
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0347AL333_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_2-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A     140      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    G     141      L     139          3.353
LGA    A     142      A     140           #
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    L     143      F     164          4.897
LGA    R     144      L     165          4.779
LGA    M     145      R     166          2.881
LGA    A     146      R     167          2.214
LGA    G     147      R     168          3.379
LGA    -       -      I     169           -
LGA    G     148      D     170          2.884
LGA    Y     149      R     171          2.615
LGA    A     150      D     172          3.526
LGA    K     151      L     173          5.121
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    V     152      F     178          0.621
LGA    I     153      D     179          4.187
LGA    I     154      D     180          2.342
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    P     155      A     183          2.222
LGA    F     156      E     184          2.450
LGA    S     157      A     185          2.288
LGA    L     182      M     186          1.355
LGA    A     183      K     187          1.113
LGA    E     184      L     188          0.940
LGA    A     185      A     189          2.403
LGA    M     186      K     190          2.642
LGA    K     187      S     191          2.271
LGA    -       -      R     192           -
LGA    L     188      E     193          3.996
LGA    A     189      A     194          3.859
LGA    K     190      R     195          3.014
LGA    S     191      H     196          3.574
LGA    R     192      L     197          3.192
LGA    E     193      P     198           #
LGA    H     196      G     199          2.718
LGA    L     197      W     200          2.637
LGA    P     198      C     201          3.427
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   71    5.0     30    3.09     6.67     26.540     0.940

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.133809 * X  +   0.397275 * Y  +   0.907892 * Z  +   8.284622
  Y_new =   0.971990 * X  +  -0.126003 * Y  +   0.198392 * Z  +  20.094276
  Z_new =   0.193213 * X  +   0.909008 * Y  +  -0.369287 * Z  +  -8.468932 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.956681   -1.184912  [ DEG:   112.1096    -67.8904 ]
  Theta =  -0.194436   -2.947157  [ DEG:   -11.1404   -168.8596 ]
  Phi   =   1.707602   -1.433991  [ DEG:    97.8384    -82.1616 ]
 
# 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: T0347AL333_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_2-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   71   5.0   30   3.09    6.67  26.540
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_2-D2
REMARK Aligment from pdb entry: 1bh9_B
ATOM    193  N   ALA   140      17.745  58.141   2.027  1.00  0.00              
ATOM    194  CA  ALA   140      17.478  59.565   1.843  1.00  0.00              
ATOM    195  C   ALA   140      15.981  59.803   1.590  1.00  0.00              
ATOM    196  O   ALA   140      15.403  60.778   2.062  1.00  0.00              
ATOM    197  N   GLY   141      15.363  58.902   0.841  1.00  0.00              
ATOM    198  CA  GLY   141      13.945  58.999   0.530  1.00  0.00              
ATOM    199  C   GLY   141      13.180  59.031   1.845  1.00  0.00              
ATOM    200  O   GLY   141      12.175  59.727   1.977  1.00  0.00              
ATOM    201  N   ALA   142      13.683  58.283   2.821  1.00  0.00              
ATOM    202  CA  ALA   142      13.072  58.212   4.133  1.00  0.00              
ATOM    203  C   ALA   142      13.200  59.529   4.889  1.00  0.00              
ATOM    204  O   ALA   142      12.249  59.952   5.547  1.00  0.00              
ATOM    205  N   LEU   143      14.370  60.166   4.803  1.00  0.00              
ATOM    206  CA  LEU   143      14.628  61.451   5.467  1.00  0.00              
ATOM    207  C   LEU   143      13.728  62.538   4.864  1.00  0.00              
ATOM    208  O   LEU   143      13.084  63.309   5.582  1.00  0.00              
ATOM    209  N   ARG   144      13.698  62.577   3.536  1.00  0.00              
ATOM    210  CA  ARG   144      12.881  63.522   2.783  1.00  0.00              
ATOM    211  C   ARG   144      11.407  63.324   3.146  1.00  0.00              
ATOM    212  O   ARG   144      10.650  64.281   3.229  1.00  0.00              
