462  49.771   5.360  1.00  1.00
ATOM    943  CD2 TYR   291      25.269  49.159   6.024  1.00  1.00
ATOM    944  CE1 TYR   291      27.308  49.087   4.164  1.00  1.00
ATOM    945  CE2 TYR   291      25.096  48.466   4.837  1.00  1.00
ATOM    946  CZ  TYR   291      26.120  48.436   3.903  1.00  1.00
ATOM    947  OH  TYR   291      25.918  47.735   2.725  1.00  1.00
ATOM    948  N   MET   292      24.127  52.516   7.992  1.00  1.00
ATOM    949  CA  MET   292      22.723  52.876   7.688  1.00  1.00
ATOM    950  C   MET   292      22.630  54.336   7.233  1.00  1.00
ATOM    951  O   MET   292      21.834  54.675   6.344  1.00  1.00
ATOM    952  CB  MET   292      21.832  52.612   8.911  1.00  1.00
ATOM    953  CG  MET   292      20.309  52.901   8.637  1.00  1.00
ATOM    954  SD  MET   292      19.352  52.580  10.050  1.00  1.00
ATOM    955  CE  MET   292      19.731  53.908  11.001  1.00  1.00
ATOM    956  N   ALA   293      23.446  55.179   7.852  1.00  1.00
ATOM    957  CA  ALA   293      23.483  56.615   7.492  1.00  1.00
ATOM    958  C   ALA   293      24.083  56.801   6.094  1.00  1.00
ATOM    959  O   ALA   293      23.645  57.671   5.326  1.00  1.00
ATOM    960  CB  ALA   293      24.266  57.407   8.549  1.00  1.00
ATOM    961  N   CYS   294      25.041  55.880   5.799  1.00  1.00
ATOM    962  CA  CYS   294      25.701  55.886   4.473  1.00  1.00
ATOM    963  C   CYS   294      24.723  55.430   3.385  1.00  1.00
ATOM    964  O   CYS   294      24.741  55.946   2.258  1.00  1.00
ATOM    965  CB  CYS   294      26.959  55.007   4.503  1.00  1.00
ATOM    966  SG  CYS   294      28.206  55.725   5.642  1.00  1.00
ATOM    967  N   LEU   295      23.959  54.465   3.666  1.00  1.00
ATOM    968  CA  LEU   295      23.004  53.930   2.668  1.00  1.00
ATOM    969  C   LEU   295      21.950  54.984   2.315  1.00  1.00
ATOM    970  O   LEU   295      21.587  55.152   1.142  1.00  1.00
ATOM    971  CB  LEU   295      22.355  52.642   3.194  1.00  1.00
ATOM    972  CG  LEU   295      23.146  51.362   2.933  1.00  1.00
ATOM    973  CD1 LEU   295      24.470  51.255   3.678  1.00  1.00
ATOM    974  CD2 LEU   295      22.212  50.178   3.236  1.00  1.00
ATOM    975  N   LYS   296      21.580  55.731   3.397  1.00  1.00
ATOM    976  CA  LYS   296      20.619  56.845   3.235  1.00  1.00
ATOM    977  C   LYS   296      21.174  57.894   2.265  1.00  1.00
ATOM    978  O   LYS   296      20.524  58.245   1.269  1.00  1.00
ATOM    979  CB  LYS   296      20.289  57.463   4.601  1.00  1.00
ATOM    980  CG  LYS   296      19.575  56.548   5.372  1.00  1.00
ATOM    981  CD  LYS   296      19.212  57.139   6.733  1.00  1.00
ATOM    982  CE  LYS   296      18.430  56.137   7.584  1.00  1.00
ATOM    983  NZ  LYS   296      18.084  56.709   8.897  1.00  1.00
ATOM    984  N   ASP   297      22.366  58.362   2.563  1.00  1.00
ATOM    985  CA  ASP   297      23.018  59.380   1.709  1.00  1.00
ATOM    986  C   ASP   297      23.275  58.820   0.305  1.00  1.00
ATOM    987  O   ASP   297      23.444  59.578  -0.661  1.00  1.00
ATOM    988  CB  ASP   297      24.318  59.868   2.365  1.00  1.00
ATOM    989  CG  ASP   297      24.082  60.722   3.602  1.00  1.00
ATOM    990  OD1 ASP   297      23.071  61.129   3.974  1.00  1.00
ATOM    991  OD2 ASP   297      25.195  60.937   4.204  1.00  1.00
ATOM    992  N   HIS   298      23.326  57.538   0.198  1.00  1.00
ATOM    993  CA  HIS   298      23.580  56.888  -1.109  1.00  1.00
ATOM    994  C   HIS   298      22.278  56.768  -1.910  1.00  1.00
ATOM    995  O   HIS   298      22.268  56.234  -3.029  1.00  1.00
ATOM    996  CB  HIS   298      24.237  55.516  -0.899  1.00  1.00
ATOM    997  CG  HIS   298      24.599  54.813  -2.032  1.00  1.00
ATOM    998  ND1 HIS   298      25.491  55.235  -3.010  1.00  1.00
ATOM    999  CD2 HIS   298      24.137  53.553  -2.390  1.00  1.00
ATOM   1000  CE1 HIS   298      25.575  54.234  -3.980  1.00  1.00
ATOM   1001  NE2 HIS   298      24.742  53.198  -3.593  1.00  1.00
TER
END
