
#######################################################
#                                                     #
#                        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   17 (   72),  selected   17 , name T0386AL170_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL170_1-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    N     219      P     220          1.284
LGA    P     220      E     221          1.651
LGA    E     221      K     222          1.052
LGA    K     222      I     223          0.706
LGA    I     223      R     224          0.311
LGA    L     226      L     225          0.611
LGA    K     227      L     226          0.459
LGA    E     228      K     227          0.582
LGA    F     229      E     228          0.623
LGA    M     230      F     229          0.601
LGA    H     231      M     230          0.559
LGA    T     232      H     231          0.939
LGA    M     233      T     232          0.906
LGA    K     234      M     233          0.953
LGA    N     235      K     234          1.021
LGA    T     236      N     235          2.154
LGA    G     237      T     236          1.909
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)   17   81    5.0     17    1.08     5.88     20.327     1.435

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.013098 * X  +   0.665427 * Y  +  -0.746348 * Z  + -36.350010
  Y_new =  -0.876607 * X  +   0.366718 * Y  +   0.311573 * Z  +  38.064640
  Z_new =   0.481028 * X  +   0.650173 * Y  +   0.588122 * Z  +  43.618515 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.835466   -2.306126  [ DEG:    47.8687   -132.1313 ]
  Theta =  -0.501827   -2.639766  [ DEG:   -28.7526   -151.2475 ]
  Phi   =  -1.555855    1.585737  [ DEG:   -89.1439     90.8561 ]
 
# 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: T0386AL170_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL170_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17   81   5.0   17   1.08    5.88  20.327
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL170_1-D2
REMARK Aligment from pdb entry: 2G03_A
ATOM    633  N   ASN   219       0.359  60.264  77.387  1.00  0.00              
ATOM    634  CA  ASN   219       1.403  59.266  77.314  1.00  0.00              
ATOM    635  C   ASN   219       2.686  59.749  78.013  1.00  0.00              
ATOM    636  O   ASN   219       3.188  60.836  77.729  1.00  0.00              
ATOM    637  N   PRO   220       3.190  58.957  78.956  1.00  0.00              
ATOM    638  CA  PRO   220       4.380  59.331  79.722  1.00  0.00              
ATOM    639  C   PRO   220       5.598  59.675  78.839  1.00  0.00              
ATOM    640  O   PRO   220       6.307  60.638  79.117  1.00  0.00              
ATOM    641  N   GLU   221       5.822  58.915  77.773  1.00  0.00              
ATOM    642  CA  GLU   221       6.979  59.133  76.920  1.00  0.00              
ATOM    643  C   GLU   221       6.874  60.440  76.123  1.00  0.00              
ATOM    644  O   GLU   221       7.851  61.201  76.010  1.00  0.00              
ATOM    645  N   LYS   222       5.687  60.710  75.579  1.00  0.00              
ATOM    646  CA  LYS   222       5.421  61.958  74.874  1.00  0.00              
ATOM    647  C   LYS   222       5.551  63.137  75.828  1.00  0.00              
ATOM    648  O   LYS   222       6.175  64.142  75.482  1.00  0.00              
ATOM    649  N   ILE   223       4.977  63.030  77.025  1.00  0.00              
ATOM    650  CA  ILE   223       5.091  64.121  77.996  1.00  0.00              
ATOM    651  C   ILE   223       6.578  64.368  78.376  1.00  0.00              
ATOM    652  O   ILE   223       7.105  65.459  78.187  1.00  0.00              
ATOM    653  N   LEU   226       7.264  63.348  78.857  1.00  0.00              
ATOM    654  CA  LEU   226       8.610  63.548  79.378  1.00  0.00              
ATOM    655  C   LEU   226       9.722  63.803  78.343  1.00  0.00              
