
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0320AL044_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228           -
LGA    N     229      N     229           -
LGA    S     230      S     230           -
LGA    L     231      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    P     232      W     249           #
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    N     233      I     252          2.820
LGA    P     234      H     253          2.241
LGA    L     236      A     254          2.670
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    S     240      K     257          4.435
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    N     241      S     264          5.360
LGA    N     242      S     265           -
LGA    P     243      A     266           #
LGA    A     244      I     267          2.716
LGA    L     245      -       -           -
LGA    H     246      -       -           -
LGA    F     247      N     268          2.671
LGA    E     248      T     269          2.577
LGA    W     249      S     270          2.188
LGA    E     250      -       -           -
LGA    I     251      -       -           -
LGA    G     256      P     271          1.051
LGA    K     257      -       -           -
LGA    D     258      -       -           -
LGA    A     259      I     272          1.669
LGA    E     260      S     273          0.988
LGA    G     261      -       -           -
LGA    E     262      V     274          5.417
LGA    R     263      V     275          2.805
LGA    S     264      D     276          4.673
LGA    S     265      K     277           #
LGA    -       -      E     278           -
LGA    A     266      R     279           #
LGA    I     267      -       -           -
LGA    N     268      F     280          3.005
LGA    T     269      S     281          3.869
LGA    S     270      K     282          4.173
LGA    P     271      Y     283           #
LGA    I     272      H     284           -
LGA    S     273      -       -           -
LGA    V     274      -       -           -
LGA    V     275      -       -           -
LGA    D     276      -       -           -
LGA    K     277      -       -           -
LGA    E     278      -       -           -
LGA    R     279      D     285           #
LGA    F     280      N     286           -
LGA    S     281      Y     287           -
LGA    H     284      Y     288           -
LGA    D     285      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   73    5.0     18    3.33     0.00     16.048     0.525

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.844774 * X  +  -0.499796 * Y  +   0.191209 * Z  + -30.352667
  Y_new =  -0.205779 * X  +  -0.026434 * Y  +  -0.978242 * Z  +  84.375359
  Z_new =   0.493976 * X  +  -0.865740 * Y  +  -0.080516 * Z  +  16.271441 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.663532    1.478060  [ DEG:   -95.3134     84.6866 ]
  Theta =  -0.516656   -2.624936  [ DEG:   -29.6022   -150.3978 ]
  Phi   =  -2.902656    0.238937  [ DEG:  -166.3099     13.6901 ]
 
# 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: T0320AL044_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   73   5.0   18   3.33    0.00  16.048
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_2-D2
REMARK Aligment from pdb entry: 1wy5_A
ATOM    729  N   ASN   228     -10.372  25.883   3.464  1.00  0.00              
ATOM    730  CA  ASN   228     -11.371  25.456   4.458  1.00  0.00              
ATOM    731  C   ASN   228     -11.171  23.982   4.845  1.00  0.00              
ATOM    732  O   ASN   228     -11.315  23.619   6.016  1.00  0.00              
ATOM    733  N   ASN   229     -10.832  23.137   3.865  1.00  0.00              
ATOM    734  CA  ASN   229     -10.591  21.720   4.141  1.00  0.00              
