
#######################################################
#                                                     #
#                        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    5 (   44),  selected    5 , name T0316TS650_1_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS650_1_3-D2.T0316_D2.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    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    Y     279      F     261          0.710
LGA    H     280      V     262          0.913
LGA    D     281      V     263          0.238
LGA    S     282      G     264          0.304
LGA    L     283      K     265          0.812
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   60    5.0      5    0.66     0.00      8.333     0.662

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.701970 * X  +  -0.530239 * Y  +   0.475484 * Z  +  48.955849
  Y_new =   0.493539 * X  +   0.119171 * Y  +   0.861521 * Z  +  -8.265161
  Z_new =  -0.513476 * X  +   0.839431 * Y  +   0.178039 * Z  +  28.678379 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.361799   -1.779794  [ DEG:    78.0253   -101.9747 ]
  Theta =   0.539230    2.602362  [ DEG:    30.8956    149.1044 ]
  Phi   =   2.528805   -0.612788  [ DEG:   144.8898    -35.1101 ]
 
# 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: T0316TS650_1_3-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS650_1_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   60   5.0    5   0.66    0.00   8.333
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS650_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0316
PARENT 1EXM_A
ATOM   2176  N   TYR   279      28.348  23.010 -17.843  1.00  0.00              
ATOM   2177  CA  TYR   279      28.565  22.492 -19.209  1.00  0.00              
ATOM   2178  CB  TYR   279      29.209  23.566 -20.100  1.00  0.00              
ATOM   2179  CG  TYR   279      29.494  22.931 -21.418  1.00  0.00              
ATOM   2180  CD1 TYR   279      28.493  22.761 -22.349  1.00  0.00              
ATOM   2181  CD2 TYR   279      30.766  22.507 -21.726  1.00  0.00              
ATOM   2182  CE1 TYR   279      28.760  22.177 -23.563  1.00  0.00              
ATOM   2183  CE2 TYR   279      31.042  21.922 -22.941  1.00  0.00              
ATOM   2184  CZ  TYR   279      30.037  21.758 -23.862  1.00  0.00              
ATOM   2185  OH  TYR   279      30.311  21.159 -25.110  1.00  0.00              
ATOM   2186  C   TYR   279      29.446  21.286 -19.229  1.00  0.00              
ATOM   2187  O   TYR   279      29.012  20.208 -19.632  1.00  0.00              
ATOM   2188  N   HIS   280      30.708  21.430 -18.776  1.00  0.00              
ATOM   2189  CA  HIS   280      31.602  20.312 -18.851  1.00  0.00              
ATOM   2190  ND1 HIS   280      34.967  22.162 -18.732  1.00  0.00              
ATOM   2191  CG  HIS   280      33.687  21.735 -19.006  1.00  0.00              
ATOM   2192  CB  HIS   280      33.008  20.605 -18.295  1.00  0.00              
ATOM   2193  NE2 HIS   280      34.199  23.483 -20.344  1.00  0.00              
ATOM   2194  CD2 HIS   280      33.231  22.557 -19.997  1.00  0.00              
ATOM   2195  CE1 HIS   280      35.223  23.205 -19.558  1.00  0.00              
ATOM   2196  C   HIS   280      31.015  19.195 -18.053  1.00  0.00              
ATOM   2197  O   HIS   280      30.831  19.301 -16.841  1.00  0.00              
ATOM   2198  N   ASP   281      30.673  18.098 -18.757  1.00  0.00              
ATOM   2199  CA  ASP   281      30.105  16.924 -18.166  1.00  0.00              
ATOM   2200  CB  ASP   281      29.608  15.919 -19.220  1.00  0.00              
ATOM   2201  CG  ASP   281      28.903  14.789 -18.489  1.00  0.00              
ATOM   2202  OD1 ASP   281      28.508  15.010 -17.314  1.00  0.00              
ATOM   2203  OD2 ASP   281      28.741  13.697 -19.096  1.00  0.00              
ATOM   2204  C   ASP   281      31.129  16.203 -17.351  1.00  0.00              
ATOM   2205  O   ASP   281      30.857  15.803 -16.220  1.00  0.00              
ATOM   2206  N   SER   282      32.348  16.029 -17.900  1.00  0.00              
ATOM   2207  CA  SER   282      33.317  15.235 -17.201  1.00  0.00              
ATOM   2208  CB  SER   282      33.655  13.915 -17.917  1.00  0.00              
ATOM   2209  OG  SER   282      34.334  14.184 -19.136  1.00  0.00              
ATOM   2210  C   SER   282      34.593  15.997 -17.120  1.00  0.00              
ATOM   2211  O   SER   282      34.911  16.800 -17.996  1.00  0.00              
ATOM   2212  N   LEU   283      35.353  15.759 -16.034  1.00  0.00              
ATOM   2213  CA  LEU   283      36.612  16.414 -15.857  1.00  0.00              
ATOM   2214  CB  LEU   283      36.543  17.657 -14.949  1.00  0.00              
ATOM   2215  CG  LEU   283      35.755  17.473 -13.631  1.00  0.00              
ATOM   2216  CD1 LEU   283      36.383  16.426 -12.696  1.00  0.00              
ATOM   2217  CD2 LEU   283      35.570  18.826 -12.931  1.00  0.00              
ATOM   2218  C   LEU   283      37.549  15.453 -15.212  1.00  0.00              
ATOM   2219  O   LEU   283      37.136  14.499 -14.556  1.00  0.00              
TER
END
