
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0386AL509_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL509_1-D2.T0386_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    K     222      N     219          0.994
LGA    I     223      P     220          0.393
LGA    R     224      E     221          1.020
LGA    L     225      K     222          0.161
LGA    L     226      I     223          0.311
LGA    K     227      R     224          0.479
LGA    E     228      L     225          0.394
LGA    F     229      L     226          0.366
LGA    M     230      K     227          0.568
LGA    H     231      E     228          0.628
LGA    T     232      F     229          0.759
LGA    M     233      M     230          0.271
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    A     261      M     233          0.757
LGA    G     262      K     234          1.238
LGA    L     263      N     235           #
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   81    5.0     14    0.67     7.14     17.641     1.817

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.286141 * X  +  -0.294429 * Y  +   0.911830 * Z  +  30.375561
  Y_new =  -0.420402 * X  +   0.816559 * Y  +   0.395593 * Z  +  10.827044
  Z_new =  -0.861037 * X  +  -0.496530 * Y  +   0.109873 * Z  +  90.008430 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.353024    1.788568  [ DEG:   -77.5226    102.4774 ]
  Theta =   1.037306    2.104286  [ DEG:    59.4333    120.5667 ]
  Phi   =  -0.973183    2.168409  [ DEG:   -55.7593    124.2407 ]
 
# 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: T0386AL509_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL509_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   81   5.0   14   0.67    7.14  17.641
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL509_1-D2
REMARK Aligment from pdb entry: 2f6sA_
ATOM    337  N   LYS   222       2.476  55.015  76.405  1.00  0.00              
ATOM    338  CA  LYS   222       3.197  55.891  75.465  1.00  0.00              
ATOM    339  C   LYS   222       2.786  57.376  75.588  1.00  0.00              
ATOM    340  O   LYS   222       3.596  58.246  75.243  1.00  0.00              
ATOM    341  N   ILE   223       1.586  57.667  76.108  1.00  0.00              
ATOM    342  CA  ILE   223       1.217  59.068  76.401  1.00  0.00              
ATOM    343  C   ILE   223       2.194  59.681  77.425  1.00  0.00              
ATOM    344  O   ILE   223       2.767  60.759  77.196  1.00  0.00              
ATOM    345  N   ARG   224       2.390  58.972  78.537  1.00  0.00              
ATOM    346  CA  ARG   224       3.338  59.355  79.579  1.00  0.00              
ATOM    347  C   ARG   224       4.750  59.551  79.009  1.00  0.00              
ATOM    348  O   ARG   224       5.436  60.513  79.344  1.00  0.00              
ATOM    349  N   LEU   225       5.155  58.640  78.132  1.00  0.00              
ATOM    350  CA  LEU   225       6.481  58.665  77.547  1.00  0.00              
ATOM    351  C   LEU   225       6.657  59.859  76.609  1.00  0.00              
ATOM    352  O   LEU   225       7.690  60.526  76.637  1.00  0.00              
ATOM    353  N   LEU   226       5.639  60.141  75.805  1.00  0.00              
ATOM    354  CA  LEU   226       5.671  61.277  74.888  1.00  0.00              
ATOM    355  C   LEU   226       5.693  62.609  75.653  1.00  0.00              
ATOM    356  O   LEU   226       6.484  63.491  75.323  1.00  0.00              
ATOM    357  N   LYS   227       4.847  62.739  76.674  1.00  0.00              
ATOM    358  CA  LYS   227       4.898  63.897  77.567  1.00  0.00              
ATOM    359  C   LYS   227       6.291  64.093  78.158  1.00  0.00              
ATOM    360  O   LYS   227       6.791  65.218  78.231  1.00  0.00              
ATOM    361  N   GLU   228       6.914  62.988  78.555  1.00  0.00              
ATOM    362  CA  GLU   228       8.259  62.995  79.070  1.00  0.00              
ATOM    363  C   GLU   228       9.272  63.514  78.068  1.00  0.00              
ATOM    364  O   GLU   228      10.095  64.388  78.394  1.00  0.00              
ATOM    365  N   PHE   229       9.224  62.991  76.847  1.00  0.00              
ATOM    366  CA  PHE   229      10.212  63.364  75.844  1.00  0.00              
ATOM    367  C   PHE   229       9.998  64.790  75.364  1.00  0.00              
ATOM    368  O   PHE   229      10.956  65.487  75.087  1.00  0.00              
ATOM    369  N   MET   230       8.742  65.230  75.290  1.00  0.00              
ATOM    370  CA  MET   230       8.433  66.607  74.945  1.00  0.00              
ATOM    371  C   MET   230       9.089  67.545  75.967  1.00  0.00              
ATOM    372  O   MET   230       9.627  68.582  75.605  1.00  0.00              
ATOM    373  N   HIS   231       9.062  67.176  77.241  1.00  0.00              
ATOM    374  CA  HIS   231       9.647  68.010  78.274  1.00  0.00              
ATOM    375  C   HIS   231      11.168  68.000  78.155  1.00  0.00              
ATOM    376  O   HIS   231      11.816  69.045  78.305  1.00  0.00              
ATOM    377  N   THR   232      11.730  66.824  77.864  1.00  0.00              
ATOM    378  CA  THR   232      13.156  66.699  77.656  1.00  0.00              
ATOM    379  C   THR   232      13.620  67.692  76.580  1.00  0.00              
ATOM    380  O   THR   232      14.624  68.383  76.758  1.00  0.00              
ATOM    381  N   MET   233      12.884  67.762  75.469  1.00  0.00              
ATOM    382  CA  MET   233      13.202  68.697  74.383  1.00  0.00              
ATOM    383  C   MET   233      12.956  70.147  74.784  1.00  0.00              
ATOM    384  O   MET   233      13.656  71.060  74.331  1.00  0.00              
ATOM    385  N   ALA   261      15.874  71.920  76.399  1.00  0.00              
ATOM    386  CA  ALA   261      16.842  72.432  75.453  1.00  0.00              
ATOM    387  C   ALA   261      16.339  73.687  74.728  1.00  0.00              
ATOM    388  O   ALA   261      17.010  74.183  73.820  1.00  0.00              
ATOM    389  N   GLY   262      15.161  74.194  75.116  1.00  0.00              
ATOM    390  CA  GLY   262      14.601  75.416  74.529  1.00  0.00              
ATOM    391  C   GLY   262      13.582  75.250  73.405  1.00  0.00              
ATOM    392  O   GLY   262      13.242  76.222  72.723  1.00  0.00              
ATOM    393  N   LEU   263      13.089  74.032  73.194  1.00  0.00              
ATOM    394  CA  LEU   263      12.036  73.804  72.201  1.00  0.00              
ATOM    395  C   LEU   263      10.660  74.038  72.823  1.00  0.00              
ATOM    396  O   LEU   263      10.269  73.331  73.754  1.00  0.00              
END