ATOM    735  C   ASN   229      -9.350  21.525   5.005  1.00  0.00              
ATOM    736  O   ASN   229      -9.346  20.699   5.915  1.00  0.00              
ATOM    737  N   SER   230      -8.293  22.276   4.710  1.00  0.00              
ATOM    738  CA  SER   230      -7.063  22.161   5.465  1.00  0.00              
ATOM    739  C   SER   230      -7.276  22.613   6.896  1.00  0.00              
ATOM    740  O   SER   230      -6.693  22.051   7.824  1.00  0.00              
ATOM    741  N   LEU   231      -8.114  23.630   7.071  1.00  0.00              
ATOM    742  CA  LEU   231      -8.393  24.165   8.399  1.00  0.00              
ATOM    743  C   LEU   231      -9.259  23.222   9.220  1.00  0.00              
ATOM    744  O   LEU   231      -9.366  23.366  10.434  1.00  0.00              
ATOM    745  N   PRO   232      -9.866  22.246   8.557  1.00  0.00              
ATOM    746  CA  PRO   232     -10.688  21.275   9.261  1.00  0.00              
ATOM    747  C   PRO   232      -9.731  20.248   9.871  1.00  0.00              
ATOM    748  O   PRO   232     -10.074  19.549  10.819  1.00  0.00              
ATOM    749  N   ASN   233      -6.318  21.265  10.594  1.00  0.00              
ATOM    750  CA  ASN   233      -5.614  22.111  11.545  1.00  0.00              
ATOM    751  C   ASN   233      -6.296  23.477  11.658  1.00  0.00              
ATOM    752  O   ASN   233      -6.218  24.322  10.762  1.00  0.00              
ATOM    753  N   PRO   234      -6.960  23.671  12.785  1.00  0.00              
ATOM    754  CA  PRO   234      -7.688  24.891  13.106  1.00  0.00              
ATOM    755  C   PRO   234      -6.844  26.175  13.037  1.00  0.00              
ATOM    756  O   PRO   234      -7.345  27.240  12.682  1.00  0.00              
ATOM    757  N   LEU   236      -5.563  26.073  13.373  1.00  0.00              
ATOM    758  CA  LEU   236      -4.693  27.243  13.350  1.00  0.00              
ATOM    759  C   LEU   236      -3.692  27.177  12.203  1.00  0.00              
ATOM    760  O   LEU   236      -2.497  27.408  12.404  1.00  0.00              
ATOM    761  N   SER   240      -4.188  26.872  11.005  1.00  0.00              
ATOM    762  CA  SER   240      -3.349  26.756   9.816  1.00  0.00              
ATOM    763  C   SER   240      -2.448  27.969   9.598  1.00  0.00              
ATOM    764  O   SER   240      -1.255  27.810   9.332  1.00  0.00              
ATOM    765  N   ASN   241      -3.011  29.175   9.720  1.00  0.00              
ATOM    766  CA  ASN   241      -2.239  30.405   9.508  1.00  0.00              
ATOM    767  C   ASN   241      -1.066  30.561  10.475  1.00  0.00              
ATOM    768  O   ASN   241       0.038  30.911  10.061  1.00  0.00              
ATOM    769  N   ASN   242      -1.294  30.300  11.758  1.00  0.00              
ATOM    770  CA  ASN   242      -0.231  30.426  12.748  1.00  0.00              
ATOM    771  C   ASN   242       0.871  29.421  12.456  1.00  0.00              
ATOM    772  O   ASN   242       2.060  29.720  12.571  1.00  0.00              
ATOM    773  N   PRO   243       0.462  28.223  12.076  1.00  0.00              
ATOM    774  CA  PRO   243       1.398  27.168  11.751  1.00  0.00              
ATOM    775  C   PRO   243       2.197  27.494  10.478  1.00  0.00              
ATOM    776  O   PRO   243       3.424  27.340  10.429  1.00  0.00              
ATOM    777  N   ALA   244       1.485  27.952   9.457  1.00  0.00              
ATOM    778  CA  ALA   244       2.082  28.321   8.191  1.00  0.00              
ATOM    779  C   ALA   244       3.158  29.403   8.376  1.00  0.00              
ATOM    780  O   ALA   244       4.251  29.304   7.806  1.00  0.00              
