
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_4-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    -       -      Y     150           -
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    L      79      F     159          0.738
LGA    E      80      Y     160          1.291
LGA    D      81      R     161          0.378
LGA    F      82      H     162          0.781
LGA    E      83      I     163          1.360
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    0.98     0.00      5.529     0.462

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.182773 * X  +   0.982857 * Y  +   0.024208 * Z  + -17.815718
  Y_new =  -0.538828 * X  +  -0.120735 * Y  +   0.833719 * Z  +  18.198330
  Z_new =   0.822350 * X  +   0.139337 * Y  +   0.551658 * Z  + -50.191608 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.247405   -2.894188  [ DEG:    14.1753   -165.8247 ]
  Theta =  -0.965528   -2.176064  [ DEG:   -55.3207   -124.6793 ]
  Phi   =  -1.897822    1.243771  [ DEG:  -108.7372     71.2628 ]
 
# 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_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_4-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   0.98    0.00   5.529
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_4-D2
REMARK Aligment from pdb entry: 1cbkA
ATOM    281  N   LEU    79       8.537  50.699   6.225  1.00  0.00              
ATOM    282  CA  LEU    79       9.773  50.034   6.662  1.00  0.00              
ATOM    283  C   LEU    79      10.195  48.916   5.713  1.00  0.00              
ATOM    284  O   LEU    79       9.685  48.834   4.603  1.00  0.00              
ATOM    285  N   GLU    80      11.083  48.033   6.161  1.00  0.00              
ATOM    286  CA  GLU    80      11.585  46.931   5.325  1.00  0.00              
ATOM    287  C   GLU    80      10.544  45.954   4.796  1.00  0.00              
ATOM    288  O   GLU    80      10.687  45.442   3.686  1.00  0.00              
ATOM    289  N   ASP    81       9.523  45.685   5.613  1.00  0.00              
ATOM    290  CA  ASP    81       8.456  44.752   5.265  1.00  0.00              
ATOM    291  C   ASP    81       7.098  45.381   4.960  1.00  0.00              
ATOM    292  O   ASP    81       6.263  44.752   4.307  1.00  0.00              
ATOM    293  N   PHE    82       6.864  46.612   5.414  1.00  0.00              
ATOM    294  CA  PHE    82       5.567  47.260   5.190  1.00  0.00              
ATOM    295  C   PHE    82       5.607  48.609   4.487  1.00  0.00              
ATOM    296  O   PHE    82       6.518  49.386   4.687  1.00  0.00              
ATOM    297  N   GLU    83       4.539  48.887   3.745  1.00  0.00              
ATOM    298  CA  GLU    83       4.345  50.126   3.000  1.00  0.00              
ATOM    299  C   GLU    83       2.865  50.426   3.230  1.00  0.00              
ATOM    300  O   GLU    83       2.009  49.992   2.453  1.00  0.00              
END