ATOM    213  N   MET   145      11.012  62.078   3.372  1.00  0.00              
ATOM    214  CA  MET   145       9.641  61.760   3.760  1.00  0.00              
ATOM    215  C   MET   145       9.357  62.263   5.198  1.00  0.00              
ATOM    216  O   MET   145       8.323  62.879   5.453  1.00  0.00              
ATOM    217  N   ALA   146      10.283  62.018   6.127  1.00  0.00              
ATOM    218  CA  ALA   146      10.102  62.447   7.516  1.00  0.00              
ATOM    219  C   ALA   146      10.262  63.954   7.767  1.00  0.00              
ATOM    220  O   ALA   146       9.757  64.468   8.763  1.00  0.00              
ATOM    221  N   GLY   147      10.968  64.667   6.888  1.00  0.00              
ATOM    222  CA  GLY   147      11.122  66.110   7.070  1.00  0.00              
ATOM    223  C   GLY   147       9.961  66.825   6.385  1.00  0.00              
ATOM    224  O   GLY   147      10.007  68.025   6.113  1.00  0.00              
ATOM    225  N   GLY   148       8.916  66.051   6.114  1.00  0.00              
ATOM    226  CA  GLY   148       7.731  66.584   5.479  1.00  0.00              
ATOM    227  C   GLY   148       7.911  67.099   4.068  1.00  0.00              
ATOM    228  O   GLY   148       7.103  67.900   3.600  1.00  0.00              
ATOM    229  N   TYR   149       8.945  66.640   3.375  1.00  0.00              
ATOM    230  CA  TYR   149       9.172  67.104   2.021  1.00  0.00              
ATOM    231  C   TYR   149       8.826  66.054   0.979  1.00  0.00              
ATOM    232  O   TYR   149       8.439  64.945   1.313  1.00  0.00              
ATOM    233  N   ALA   150       8.943  66.439  -0.285  1.00  0.00              
ATOM    234  CA  ALA   150       8.660  65.574  -1.433  1.00  0.00              
ATOM    235  C   ALA   150       9.905  65.442  -2.326  1.00  0.00              
ATOM    236  O   ALA   150      10.797  66.291  -2.313  1.00  0.00              
ATOM    237  N   LYS   151       9.984  64.364  -3.109  1.00  0.00              
ATOM    238  CA  LYS   151      11.135  64.204  -3.996  1.00  0.00              
ATOM    239  C   LYS   151      11.057  65.392  -4.978  1.00  0.00              
ATOM    240  O   LYS   151      10.074  66.130  -4.973  1.00  0.00              
ATOM    241  N   VAL   152      12.075  65.602  -5.822  1.00  0.00              
ATOM    242  CA  VAL   152      13.332  64.880  -5.999  1.00  0.00              
ATOM    243  C   VAL   152      14.168  65.006  -4.742  1.00  0.00              
ATOM    244  O   VAL   152      13.987  65.945  -3.969  1.00  0.00              
ATOM    245  N   ILE   153      15.081  64.067  -4.534  1.00  0.00              
ATOM    246  CA  ILE   153      15.961  64.115  -3.377  1.00  0.00              
ATOM    247  C   ILE   153      16.907  65.306  -3.507  1.00  0.00              
ATOM    248  O   ILE   153      17.452  65.559  -4.580  1.00  0.00              
ATOM    249  N   ILE   154      17.085  66.037  -2.412  1.00  0.00              
ATOM    250  CA  ILE   154      17.975  67.195  -2.390  1.00  0.00              
ATOM    251  C   ILE   154      19.270  66.785  -1.698  1.00  0.00              
ATOM    252  O   ILE   154      19.308  65.797  -0.966  1.00  0.00              
ATOM    253  N   PRO   155      20.350  67.548  -1.922  1.00  0.00              
ATOM    254  CA  PRO   155      21.658  67.292  -1.325  1.00  0.00              
ATOM    255  C   PRO   155      21.585  67.075   0.190  1.00  0.00              
ATOM    256  O   PRO   155      22.237  66.187   0.733  1.00  0.00              
ATOM    257  N   PHE   156      20.786  67.892   0.867  1.00  0.00              
ATOM    258  CA  PHE   156      20.653  67.783   2.312  1.00  0.00              
ATOM    259  C   PHE   156      20.100  66.429   2.724  1.00  0.00              
ATOM    260  O   PHE   156      20.304  65.997   3.858  1.00  0.00              
ATOM    261  N   SER   157      19.402  65.762   1.807  1.00  0.00              
ATOM    262  CA  SER   157      18.819  64.453   2.091  1.00  0.00              
ATOM    263  C   SER   157      19.857  63.349   2.006  1.00  0.00              
ATOM    264  O   SER   157      19.827  62.400   2.788  1.00  0.00              
ATOM    265  N   LEU   182      20.757  63.483   1.033  1.00  0.00              
ATOM    266  CA  LEU   182      21.805  62.505   0.775  1.00  0.00              
ATOM    267  C   LEU   182      22.811  62.488   1.913  1.00  0.00              
ATOM    268  O   LEU   182      23.187  61.437   2.430  1.00  0.00              