ATOM    781  N   LEU   245       2.850  30.432   9.170  1.00  0.00              
ATOM    782  CA  LEU   245       3.808  31.511   9.417  1.00  0.00              
ATOM    783  C   LEU   245       5.130  30.983   9.961  1.00  0.00              
ATOM    784  O   LEU   245       6.194  31.488   9.611  1.00  0.00              
ATOM    785  N   HIS   246       5.075  29.970  10.821  1.00  0.00              
ATOM    786  CA  HIS   246       6.304  29.413  11.370  1.00  0.00              
ATOM    787  C   HIS   246       7.130  28.753  10.269  1.00  0.00              
ATOM    788  O   HIS   246       8.360  28.841  10.274  1.00  0.00              
ATOM    789  N   PHE   247       6.451  28.102   9.327  1.00  0.00              
ATOM    790  CA  PHE   247       7.122  27.448   8.207  1.00  0.00              
ATOM    791  C   PHE   247       7.837  28.527   7.403  1.00  0.00              
ATOM    792  O   PHE   247       9.017  28.400   7.087  1.00  0.00              
ATOM    793  N   GLU   248       7.113  29.596   7.082  1.00  0.00              
ATOM    794  CA  GLU   248       7.686  30.698   6.318  1.00  0.00              
ATOM    795  C   GLU   248       8.967  31.209   6.982  1.00  0.00              
ATOM    796  O   GLU   248       9.990  31.379   6.324  1.00  0.00              
ATOM    797  N   TRP   249       8.918  31.437   8.289  1.00  0.00              
ATOM    798  CA  TRP   249      10.098  31.918   8.992  1.00  0.00              
ATOM    799  C   TRP   249      11.240  30.901   8.940  1.00  0.00              
ATOM    800  O   TRP   249      12.403  31.274   8.789  1.00  0.00              
ATOM    801  N   GLU   250      10.924  29.619   9.064  1.00  0.00              
ATOM    802  CA  GLU   250      11.982  28.626   8.983  1.00  0.00              
ATOM    803  C   GLU   250      12.550  28.653   7.552  1.00  0.00              
ATOM    804  O   GLU   250      13.770  28.736   7.355  1.00  0.00              
ATOM    805  N   ILE   251      11.663  28.610   6.558  1.00  0.00              
ATOM    806  CA  ILE   251      12.082  28.626   5.162  1.00  0.00              
ATOM    807  C   ILE   251      12.933  29.846   4.813  1.00  0.00              
ATOM    808  O   ILE   251      13.967  29.708   4.159  1.00  0.00              
ATOM    809  N   GLY   256      12.525  31.033   5.257  1.00  0.00              
ATOM    810  CA  GLY   256      13.295  32.240   4.958  1.00  0.00              
ATOM    811  C   GLY   256      14.713  32.247   5.531  1.00  0.00              
ATOM    812  O   GLY   256      15.616  32.797   4.909  1.00  0.00              
ATOM    813  N   LYS   257      14.921  31.645   6.701  1.00  0.00              
ATOM    814  CA  LYS   257      16.265  31.603   7.273  1.00  0.00              
ATOM    815  C   LYS   257      17.087  30.595   6.475  1.00  0.00              
ATOM    816  O   LYS   257      18.259  30.822   6.178  1.00  0.00              
ATOM    817  N   ASP   258      16.457  29.483   6.107  1.00  0.00              
ATOM    818  CA  ASP   258      17.145  28.460   5.329  1.00  0.00              
ATOM    819  C   ASP   258      17.505  28.992   3.936  1.00  0.00              
ATOM    820  O   ASP   258      18.573  28.684   3.407  1.00  0.00              
ATOM    821  N   ALA   259      16.626  29.801   3.348  1.00  0.00              
ATOM    822  CA  ALA   259      16.896  30.364   2.026  1.00  0.00              
ATOM    823  C   ALA   259      18.048  31.358   2.132  1.00  0.00              
ATOM    824  O   ALA   259      18.976  31.347   1.324  1.00  0.00              
ATOM    825  N   GLU   260      17.981  32.212   3.144  1.00  0.00              
ATOM    826  CA  GLU   260      19.013  33.210   3.367  1.00  0.00              
ATOM    827  C   GLU   260      20.381  32.526   3.426  1.00  0.00              
