
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0289AL333_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL333_5-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I     224           -
LGA    -       -      M     225           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    F     261      Y     230          2.070
LGA    V     262      P     231          4.134
LGA    S     263      R     232          0.825
LGA    L     264      N     233          5.039
LGA    D     265      E     234           -
LGA    G     266      S     235           -
LGA    K     267      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    V     268      A     239          4.062
LGA    I     269      A     240          2.448
LGA    P     270      V     241          4.231
LGA    L     271      -       -           -
LGA    G     272      I     242          3.059
LGA    G     273      H     243          2.450
LGA    D     274      P     244          2.141
LGA    C     275      N     245          1.586
LGA    Y     288      L     246          1.794
LGA    E     289      Q     247          1.782
LGA    K     290      D     248          2.527
LGA    K     291      Q     249          2.927
LGA    E     292      D     250          3.952
LGA    A     293      -       -           -
LGA    F     294      W     251          2.814
LGA    A     295      K     252          4.274
LGA    -       -      P     253           -
LGA    -       -      L     254           -
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    -       -      L     271           -
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    -       -      P     279           -
LGA    K     296      V     280          2.040
LGA    T     297      F     281           -
LGA    -       -      V     282           -
LGA    -       -      N     283           -
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   74    5.0     19    3.06     0.00     16.347     0.602

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.969816 * X  +   0.120698 * Y  +   0.211870 * Z  +  -8.963687
  Y_new =   0.230442 * X  +  -0.169649 * Y  +  -0.958184 * Z  +  89.584114
  Z_new =  -0.079707 * X  +   0.978086 * Y  +  -0.192342 * Z  +   7.373844 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.764970   -1.376623  [ DEG:   101.1253    -78.8747 ]
  Theta =   0.079792    3.061801  [ DEG:     4.5717    175.4283 ]
  Phi   =   0.233288   -2.908305  [ DEG:    13.3664   -166.6336 ]
 
# 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: T0289AL333_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL333_5-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   74   5.0   19   3.06    0.00  16.347
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL333_5-D2
REMARK Aligment from pdb entry: 1jwq_A
ATOM    521  N   PHE   261      19.787  39.955  30.702  1.00  0.00              
ATOM    522  CA  PHE   261      18.490  40.550  31.031  1.00  0.00              
ATOM    523  C   PHE   261      18.570  41.991  31.502  1.00  0.00              
ATOM    524  O   PHE   261      19.254  42.299  32.474  1.00  0.00              
ATOM    525  N   VAL   262      17.853  42.867  30.805  1.00  0.00              
ATOM    526  CA  VAL   262      17.819  44.281  31.146  1.00  0.00              
ATOM    527  C   VAL   262      16.826  44.523  32.275  1.00  0.00              
ATOM    528  O   VAL   262      16.741  45.627  32.808  1.00  0.00              
ATOM    529  N   SER   263      16.074  43.482  32.619  1.00  0.00              
ATOM    530  CA  SER   263      15.072  43.556  33.679  1.00  0.00              
ATOM    531  C   SER   263      15.672  43.297  35.060  1.00  0.00              
ATOM    532  O   SER   263      14.991  43.426  36.079  1.00  0.00              
ATOM    533  N   LEU   264      16.946  42.918  35.083  1.00  0.00              
ATOM    534  CA  LEU   264      17.662  42.665  36.328  1.00  0.00              
ATOM    535  C   LEU   264      18.590  43.859  36.533  1.00  0.00              
ATOM    536  O   LEU   264      19.374  44.199  35.654  1.00  0.00              
ATOM    537  N   ASP   265      18.484  44.502  37.690  1.00  0.00              
ATOM    538  CA  ASP   265      19.290  45.682  37.990  1.00  0.00              
ATOM    539  C   ASP   265      20.789  45.511  37.771  1.00  0.00              
ATOM    540  O   ASP   265      21.414  46.307  37.066  1.00  0.00              
ATOM    541  N   GLY   266      21.372  44.485  38.380  1.00  0.00              
ATOM    542  CA  GLY   266      22.807  44.251  38.240  1.00  0.00              
ATOM    543  C   GLY   266      23.198  43.898  36.809  1.00  0.00              
ATOM    544  O   GLY   266      24.176  44.423  36.276  1.00  0.00              
ATOM    545  N   LYS   267      22.426  43.013  36.187  1.00  0.00              
ATOM    546  CA  LYS   267      22.724  42.593  34.828  1.00  0.00              
ATOM    547  C   LYS   267      22.586  43.731  33.818  1.00  0.00              
ATOM    548  O   LYS   267      23.380  43.832  32.882  1.00  0.00              
ATOM    549  N   VAL   268      21.585  44.587  33.999  1.00  0.00              
ATOM    550  CA  VAL   268      21.412  45.719  33.093  1.00  0.00              
ATOM    551  C   VAL   268      22.662  46.596  33.142  1.00  0.00              
ATOM    552  O   VAL   268      23.187  47.007  32.109  1.00  0.00              
ATOM    553  N   ILE   269      23.129  46.891  34.353  1.00  0.00              
