
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0386AL381_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL381_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    -       -      N     219           -
LGA    K     234      P     220          1.796
LGA    N     235      E     221          1.336
LGA    T     236      K     222          1.919
LGA    G     237      I     223          3.514
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    R     238      K     227          2.124
LGA    N     239      E     228          1.149
LGA    V     240      F     229          2.619
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      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    N     241      G     260          5.769
LGA    D     242      A     261          4.494
LGA    R     243      G     262          2.041
LGA    P     244      L     263          1.548
LGA    V     245      E     264          1.384
LGA    M     246      G     265          2.742
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)   13   81    5.0     13    2.82     0.00     11.642     0.446

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.123865 * X  +   0.260031 * Y  +   0.957623 * Z  +  -0.478944
  Y_new =   0.918850 * X  +  -0.394433 * Y  +  -0.011746 * Z  +  91.986534
  Z_new =   0.374664 * X  +   0.881366 * Y  +  -0.287785 * Z  +  36.207306 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.886404   -1.255189  [ DEG:   108.0830    -71.9170 ]
  Theta =  -0.384034   -2.757558  [ DEG:   -22.0035   -157.9965 ]
  Phi   =   1.436800   -1.704792  [ DEG:    82.3226    -97.6774 ]
 
# 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: T0386AL381_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL381_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   81   5.0   13   2.82    0.00  11.642
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL381_1-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    617  N   LYS   234       1.441  56.629  74.873  1.00  0.00              
ATOM    618  CA  LYS   234       0.502  57.618  75.418  1.00  0.00              
ATOM    619  C   LYS   234       1.114  58.556  76.466  1.00  0.00              
ATOM    620  O   LYS   234       0.525  59.575  76.812  1.00  0.00              
ATOM    621  N   ASN   235       2.267  58.187  77.003  1.00  0.00              
ATOM    622  CA  ASN   235       2.761  58.868  78.169  1.00  0.00              
ATOM    623  C   ASN   235       4.213  59.315  78.023  1.00  0.00              
ATOM    624  O   ASN   235       4.904  59.463  79.011  1.00  0.00              
ATOM    625  N   THR   236       4.669  59.566  76.800  1.00  0.00              
ATOM    626  CA  THR   236       6.012  60.118  76.617  1.00  0.00              
ATOM    627  C   THR   236       5.936  61.615  76.822  1.00  0.00              
ATOM    628  O   THR   236       4.863  62.203  76.661  1.00  0.00              
ATOM    629  N   GLY   237       7.058  62.230  77.200  1.00  0.00              
ATOM    630  CA  GLY   237       7.164  63.682  77.279  1.00  0.00              
ATOM    631  C   GLY   237       8.527  64.054  76.735  1.00  0.00              
ATOM    632  O   GLY   237       9.479  63.314  76.922  1.00  0.00              
ATOM    633  N   ARG   238       8.652  65.189  76.058  1.00  0.00              
ATOM    634  CA  ARG   238       9.994  65.616  75.693  1.00  0.00              
ATOM    635  C   ARG   238      10.601  66.600  76.677  1.00  0.00              
ATOM    636  O   ARG   238      11.672  67.136  76.433  1.00  0.00              
ATOM    637  N   ASN   239       9.937  66.788  77.808  1.00  0.00              
ATOM    638  CA  ASN   239      10.454  67.665  78.855  1.00  0.00              
ATOM    639  C   ASN   239      11.348  66.810  79.775  1.00  0.00              
ATOM    640  O   ASN   239      11.005  66.566  80.927  1.00  0.00              
ATOM    641  N   VAL   240      12.493  66.372  79.253  1.00  0.00              
ATOM    642  CA  VAL   240      13.223  65.219  79.797  1.00  0.00              
ATOM    643  C   VAL   240      13.972  65.530  81.102  1.00  0.00              
ATOM    644  O   VAL   240      14.402  64.599  81.809  1.00  0.00              
ATOM    645  N   ASN   241      14.119  66.818  81.410  1.00  0.00              
ATOM    646  CA  ASN   241      14.907  67.259  82.556  1.00  0.00              
ATOM    647  C   ASN   241      14.074  68.034  83.568  1.00  0.00              
ATOM    648  O   ASN   241      14.610  68.670  84.462  1.00  0.00              
ATOM    649  N   ASP   242      12.765  67.974  83.416  1.00  0.00              
ATOM    650  CA  ASP   242      11.859  68.661  84.309  1.00  0.00              
ATOM    651  C   ASP   242      11.857  68.015  85.706  1.00  0.00              
ATOM    652  O   ASP   242      11.671  66.806  85.842  1.00  0.00              
ATOM    653  N   ARG   243      12.105  68.817  86.739  1.00  0.00              
ATOM    654  CA  ARG   243      12.177  68.310  88.110  1.00  0.00              
ATOM    655  C   ARG   243      10.918  67.530  88.544  1.00  0.00              
ATOM    656  O   ARG   243      11.030  66.490  89.186  1.00  0.00              
ATOM    657  N   PRO   244       9.736  68.010  88.174  1.00  0.00              
ATOM    658  CA  PRO   244       8.498  67.370  88.588  1.00  0.00              
ATOM    659  C   PRO   244       8.296  66.006  87.913  1.00  0.00              
ATOM    660  O   PRO   244       7.896  65.024  88.563  1.00  0.00              
ATOM    661  N   VAL   245       8.583  65.938  86.613  1.00  0.00              
ATOM    662  CA  VAL   245       8.525  64.687  85.869  1.00  0.00              
ATOM    663  C   VAL   245       9.546  63.701  86.419  1.00  0.00              
ATOM    664  O   VAL   245       9.221  62.530  86.624  1.00  0.00              
ATOM    665  N   MET   246      10.773  64.156  86.665  1.00  0.00              
ATOM    666  CA  MET   246      11.792  63.261  87.221  1.00  0.00              
ATOM    667  C   MET   246      11.360  62.734  88.618  1.00  0.00              
ATOM    668  O   MET   246      11.237  61.531  88.829  1.00  0.00              
END