ATOM    828  O   GLU   260      21.340  32.977   2.799  1.00  0.00              
ATOM    829  N   GLY   261      20.459  31.435   4.182  1.00  0.00              
ATOM    830  CA  GLY   261      21.692  30.668   4.320  1.00  0.00              
ATOM    831  C   GLY   261      22.167  30.130   2.958  1.00  0.00              
ATOM    832  O   GLY   261      23.336  30.287   2.589  1.00  0.00              
ATOM    833  N   GLU   262      21.257  29.491   2.224  1.00  0.00              
ATOM    834  CA  GLU   262      21.571  28.949   0.906  1.00  0.00              
ATOM    835  C   GLU   262      22.085  30.049  -0.031  1.00  0.00              
ATOM    836  O   GLU   262      23.003  29.825  -0.820  1.00  0.00              
ATOM    837  N   ARG   263      21.499  31.240   0.061  1.00  0.00              
ATOM    838  CA  ARG   263      21.931  32.353  -0.775  1.00  0.00              
ATOM    839  C   ARG   263      23.330  32.856  -0.382  1.00  0.00              
ATOM    840  O   ARG   263      24.174  33.082  -1.254  1.00  0.00              
ATOM    841  N   SER   264      23.585  33.003   0.920  1.00  0.00              
ATOM    842  CA  SER   264      24.892  33.468   1.405  1.00  0.00              
ATOM    843  C   SER   264      25.998  32.500   1.002  1.00  0.00              
ATOM    844  O   SER   264      27.100  32.914   0.638  1.00  0.00              
ATOM    845  N   SER   265      25.704  31.207   1.084  1.00  0.00              
ATOM    846  CA  SER   265      26.687  30.194   0.732  1.00  0.00              
ATOM    847  C   SER   265      26.892  30.123  -0.775  1.00  0.00              
ATOM    848  O   SER   265      28.020  30.002  -1.246  1.00  0.00              
ATOM    849  N   ALA   266      28.334  20.717  -3.255  1.00  0.00              
ATOM    850  CA  ALA   266      26.992  20.172  -3.011  1.00  0.00              
ATOM    851  C   ALA   266      26.004  20.494  -4.134  1.00  0.00              
ATOM    852  O   ALA   266      26.011  21.598  -4.682  1.00  0.00              
ATOM    853  N   ILE   267      25.146  19.534  -4.462  1.00  0.00              
ATOM    854  CA  ILE   267      24.160  19.712  -5.528  1.00  0.00              
ATOM    855  C   ILE   267      23.393  21.031  -5.406  1.00  0.00              
ATOM    856  O   ILE   267      23.231  21.763  -6.388  1.00  0.00              
ATOM    857  N   ASN   268      22.919  21.328  -4.197  1.00  0.00              
ATOM    858  CA  ASN   268      22.151  22.542  -3.947  1.00  0.00              
ATOM    859  C   ASN   268      22.889  23.799  -4.379  1.00  0.00              
ATOM    860  O   ASN   268      22.324  24.652  -5.062  1.00  0.00              
ATOM    861  N   THR   269      24.153  23.916  -3.986  1.00  0.00              
ATOM    862  CA  THR   269      24.930  25.094  -4.347  1.00  0.00              
ATOM    863  C   THR   269      25.297  25.118  -5.831  1.00  0.00              
ATOM    864  O   THR   269      25.449  26.190  -6.418  1.00  0.00              
ATOM    865  N   SER   270      25.430  23.940  -6.437  1.00  0.00              
ATOM    866  CA  SER   270      25.763  23.854  -7.854  1.00  0.00              
ATOM    867  C   SER   270      24.665  24.512  -8.670  1.00  0.00              
ATOM    868  O   SER   270      24.940  25.240  -9.625  1.00  0.00              
ATOM    869  N   PRO   271      23.420  24.237  -8.290  1.00  0.00              
ATOM    870  CA  PRO   271      22.257  24.784  -8.977  1.00  0.00              
ATOM    871  C   PRO   271      22.074  26.272  -8.706  1.00  0.00              
ATOM    872  O   PRO   271      21.688  27.028  -9.591  1.00  0.00              
ATOM    873  N   ILE   272      22.333  26.691  -7.475  1.00  0.00              