ATOM    656  O   LEU   226      10.576  64.640  78.590  1.00  0.00              
ATOM    657  N   LYS   227       9.704  63.102  77.209  1.00  0.00              
ATOM    658  CA  LYS   227      10.636  63.400  76.120  1.00  0.00              
ATOM    659  C   LYS   227      10.341  64.773  75.529  1.00  0.00              
ATOM    660  O   LYS   227      11.252  65.448  75.043  1.00  0.00              
ATOM    661  N   GLU   228       9.071  65.183  75.582  1.00  0.00              
ATOM    662  CA  GLU   228       8.644  66.498  75.146  1.00  0.00              
ATOM    663  C   GLU   228       9.162  67.621  76.023  1.00  0.00              
ATOM    664  O   GLU   228       9.630  68.634  75.518  1.00  0.00              
ATOM    665  N   PHE   229       9.036  67.468  77.339  1.00  0.00              
ATOM    666  CA  PHE   229       9.618  68.393  78.311  1.00  0.00              
ATOM    667  C   PHE   229      11.133  68.511  78.106  1.00  0.00              
ATOM    668  O   PHE   229      11.671  69.609  78.107  1.00  0.00              
ATOM    669  N   MET   230      11.820  67.387  77.945  1.00  0.00              
ATOM    670  CA  MET   230      13.245  67.438  77.635  1.00  0.00              
ATOM    671  C   MET   230      13.571  68.216  76.357  1.00  0.00              
ATOM    672  O   MET   230      14.553  68.945  76.326  1.00  0.00              
ATOM    673  N   HIS   231      12.766  68.051  75.312  1.00  0.00              
ATOM    674  CA  HIS   231      13.019  68.741  74.054  1.00  0.00              
ATOM    675  C   HIS   231      12.734  70.232  74.215  1.00  0.00              
ATOM    676  O   HIS   231      13.520  71.058  73.790  1.00  0.00              
ATOM    677  N   THR   232      11.612  70.568  74.849  1.00  0.00              
ATOM    678  CA  THR   232      11.248  71.940  75.157  1.00  0.00              
ATOM    679  C   THR   232      12.359  72.712  75.875  1.00  0.00              
ATOM    680  O   THR   232      12.646  73.873  75.537  1.00  0.00              
ATOM    681  N  AMET   233      12.964  72.078  76.878  1.00  0.00              
ATOM    682  N  BMET   233      12.944  72.072  76.871  1.00  0.00              
ATOM    683  CA AMET   233      14.051  72.678  77.664  1.00  0.00              
ATOM    684  CA BMET   233      14.009  72.654  77.655  1.00  0.00              
ATOM    685  C  AMET   233      15.352  72.799  76.867  1.00  0.00              
ATOM    686  C  BMET   233      15.271  72.855  76.806  1.00  0.00              
ATOM    687  O  AMET   233      16.203  73.659  77.160  1.00  0.00              
ATOM    688  O  BMET   233      16.026  73.813  77.024  1.00  0.00              
ATOM    689  N   LYS   234      15.499  71.937  75.865  1.00  0.00              
ATOM    690  CA  LYS   234      16.634  71.993  74.938  1.00  0.00              
ATOM    691  C   LYS   234      16.557  73.206  73.964  1.00  0.00              
ATOM    692  O   LYS   234      17.582  73.777  73.593  1.00  0.00              
ATOM    693  N   ASN   235      15.346  73.616  73.593  1.00  0.00              
ATOM    694  CA  ASN   235      15.146  74.688  72.627  1.00  0.00              
ATOM    695  C   ASN   235      15.812  75.961  73.091  1.00  0.00              
ATOM    696  O   ASN   235      16.294  76.749  72.275  1.00  0.00              
ATOM    697  N   THR   236      15.870  76.179  74.399  1.00  0.00              
ATOM    698  CA  THR   236      16.474  77.438  74.844  1.00  0.00              
ATOM    699  C   THR   236      17.692  77.242  75.717  1.00  0.00              
ATOM    700  O   THR   236      18.027  78.125  76.485  1.00  0.00              
ATOM    701  N   GLY   237      18.390  76.119  75.552  1.00  0.00              
ATOM    702  CA  GLY   237      19.577  75.815  76.368  1.00  0.00              
ATOM    703  C   GLY   237      20.365  74.627  75.847  1.00  0.00              
ATOM    704  O   GLY   237      21.095  73.954  76.598  1.00  0.00              
END