ATOM    269  N   ALA   183      23.261  63.670   2.293  1.00  0.00              
ATOM    270  CA  ALA   183      24.226  63.753   3.344  1.00  0.00              
ATOM    271  C   ALA   183      23.651  63.340   4.671  1.00  0.00              
ATOM    272  O   ALA   183      24.333  62.688   5.442  1.00  0.00              
ATOM    273  N   GLU   184      22.394  63.681   4.939  1.00  0.00              
ATOM    274  CA  GLU   184      21.786  63.277   6.206  1.00  0.00              
ATOM    275  C   GLU   184      21.648  61.764   6.248  1.00  0.00              
ATOM    276  O   GLU   184      21.874  61.138   7.284  1.00  0.00              
ATOM    277  N   ALA   185      21.283  61.187   5.106  1.00  0.00              
ATOM    278  CA  ALA   185      21.119  59.745   4.979  1.00  0.00              
ATOM    279  C   ALA   185      22.427  59.043   5.266  1.00  0.00              
ATOM    280  O   ALA   185      22.460  58.018   5.938  1.00  0.00              
ATOM    281  N   MET   186      23.503  59.607   4.735  1.00  0.00              
ATOM    282  CA  MET   186      24.826  59.058   4.908  1.00  0.00              
ATOM    283  C   MET   186      25.232  59.038   6.371  1.00  0.00              
ATOM    284  O   MET   186      25.894  58.109   6.811  1.00  0.00              
ATOM    285  N   LYS   187      24.819  60.046   7.127  1.00  0.00              
ATOM    286  CA  LYS   187      25.142  60.095   8.546  1.00  0.00              
ATOM    287  C   LYS   187      24.401  59.019   9.325  1.00  0.00              
ATOM    288  O   LYS   187      24.959  58.454  10.266  1.00  0.00              
ATOM    289  N   LEU   188      23.154  58.736   8.936  1.00  0.00              
ATOM    290  CA  LEU   188      22.353  57.717   9.617  1.00  0.00              
ATOM    291  C   LEU   188      22.876  56.325   9.290  1.00  0.00              
ATOM    292  O   LEU   188      22.979  55.469  10.175  1.00  0.00              
ATOM    293  N   ALA   189      23.201  56.098   8.021  1.00  0.00              
ATOM    294  CA  ALA   189      23.737  54.809   7.614  1.00  0.00              
ATOM    295  C   ALA   189      25.021  54.516   8.391  1.00  0.00              
ATOM    296  O   ALA   189      25.220  53.397   8.848  1.00  0.00              
ATOM    297  N   LYS   190      25.887  55.518   8.544  1.00  0.00              
ATOM    298  CA  LYS   190      27.127  55.331   9.294  1.00  0.00              
ATOM    299  C   LYS   190      26.826  55.021  10.757  1.00  0.00              
ATOM    300  O   LYS   190      27.478  54.181  11.356  1.00  0.00              
ATOM    301  N   SER   191      25.831  55.681  11.338  1.00  0.00              
ATOM    302  CA  SER   191      25.478  55.384  12.721  1.00  0.00              
ATOM    303  C   SER   191      25.034  53.936  12.833  1.00  0.00              
ATOM    304  O   SER   191      25.542  53.198  13.676  1.00  0.00              
ATOM    305  N   ARG   192      24.090  53.531  11.987  1.00  0.00              
ATOM    306  CA  ARG   192      23.614  52.154  11.986  1.00  0.00              
ATOM    307  C   ARG   192      24.774  51.240  11.612  1.00  0.00              
ATOM    308  O   ARG   192      24.664  50.018  11.668  1.00  0.00              
ATOM    309  N   GLU   193      25.884  51.850  11.214  1.00  0.00              
ATOM    310  CA  GLU   193      27.058  51.095  10.828  1.00  0.00              
ATOM    311  C   GLU   193      26.831  50.180   9.642  1.00  0.00              
ATOM    312  O   GLU   193      27.557  49.193   9.482  1.00  0.00              
ATOM    313  N   HIS   196      25.843  50.491   8.796  1.00  0.00              
ATOM    314  CA  HIS   196      25.584  49.635   7.649  1.00  0.00              
ATOM    315  C   HIS   196      26.305  50.003   6.361  1.00  0.00              
ATOM    316  O   HIS   196      26.255  49.246   5.391  1.00  0.00              
ATOM    317  N   LEU   197      26.960  51.162   6.330  1.00  0.00              
ATOM    318  CA  LEU   197      27.757  51.531   5.166  1.00  0.00              
ATOM    319  C   LEU   197      29.102  51.888   5.740  1.00  0.00              
ATOM    320  O   LEU   197      29.194  52.300   6.885  1.00  0.00              
ATOM    321  N   PRO   198      30.174  51.681   4.970  1.00  0.00              
ATOM    322  CA  PRO   198      31.510  52.013   5.453  1.00  0.00              
ATOM    323  C   PRO   198      31.653  53.528   5.672  1.00  0.00              
ATOM    324  O   PRO   198      30.622  54.244   5.626  1.00  0.00              
END
