
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_3-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      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    N     228      W     249           #
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    N     229      H     253          4.905
LGA    S     230      A     254          3.545
LGA    L     231      F     255          4.834
LGA    P     232      -       -           -
LGA    N     233      -       -           -
LGA    P     234      G     256          3.617
LGA    L     236      K     257          2.065
LGA    S     240      -       -           -
LGA    N     241      D     258           #
LGA    N     242      R     263          4.635
LGA    P     243      S     264           -
LGA    -       -      S     265           -
LGA    A     244      A     266          4.930
LGA    L     245      I     267          4.092
LGA    H     246      -       -           -
LGA    F     247      N     268          2.265
LGA    E     248      T     269          2.510
LGA    W     249      -       -           -
LGA    E     250      -       -           -
LGA    I     251      S     270          2.910
LGA    G     256      -       -           -
LGA    K     257      P     271          2.696
LGA    D     258      I     272          1.595
LGA    A     259      S     273          4.534
LGA    E     260      V     274          3.665
LGA    G     261      V     275          4.635
LGA    E     262      D     276          1.969
LGA    R     263      K     277          2.472
LGA    S     264      E     278          5.262
LGA    S     265      -       -           -
LGA    A     266      -       -           -
LGA    I     267      -       -           -
LGA    N     268      -       -           -
LGA    T     269      -       -           -
LGA    S     270      -       -           -
LGA    P     271      -       -           -
LGA    I     272      -       -           -
LGA    S     273      R     279          3.970
LGA    V     274      F     280          4.554
LGA    V     275      S     281          3.311
LGA    D     276      K     282          2.077
LGA    K     277      Y     283          3.603
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      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    E     278      G     302          4.126
LGA    R     279      R     303          3.482
LGA    F     280      I     304           #
LGA    S     281      -       -           -
LGA    H     284      -       -           -
LGA    D     285      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   73    5.0     26    3.70     7.69     18.955     0.684

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.025571 * X  +  -0.959818 * Y  +   0.279455 * Z  +  68.965225
  Y_new =  -0.310240 * X  +  -0.258124 * Y  +  -0.914944 * Z  +  52.165310
  Z_new =   0.950314 * X  +  -0.110094 * Y  +  -0.291174 * Z  + -15.216266 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.780104    0.361489  [ DEG:  -159.2882     20.7118 ]
  Theta =  -1.254244   -1.887349  [ DEG:   -71.8629   -108.1371 ]
  Phi   =  -1.653033    1.488560  [ DEG:   -94.7118     85.2882 ]
 
# 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_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_3-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   26   3.70    7.69  18.955
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_3-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    637  N   ASN   228      -7.514  22.529  12.704  1.00  0.00              
ATOM    638  CA  ASN   228      -8.683  23.214  13.271  1.00  0.00              
ATOM    639  C   ASN   228      -8.498  23.463  14.757  1.00  0.00              
ATOM    640  O   ASN   228      -8.766  24.559  15.254  1.00  0.00              