ATOM    554  CA  ILE   269      24.323  47.716  34.522  1.00  0.00              
ATOM    555  C   ILE   269      25.503  47.061  33.812  1.00  0.00              
ATOM    556  O   ILE   269      26.282  47.725  33.125  1.00  0.00              
ATOM    557  N   PRO   270      25.625  45.751  33.979  1.00  0.00              
ATOM    558  CA  PRO   270      26.701  44.996  33.358  1.00  0.00              
ATOM    559  C   PRO   270      26.639  45.062  31.835  1.00  0.00              
ATOM    560  O   PRO   270      27.657  45.273  31.180  1.00  0.00              
ATOM    561  N   LEU   271      25.450  44.882  31.266  1.00  0.00              
ATOM    562  CA  LEU   271      25.318  44.924  29.814  1.00  0.00              
ATOM    563  C   LEU   271      25.710  46.280  29.239  1.00  0.00              
ATOM    564  O   LEU   271      26.153  46.366  28.094  1.00  0.00              
ATOM    565  N   GLY   272      25.551  47.340  30.027  1.00  0.00              
ATOM    566  CA  GLY   272      25.926  48.661  29.545  1.00  0.00              
ATOM    567  C   GLY   272      27.306  49.086  30.016  1.00  0.00              
ATOM    568  O   GLY   272      27.664  50.261  29.943  1.00  0.00              
ATOM    569  N   GLY   273      28.081  48.118  30.490  1.00  0.00              
ATOM    570  CA  GLY   273      29.445  48.373  30.931  1.00  0.00              
ATOM    571  C   GLY   273      30.340  48.192  29.707  1.00  0.00              
ATOM    572  O   GLY   273      30.278  47.165  29.029  1.00  0.00              
ATOM    573  N   ASP   274      31.166  49.193  29.424  1.00  0.00              
ATOM    574  CA  ASP   274      32.054  49.145  28.269  1.00  0.00              
ATOM    575  C   ASP   274      32.963  47.934  28.182  1.00  0.00              
ATOM    576  O   ASP   274      33.092  47.333  27.117  1.00  0.00              
ATOM    577  N   CYS   275      33.598  47.571  29.292  1.00  0.00              
ATOM    578  CA  CYS   275      34.499  46.428  29.284  1.00  0.00              
ATOM    579  C   CYS   275      33.741  45.141  28.982  1.00  0.00              
ATOM    580  O   CYS   275      34.223  44.289  28.239  1.00  0.00              
ATOM    581  N   TYR   288      32.554  45.011  29.562  1.00  0.00              
ATOM    582  CA  TYR   288      31.711  43.840  29.339  1.00  0.00              
ATOM    583  C   TYR   288      31.424  43.716  27.848  1.00  0.00              
ATOM    584  O   TYR   288      31.624  42.657  27.254  1.00  0.00              
ATOM    585  N   GLU   289      30.961  44.808  27.250  1.00  0.00              
ATOM    586  CA  GLU   289      30.635  44.820  25.828  1.00  0.00              
ATOM    587  C   GLU   289      31.820  44.425  24.959  1.00  0.00              
ATOM    588  O   GLU   289      31.683  43.624  24.038  1.00  0.00              
ATOM    589  N   LYS   290      32.988  44.984  25.250  1.00  0.00              
ATOM    590  CA  LYS   290      34.172  44.668  24.463  1.00  0.00              
ATOM    591  C   LYS   290      34.540  43.196  24.549  1.00  0.00              
ATOM    592  O   LYS   290      34.904  42.579  23.550  1.00  0.00              
ATOM    593  N   LYS   291      34.440  42.640  25.749  1.00  0.00              
ATOM    594  CA  LYS   291      34.762  41.241  25.982  1.00  0.00              
ATOM    595  C   LYS   291      33.777  40.335  25.241  1.00  0.00              
ATOM    596  O   LYS   291      34.166  39.364  24.587  1.00  0.00              
ATOM    597  N   GLU   292      32.496  40.669  25.347  1.00  0.00              
ATOM    598  CA  GLU   292      31.442  39.897  24.704  1.00  0.00              
ATOM    599  C   GLU   292      31.508  40.037  23.190  1.00  0.00              
ATOM    600  O   GLU   292      31.298  39.067  22.466  1.00  0.00              
ATOM    601  N   ALA   293      31.811  41.243  22.717  1.00  0.00              
ATOM    602  CA  ALA   293      31.918  41.485  21.284  1.00  0.00              
ATOM    603  C   ALA   293      33.019  40.601  20.714  1.00  0.00              
ATOM    604  O   ALA   293      32.900  40.076  19.606  1.00  0.00              
ATOM    605  N   PHE   294      34.099  40.439  21.471  1.00  0.00              
ATOM    606  CA  PHE   294      35.195  39.601  21.003  1.00  0.00              
ATOM    607  C   PHE   294      34.742  38.150  20.976  1.00  0.00              
ATOM    608  O   PHE   294      35.106  37.397  20.076  1.00  0.00              
ATOM    609  N   ALA   295      33.949  37.764  21.970  1.00  0.00              
ATOM    610  CA  ALA   295      33.451  36.402  22.029  1.00  0.00              
ATOM    611  C   ALA   295      32.556  36.108  20.838  1.00  0.00              
ATOM    612  O   ALA   295      32.647  35.044  20.225  1.00  0.00              
ATOM    613  N   LYS   296      31.685  37.054  20.509  1.00  0.00              
ATOM    614  CA  LYS   296      30.782  36.895  19.375  1.00  0.00              
ATOM    615  C   LYS   296      31.602  36.822  18.087  1.00  0.00              
ATOM    616  O   LYS   296      31.338  35.995  17.208  1.00  0.00              
ATOM    617  N   THR   297      32.612  37.679  17.990  1.00  0.00              
ATOM    618  CA  THR   297      33.478  37.689  16.819  1.00  0.00              
ATOM    619  C   THR   297      34.166  36.332  16.679  1.00  0.00              
ATOM    620  O   THR   297      34.249  35.789  15.584  1.00  0.00              
END