ATOM    874  CA  ILE   272      22.187  28.095  -7.123  1.00  0.00              
ATOM    875  C   ILE   272      23.211  28.933  -7.879  1.00  0.00              
ATOM    876  O   ILE   272      22.887  29.994  -8.418  1.00  0.00              
ATOM    877  N   SER   273      24.451  28.450  -7.911  1.00  0.00              
ATOM    878  CA  SER   273      25.527  29.146  -8.604  1.00  0.00              
ATOM    879  C   SER   273      25.184  29.257 -10.079  1.00  0.00              
ATOM    880  O   SER   273      25.405  30.292 -10.703  1.00  0.00              
ATOM    881  N   VAL   274      22.051  29.079 -11.379  1.00  0.00              
ATOM    882  CA  VAL   274      20.873  29.940 -11.548  1.00  0.00              
ATOM    883  C   VAL   274      21.326  31.376 -11.744  1.00  0.00              
ATOM    884  O   VAL   274      20.852  32.074 -12.637  1.00  0.00              
ATOM    885  N   VAL   275      22.247  31.813 -10.891  1.00  0.00              
ATOM    886  CA  VAL   275      22.755  33.175 -10.952  1.00  0.00              
ATOM    887  C   VAL   275      23.595  33.425 -12.198  1.00  0.00              
ATOM    888  O   VAL   275      23.335  34.356 -12.956  1.00  0.00              
ATOM    889  N   ASP   276      24.595  32.583 -12.407  1.00  0.00              
ATOM    890  CA  ASP   276      25.481  32.715 -13.553  1.00  0.00              
ATOM    891  C   ASP   276      24.752  32.807 -14.898  1.00  0.00              
ATOM    892  O   ASP   276      25.299  33.336 -15.865  1.00  0.00              
ATOM    893  N   LYS   277      23.521  32.309 -14.965  1.00  0.00              
ATOM    894  CA  LYS   277      22.785  32.340 -16.224  1.00  0.00              
ATOM    895  C   LYS   277      21.451  33.077 -16.166  1.00  0.00              
ATOM    896  O   LYS   277      20.726  33.128 -17.160  1.00  0.00              
ATOM    897  N   GLU   278      18.442  24.979 -15.772  1.00  0.00              
ATOM    898  CA  GLU   278      19.516  24.833 -14.796  1.00  0.00              
ATOM    899  C   GLU   278      20.242  23.487 -14.909  1.00  0.00              
ATOM    900  O   GLU   278      21.468  23.443 -15.029  1.00  0.00              
ATOM    901  N   ARG   279      19.484  22.394 -14.869  1.00  0.00              
ATOM    902  CA  ARG   279      20.058  21.052 -14.957  1.00  0.00              
ATOM    903  C   ARG   279      20.717  20.777 -16.313  1.00  0.00              
ATOM    904  O   ARG   279      21.744  20.096 -16.390  1.00  0.00              
ATOM    905  N   PHE   280      20.122  21.301 -17.380  1.00  0.00              
ATOM    906  CA  PHE   280      20.661  21.104 -18.722  1.00  0.00              
ATOM    907  C   PHE   280      22.055  21.736 -18.773  1.00  0.00              
ATOM    908  O   PHE   280      22.979  21.194 -19.378  1.00  0.00              
ATOM    909  N   SER   281      22.190  22.881 -18.113  1.00  0.00              
ATOM    910  CA  SER   281      23.449  23.604 -18.043  1.00  0.00              
ATOM    911  C   SER   281      24.363  22.911 -17.031  1.00  0.00              
ATOM    912  O   SER   281      25.567  22.788 -17.244  1.00  0.00              
ATOM    913  N   HIS   284      23.787  22.435 -15.935  1.00  0.00              
ATOM    914  CA  HIS   284      24.573  21.766 -14.907  1.00  0.00              
ATOM    915  C   HIS   284      25.326  20.552 -15.450  1.00  0.00              
ATOM    916  O   HIS   284      26.444  20.265 -15.018  1.00  0.00              
ATOM    917  N   ASP   285      24.716  19.847 -16.400  1.00  0.00              
ATOM    918  CA  ASP   285      25.334  18.659 -16.980  1.00  0.00              
ATOM    919  C   ASP   285      26.664  18.938 -17.673  1.00  0.00              
ATOM    920  O   ASP   285      27.500  18.041 -17.796  1.00  0.00              
END