ATOM    641  N   ASN   229      -8.030  22.436  15.456  1.00  0.00              
ATOM    642  CA  ASN   229      -7.791  22.530  16.887  1.00  0.00              
ATOM    643  C   ASN   229      -6.891  23.730  17.146  1.00  0.00              
ATOM    644  O   ASN   229      -7.012  24.407  18.166  1.00  0.00              
ATOM    645  N   SER   230      -5.991  23.989  16.206  1.00  0.00              
ATOM    646  CA  SER   230      -5.064  25.103  16.323  1.00  0.00              
ATOM    647  C   SER   230      -5.756  26.427  16.000  1.00  0.00              
ATOM    648  O   SER   230      -5.599  27.419  16.721  1.00  0.00              
ATOM    649  N   LEU   231      -6.530  26.434  14.920  1.00  0.00              
ATOM    650  CA  LEU   231      -7.230  27.642  14.504  1.00  0.00              
ATOM    651  C   LEU   231      -8.207  28.108  15.582  1.00  0.00              
ATOM    652  O   LEU   231      -8.719  29.229  15.528  1.00  0.00              
ATOM    653  N   PRO   232      -8.462  27.249  16.565  1.00  0.00              
ATOM    654  CA  PRO   232      -9.367  27.605  17.650  1.00  0.00              
ATOM    655  C   PRO   232      -8.790  28.765  18.451  1.00  0.00              
ATOM    656  O   PRO   232      -9.327  29.874  18.432  1.00  0.00              
ATOM    657  N   ASN   233      -5.904  29.974  17.884  1.00  0.00              
ATOM    658  CA  ASN   233      -5.132  30.760  16.923  1.00  0.00              
ATOM    659  C   ASN   233      -5.834  30.672  15.574  1.00  0.00              
ATOM    660  O   ASN   233      -5.501  29.839  14.734  1.00  0.00              
ATOM    661  N   PRO   234      -6.826  31.547  15.354  1.00  0.00              
ATOM    662  CA  PRO   234      -7.612  31.599  14.119  1.00  0.00              
ATOM    663  C   PRO   234      -6.807  31.746  12.836  1.00  0.00              
ATOM    664  O   PRO   234      -7.236  31.285  11.777  1.00  0.00              
ATOM    665  N   LEU   236      -5.646  32.386  12.928  1.00  0.00              
ATOM    666  CA  LEU   236      -4.821  32.591  11.745  1.00  0.00              
ATOM    667  C   LEU   236      -3.536  31.757  11.795  1.00  0.00              
ATOM    668  O   LEU   236      -2.508  32.136  11.230  1.00  0.00              
ATOM    669  N   SER   240      -3.597  30.612  12.461  1.00  0.00              
ATOM    670  CA  SER   240      -2.423  29.767  12.563  1.00  0.00              
ATOM    671  C   SER   240      -1.839  29.432  11.201  1.00  0.00              
ATOM    672  O   SER   240      -0.633  29.552  10.987  1.00  0.00              
ATOM    673  N   ASN   241      -2.693  29.000  10.283  1.00  0.00              
ATOM    674  CA  ASN   241      -2.225  28.631   8.955  1.00  0.00              
ATOM    675  C   ASN   241      -1.539  29.786   8.228  1.00  0.00              
ATOM    676  O   ASN   241      -0.675  29.566   7.380  1.00  0.00              
ATOM    677  N   ASN   242      -1.919  31.013   8.562  1.00  0.00              
ATOM    678  CA  ASN   242      -1.337  32.180   7.926  1.00  0.00              
ATOM    679  C   ASN   242       0.064  32.416   8.488  1.00  0.00              
ATOM    680  O   ASN   242       0.992  32.770   7.761  1.00  0.00              
ATOM    681  N   PRO   243       0.212  32.201   9.787  1.00  0.00              
ATOM    682  CA  PRO   243       1.498  32.380  10.450  1.00  0.00              
ATOM    683  C   PRO   243       2.525  31.384   9.919  1.00  0.00              
ATOM    684  O   PRO   243       3.712  31.699   9.800  1.00  0.00              
ATOM    685  N   ALA   244       2.053  30.184   9.597  1.00  0.00              
ATOM    686  CA  ALA   244       2.904  29.113   9.106  1.00  0.00              
ATOM    687  C   ALA   244       3.477  29.384   7.725  1.00  0.00              
