
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0299AL243_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_5-D2.T0299_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    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      F      82           -
LGA    -       -      E      83           -
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    -       -      W      93           -
LGA    -       -      S      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      R      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      F     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
LGA    -       -      K     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    -       -      G     138           -
LGA    -       -      K     139           -
LGA    -       -      F     140           -
LGA    -       -      S     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      S     144           -
LGA    -       -      Y     145           -
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    -       -      T     148           -
LGA    -       -      A     149           -
LGA    L      79      Y     150          0.343
LGA    E      80      H     151          0.446
LGA    D      81      K     152          0.153
LGA    F      82      Y     153          0.549
LGA    E      83      L     154          0.759
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    -       -      F     159           -
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    -       -      I     163           -
LGA    -       -      T     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   89    5.0      5    0.49     0.00      5.618     0.842

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.034587 * X  +   0.926653 * Y  +  -0.374322 * Z  +  -4.465743
  Y_new =   0.998309 * X  +  -0.014527 * Y  +   0.056280 * Z  +  17.955750
  Z_new =   0.046714 * X  +  -0.375636 * Y  +  -0.925589 * Z  +  37.590881 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.756067    0.385526  [ DEG:  -157.9110     22.0890 ]
  Theta =  -0.046731   -3.094862  [ DEG:    -2.6775   -177.3225 ]
  Phi   =   1.536165   -1.605428  [ DEG:    88.0158    -91.9842 ]
 
# 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: T0299AL243_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_5-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   89   5.0    5   0.49    0.00   5.618
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_5-D2
REMARK Aligment from pdb entry: 1dy3A
ATOM    273  N   LEU    79      16.329  52.922  -2.076  1.00  0.00              
ATOM    274  CA  LEU    79      17.350  53.042  -3.112  1.00  0.00              
ATOM    275  C   LEU    79      17.961  51.674  -3.386  1.00  0.00              
ATOM    276  O   LEU    79      17.687  50.737  -2.651  1.00  0.00              
ATOM    277  N   GLU    80      18.835  51.577  -4.384  1.00  0.00              
ATOM    278  CA  GLU    80      19.467  50.287  -4.708  1.00  0.00              
ATOM    279  C   GLU    80      20.371  49.834  -3.587  1.00  0.00              
ATOM    280  O   GLU    80      20.509  48.630  -3.321  1.00  0.00              
ATOM    281  N   ASP    81      20.985  50.772  -2.833  1.00  0.00              
ATOM    282  CA  ASP    81      21.839  50.380  -1.733  1.00  0.00              
ATOM    283  C   ASP    81      21.079  50.226  -0.411  1.00  0.00              
ATOM    284  O   ASP    81      21.506  49.475   0.461  1.00  0.00              
ATOM    285  N   PHE    82      20.013  51.002  -0.259  1.00  0.00              
ATOM    286  CA  PHE    82      19.350  50.994   1.052  1.00  0.00              
ATOM    287  C   PHE    82      17.849  51.066   1.041  1.00  0.00              
ATOM    288  O   PHE    82      17.219  51.939   0.431  1.00  0.00              
ATOM    289  N   GLU    83      17.255  50.060   1.687  1.00  0.00              
ATOM    290  CA  GLU    83      15.797  49.959   1.843  1.00  0.00              
ATOM    291  C   GLU    83      15.536  49.980   3.346  1.00  0.00              
ATOM    292  O   GLU    83      16.006  49.130   4.096  1.00  0.00              
END
