
#######################################################
#                                                     #
#                        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    8 (   40),  selected    8 , name T0372TS103_2_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_2_2-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    -       -      R      24           -
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    K     290      Y      64          1.901
LGA    Y     291      M      65          0.986
LGA    M     292      M      66          1.843
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    A     293      L      94          1.866
LGA    C     294      G      95          1.047
LGA    L     295      V      96          3.052
LGA    D     297      C      97          2.852
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
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    H     298      K     290          0.655
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)    8  126    5.0      8    1.95    12.50      5.820     0.390

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.681552 * X  +   0.626083 * Y  +   0.378822 * Z  +  17.797647
  Y_new =   0.729991 * X  +  -0.617771 * Y  +  -0.292356 * Z  +  64.668098
  Z_new =   0.050986 * X  +   0.475793 * Y  +  -0.878078 * Z  +  15.316871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.645023   -0.496570  [ DEG:   151.5486    -28.4514 ]
  Theta =  -0.051008   -3.090585  [ DEG:    -2.9225   -177.0775 ]
  Phi   =   0.819701   -2.321892  [ DEG:    46.9654   -133.0346 ]
 
# 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: T0372TS103_2_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_2_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  126   5.0    8   1.95   12.50   5.820
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1kaf_A
ATOM    451  N   LYS   290      34.831  49.641  -0.933  1.00  1.00
ATOM    452  CA  LYS   290      34.932  48.853   0.290  1.00  1.00
ATOM    453  C   LYS   290      34.468  49.634   1.518  1.00  1.00
ATOM    454  O   LYS   290      33.747  49.105   2.367  1.00  1.00
ATOM    455  CB  LYS   290      36.373  48.382   0.485  1.00  1.00
ATOM    456  N   TYR   291      34.872  50.895   1.607  1.00  1.00
ATOM    457  CA  TYR   291      34.505  51.731   2.746  1.00  1.00
ATOM    458  C   TYR   291      33.005  51.954   2.875  1.00  1.00
ATOM    459  O   TYR   291      32.438  51.814   3.957  1.00  1.00
ATOM    460  CB  TYR   291      35.194  53.109   2.664  1.00  1.00
ATOM    461  N   MET   292      32.365  52.314   1.770  1.00  1.00
ATOM    462  CA  MET   292      30.931  52.568   1.776  1.00  1.00
ATOM    463  C   MET   292      30.159  51.281   2.045  1.00  1.00
ATOM    464  O   MET   292      29.133  51.289   2.724  1.00  1.00
ATOM    465  CB  MET   292      30.484  53.193   0.441  1.00  1.00
ATOM    466  N   ALA   293      30.661  50.174   1.516  1.00  1.00
ATOM    467  CA  ALA   293      30.023  48.885   1.733  1.00  1.00
ATOM    468  C   ALA   293      29.988  48.580   3.228  1.00  1.00
ATOM    469  O   ALA   293      28.966  48.150   3.751  1.00  1.00
ATOM    470  CB  ALA   293      30.775  47.757   1.004  1.00  1.00
ATOM    471  N   CYS   294      31.106  48.811   3.911  1.00  1.00
ATOM    472  CA  CYS   294      31.173  48.557   5.346  1.00  1.00
ATOM    473  C   CYS   294      30.232  49.499   6.100  1.00  1.00
ATOM    474  O   CYS   294      29.483  49.070   6.977  1.00  1.00
ATOM    475  CB  CYS   294      32.622  48.731   5.883  1.00  1.00
ATOM    476  N   LEU   295      30.262  50.781   5.752  1.00  1.00
ATOM    477  CA  LEU   295      29.405  51.754   6.417  1.00  1.00
ATOM    478  C   LEU   295      27.931  51.380   6.270  1.00  1.00
ATOM    479  O   LEU   295      27.129  51.625   7.172  1.00  1.00
ATOM    480  CB  LEU   295      29.652  53.146   5.845  1.00  1.00
ATOM    481  N   ASP   297      27.586  50.777   5.135  1.00  1.00
ATOM    482  CA  ASP   297      26.207  50.383   4.854  1.00  1.00
ATOM    483  C   ASP   297      25.739  49.132   5.595  1.00  1.00
ATOM    484  O   ASP   297      24.538  48.941   5.796  1.00  1.00
ATOM    485  CB  ASP   297      26.026  50.164   3.352  1.00  1.00
ATOM    486  N   HIS   298      26.681  48.283   5.992  1.00  1.00
ATOM    487  CA  HIS   298      26.347  47.048   6.697  1.00  1.00
ATOM    488  C   HIS   298      26.446  47.171   8.216  1.00  1.00
ATOM    489  O   HIS   298      26.273  46.185   8.936  1.00  1.00
ATOM    490  CB  HIS   298      27.256  45.912   6.219  1.00  1.00
TER
END