ATOM    688  O   ALA   244       4.625  29.040   7.448  1.00  0.00              
ATOM    689  N   LEU   245       2.679  30.001   6.860  1.00  0.00              
ATOM    690  CA  LEU   245       3.141  30.338   5.515  1.00  0.00              
ATOM    691  C   LEU   245       4.206  31.406   5.687  1.00  0.00              
ATOM    692  O   LEU   245       5.184  31.461   4.942  1.00  0.00              
ATOM    693  N   HIS   246       3.998  32.251   6.689  1.00  0.00              
ATOM    694  CA  HIS   246       4.931  33.316   6.998  1.00  0.00              
ATOM    695  C   HIS   246       6.264  32.681   7.366  1.00  0.00              
ATOM    696  O   HIS   246       7.309  33.085   6.854  1.00  0.00              
ATOM    697  N   PHE   247       6.236  31.682   8.245  1.00  0.00              
ATOM    698  CA  PHE   247       7.474  31.013   8.625  1.00  0.00              
ATOM    699  C   PHE   247       8.087  30.323   7.411  1.00  0.00              
ATOM    700  O   PHE   247       9.290  30.426   7.169  1.00  0.00              
ATOM    701  N   GLU   248       7.268  29.611   6.647  1.00  0.00              
ATOM    702  CA  GLU   248       7.786  28.931   5.475  1.00  0.00              
ATOM    703  C   GLU   248       8.523  29.956   4.633  1.00  0.00              
ATOM    704  O   GLU   248       9.669  29.744   4.241  1.00  0.00              
ATOM    705  N   TRP   249       7.867  31.082   4.381  1.00  0.00              
ATOM    706  CA  TRP   249       8.447  32.130   3.560  1.00  0.00              
ATOM    707  C   TRP   249       9.769  32.623   4.097  1.00  0.00              
ATOM    708  O   TRP   249      10.692  32.893   3.328  1.00  0.00              
ATOM    709  N   GLU   250       9.870  32.752   5.414  1.00  0.00              
ATOM    710  CA  GLU   250      11.108  33.236   6.015  1.00  0.00              
ATOM    711  C   GLU   250      12.240  32.218   5.884  1.00  0.00              
ATOM    712  O   GLU   250      13.401  32.590   5.708  1.00  0.00              
ATOM    713  N   ILE   251      11.902  30.935   5.969  1.00  0.00              
ATOM    714  CA  ILE   251      12.904  29.905   5.829  1.00  0.00              
ATOM    715  C   ILE   251      13.439  29.992   4.421  1.00  0.00              
ATOM    716  O   ILE   251      14.645  29.889   4.193  1.00  0.00              
ATOM    717  N   GLY   256      12.533  30.187   3.472  1.00  0.00              
ATOM    718  CA  GLY   256      12.923  30.301   2.079  1.00  0.00              
ATOM    719  C   GLY   256      13.846  31.508   1.884  1.00  0.00              
ATOM    720  O   GLY   256      14.895  31.390   1.256  1.00  0.00              
ATOM    721  N   LYS   257      13.476  32.662   2.430  1.00  0.00              
ATOM    722  CA  LYS   257      14.320  33.836   2.280  1.00  0.00              
ATOM    723  C   LYS   257      15.736  33.568   2.756  1.00  0.00              
ATOM    724  O   LYS   257      16.701  34.021   2.149  1.00  0.00              
ATOM    725  N   ASP   258      15.865  32.831   3.847  1.00  0.00              
ATOM    726  CA  ASP   258      17.185  32.534   4.386  1.00  0.00              
ATOM    727  C   ASP   258      17.968  31.585   3.486  1.00  0.00              
ATOM    728  O   ASP   258      19.172  31.753   3.298  1.00  0.00              
ATOM    729  N   ALA   259      17.294  30.580   2.932  1.00  0.00              
ATOM    730  CA  ALA   259      17.982  29.633   2.058  1.00  0.00              
ATOM    731  C   ALA   259      18.480  30.367   0.824  1.00  0.00              
ATOM    732  O   ALA   259      19.534  30.044   0.288  1.00  0.00              
ATOM    733  N   GLU   260      17.733  31.367   0.379  1.00  0.00              
ATOM    734  CA  GLU   260      18.154  32.112  -0.791  1.00  0.00              
ATOM    735  C   GLU   260      19.285  33.037  -0.383  1.00  0.00              
ATOM    736  O   GLU   260      20.141  33.364  -1.199  1.00  0.00              
ATOM    737  N   GLY   261      19.289  33.458   0.882  1.00  0.00              
ATOM    738  CA  GLY   261      20.356  34.326   1.370  1.00  0.00              
ATOM    739  C   GLY   261      21.629  33.497   1.278  1.00  0.00              
ATOM    740  O   GLY   261      22.654  33.975   0.794  1.00  0.00              
ATOM    741  N   GLU   262      21.560  32.251   1.733  1.00  0.00              
ATOM    742  CA  GLU   262      22.716  31.375   1.658  1.00  0.00              
ATOM    743  C   GLU   262      23.084  31.155   0.207  1.00  0.00              
ATOM    744  O   GLU   262      24.264  31.115  -0.127  1.00  0.00              
ATOM    745  N   ARG   263      22.083  31.004  -0.656  1.00  0.00              
ATOM    746  CA  ARG   263      22.351  30.807  -2.078  1.00  0.00              
ATOM    747  C   ARG   263      23.286  31.919  -2.553  1.00  0.00              
ATOM    748  O   ARG   263      24.300  31.680  -3.223  1.00  0.00              
ATOM    749  N   SER   264      22.934  33.141  -2.191  1.00  0.00              
ATOM    750  CA  SER   264      23.724  34.293  -2.558  1.00  0.00              
ATOM    751  C   SER   264      25.098  34.122  -1.936  1.00  0.00              
ATOM    752  O   SER   264      26.100  34.025  -2.630  1.00  0.00              
ATOM    753  N   SER   265      25.127  34.040  -0.616  1.00  0.00              
ATOM    754  CA  SER   265      26.366  33.906   0.130  1.00  0.00              
ATOM    755  C   SER   265      27.296  32.778  -0.254  1.00  0.00              
ATOM    756  O   SER   265      28.506  32.888  -0.047  1.00  0.00              
ATOM    757  N   ALA   266      33.840  24.074   7.015  1.00  0.00              
ATOM    758  CA  ALA   266      33.160  23.581   8.197  1.00  0.00              
ATOM    759  C   ALA   266      32.009  22.693   7.778  1.00  0.00              
ATOM    760  O   ALA   266      31.514  22.774   6.648  1.00  0.00              
ATOM    761  N   ILE   267      31.576  21.848   8.702  1.00  0.00              
ATOM    762  CA  ILE   267      30.482  20.924   8.435  1.00  0.00              
ATOM    763  C   ILE   267      29.243  21.567   7.807  1.00  0.00              
ATOM    764  O   ILE   267      28.734  21.064   6.811  1.00  0.00              
ATOM    765  N   ASN   268      28.773  22.679   8.370  1.00  0.00              
ATOM    766  CA  ASN   268      27.587  23.342   7.839  1.00  0.00              
ATOM    767  C   ASN   268      27.843  23.860   6.447  1.00  0.00              
ATOM    768  O   ASN   268      26.992  23.744   5.574  1.00  0.00              
ATOM    769  N   THR   269      29.013  24.452   6.243  1.00  0.00              
ATOM    770  CA  THR   269      29.364  24.975   4.934  1.00  0.00              
ATOM    771  C   THR   269      29.218  23.825   3.955  1.00  0.00              
ATOM    772  O   THR   269      28.376  23.856   3.060  1.00  0.00              
ATOM    773  N   SER   270      30.041  22.802   4.144  1.00  0.00              
ATOM    774  CA  SER   270      30.007  21.641   3.283  1.00  0.00              
ATOM    775  C   SER   270      28.585  21.160   2.989  1.00  0.00              
ATOM    776  O   SER   270      28.185  21.074   1.827  1.00  0.00              
ATOM    777  N   PRO   271      27.817  20.864   4.034  1.00  0.00              
ATOM    778  CA  PRO   271      26.455  20.378   3.858  1.00  0.00              
ATOM    779  C   PRO   271      25.613  21.309   2.990  1.00  0.00              
ATOM    780  O   PRO   271      24.919  20.863   2.087  1.00  0.00              
ATOM    781  N   ILE   272      25.671  22.602   3.249  1.00  0.00              
ATOM    782  CA  ILE   272      24.885  23.542   2.461  1.00  0.00              
ATOM    783  C   ILE   272      25.266  23.483   0.988  1.00  0.00              
ATOM    784  O   ILE   272      24.418  23.671   0.108  1.00  0.00              
ATOM    785  N   SER   273      26.547  23.232   0.731  1.00  0.00              
ATOM    786  CA  SER   273      27.068  23.140  -0.627  1.00  0.00              
ATOM    787  C   SER   273      26.634  21.811  -1.232  1.00  0.00              
ATOM    788  O   SER   273      26.010  21.782  -2.290  1.00  0.00              
ATOM    789  N   VAL   274      24.336  20.064  -0.496  1.00  0.00              
ATOM    790  CA  VAL   274      22.896  20.189  -0.634  1.00  0.00              
ATOM    791  C   VAL   274      22.549  20.916  -1.926  1.00  0.00              
ATOM    792  O   VAL   274      21.812  20.405  -2.767  1.00  0.00              
ATOM    793  N   VAL   275      23.082  22.122  -2.070  1.00  0.00              
ATOM    794  CA  VAL   275      22.834  22.928  -3.255  1.00  0.00              
ATOM    795  C   VAL   275      23.320  22.221  -4.529  1.00  0.00              
ATOM    796  O   VAL   275      22.706  22.336  -5.585  1.00  0.00              
ATOM    797  N   ASP   276      24.420  21.480  -4.423  1.00  0.00              
ATOM    798  CA  ASP   276      24.973  20.751  -5.566  1.00  0.00              
ATOM    799  C   ASP   276      23.993  19.667  -6.005  1.00  0.00              
ATOM    800  O   ASP   276      23.680  19.555  -7.196  1.00  0.00              
ATOM    801  N   LYS   277      23.513  18.882  -5.041  1.00  0.00              
ATOM    802  CA  LYS   277      22.562  17.814  -5.317  1.00  0.00              
ATOM    803  C   LYS   277      21.280  18.374  -5.930  1.00  0.00              
ATOM    804  O   LYS   277      20.615  17.712  -6.727  1.00  0.00              
ATOM    805  N   GLU   278      23.556  13.987   4.120  1.00  0.00              
ATOM    806  CA  GLU   278      24.610  14.945   3.831  1.00  0.00              
ATOM    807  C   GLU   278      25.843  14.639   4.686  1.00  0.00              
ATOM    808  O   GLU   278      26.977  14.775   4.224  1.00  0.00              
ATOM    809  N   ARG   279      25.623  14.209   5.924  1.00  0.00              
ATOM    810  CA  ARG   279      26.729  13.879   6.812  1.00  0.00              
ATOM    811  C   ARG   279      27.477  12.649   6.308  1.00  0.00              
ATOM    812  O   ARG   279      28.703  12.650   6.238  1.00  0.00              
ATOM    813  N   PHE   280      26.734  11.603   5.956  1.00  0.00              
ATOM    814  CA  PHE   280      27.331  10.356   5.473  1.00  0.00              
ATOM    815  C   PHE   280      28.130  10.571   4.202  1.00  0.00              
ATOM    816  O   PHE   280      29.246  10.075   4.073  1.00  0.00              
ATOM    817  N   SER   281      27.537  11.293   3.258  1.00  0.00              
ATOM    818  CA  SER   281      28.185  11.572   1.993  1.00  0.00              
ATOM    819  C   SER   281      29.618  12.040   2.187  1.00  0.00              
ATOM    820  O   SER   281      30.536  11.523   1.554  1.00  0.00              
ATOM    821  N   HIS   284      29.818  13.010   3.069  1.00  0.00              
ATOM    822  CA  HIS   284      31.158  13.528   3.311  1.00  0.00              
ATOM    823  C   HIS   284      32.069  12.594   4.108  1.00  0.00              
ATOM    824  O   HIS   284      33.217  12.368   3.732  1.00  0.00              
ATOM    825  N   ASP   285      31.559  12.061   5.209  1.00  0.00              
ATOM    826  CA  ASP   285      32.338  11.173   6.052  1.00  0.00              
ATOM    827  C   ASP   285      32.638   9.810   5.440  1.00  0.00              
ATOM    828  O   ASP   285      33.727   9.271   5.631  1.00  0.00              
END
