
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0347AL257_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL257_4-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      -       -           -
LGA    P     135      D     134          4.279
LGA    F     136      P     135          4.883
LGA    R     137      F     136          1.243
LGA    S     138      R     137          3.283
LGA    -       -      S     138           -
LGA    L     139      L     139          0.989
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    A     140      A     142          1.168
LGA    G     141      L     143          2.318
LGA    -       -      R     144           -
LGA    A     142      M     145          3.040
LGA    L     143      A     146          4.111
LGA    R     144      -       -           -
LGA    M     145      G     147          4.378
LGA    A     146      G     148          3.675
LGA    G     147      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    G     148      W     161           #
LGA    Y     149      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    A     150      L     174           #
LGA    K     151      S     175           #
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    L     165      F     178          0.924
LGA    R     166      D     179          0.994
LGA    R     167      D     180          2.067
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    R     168      A     183          1.336
LGA    I     169      E     184          2.770
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    D     170      L     188          0.992
LGA    R     171      A     189          2.331
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    D     172      E     193          3.216
LGA    L     173      A     194           #
LGA    L     174      R     195           -
LGA    S     175      -       -           -
LGA    D     176      H     196          2.272
LGA    S     177      L     197          3.189
LGA    F     178      -       -           -
LGA    D     179      -       -           -
LGA    D     180      P     198          2.042
LGA    A     181      -       -           -
LGA    L     182      G     199          3.827
LGA    A     183      W     200          3.047
LGA    E     184      -       -           -
LGA    A     185      -       -           -
LGA    M     186      C     201           #
LGA    K     187      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   71    5.0     24    2.86     8.33     21.487     0.810

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.647467 * X  +  -0.744492 * Y  +  -0.162844 * Z  +  30.929533
  Y_new =   0.723671 * X  +  -0.667615 * Y  +   0.174900 * Z  + 101.294052
  Z_new =  -0.238929 * X  +  -0.004604 * Y  +   0.971026 * Z  +  24.545259 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.004741    3.136852  [ DEG:    -0.2716    179.7284 ]
  Theta =   0.241263    2.900330  [ DEG:    13.8234    166.1767 ]
  Phi   =   2.300674   -0.840918  [ DEG:   131.8189    -48.1811 ]
 
# 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: T0347AL257_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL257_4-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   71   5.0   24   2.86    8.33  21.487
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL257_4-D2
REMARK Aligment from pdb entry: 2czr_A
ATOM    533  N   ASP   134       0.016  51.868   4.065  1.00  0.00              
ATOM    534  CA  ASP   134       1.273  52.519   4.353  1.00  0.00              
ATOM    535  C   ASP   134       1.871  53.118   3.095  1.00  0.00              
ATOM    536  O   ASP   134       1.670  52.619   1.986  1.00  0.00              
ATOM    537  N   PRO   135       2.577  54.224   3.286  1.00  0.00              
ATOM    538  CA  PRO   135       3.190  54.947   2.188  1.00  0.00              
ATOM    539  C   PRO   135       4.655  55.180   2.506  1.00  0.00              
ATOM    540  O   PRO   135       5.029  55.435   3.659  1.00  0.00              
ATOM    541  N   PHE   136       5.481  55.066   1.474  1.00  0.00              
ATOM    542  CA  PHE   136       6.914  55.221   1.611  1.00  0.00              
ATOM    543  C   PHE   136       7.452  56.336   0.746  1.00  0.00              
ATOM    544  O   PHE   136       6.824  56.743  -0.227  1.00  0.00              
ATOM    545  N   ARG   137       8.628  56.827   1.113  1.00  0.00              
ATOM    546  CA  ARG   137       9.305  57.850   0.332  1.00  0.00              
ATOM    547  C   ARG   137      10.216  57.005  -0.545  1.00  0.00              
ATOM    548  O   ARG   137      10.720  55.975  -0.092  1.00  0.00              
ATOM    549  N   SER   138      10.410  57.404  -1.795  1.00  0.00              
ATOM    550  CA  SER   138      11.302  56.644  -2.657  1.00  0.00              
ATOM    551  C   SER   138      12.590  57.427  -2.764  1.00  0.00              
ATOM    552  O   SER   138      12.589  58.578  -3.184  1.00  0.00              
ATOM    553  N   LEU   139      13.684  56.798  -2.356  1.00  0.00              
ATOM    554  CA  LEU   139      14.994  57.421  -2.389  1.00  0.00              
ATOM    555  C   LEU   139      15.876  56.703  -3.395  1.00  0.00              
ATOM    556  O   LEU   139      15.622  55.554  -3.759  1.00  0.00              
ATOM    557  N   ALA   140      16.918  57.397  -3.839  1.00  0.00              
ATOM    558  CA  ALA   140      17.869  56.837  -4.786  1.00  0.00              
ATOM    559  C   ALA   140      19.162  56.512  -4.038  1.00  0.00              
ATOM    560  O   ALA   140      19.710  57.359  -3.339  1.00  0.00              
ATOM    561  N   GLY   141      19.626  55.276  -4.165  1.00  0.00              
ATOM    562  CA  GLY   141      20.879  54.875  -3.540  1.00  0.00              
ATOM    563  C   GLY   141      21.866  54.890  -4.697  1.00  0.00              
ATOM    564  O   GLY   141      21.881  53.987  -5.519  1.00  0.00              
ATOM    565  N   ALA   142      22.677  55.933  -4.765  1.00  0.00              
ATOM    566  CA  ALA   142      23.628  56.080  -5.860  1.00  0.00              
ATOM    567  C   ALA   142      24.988  55.422  -5.600  1.00  0.00              
ATOM    568  O   ALA   142      25.766  55.887  -4.768  1.00  0.00              
ATOM    569  N   LEU   143      25.250  54.343  -6.340  1.00  0.00              
ATOM    570  CA  LEU   143      26.489  53.563  -6.252  1.00  0.00              
ATOM    571  C   LEU   143      27.727  54.392  -6.583  1.00  0.00              
ATOM    572  O   LEU   143      28.814  54.144  -6.060  1.00  0.00              
ATOM    573  N   ARG   144      27.563  55.363  -7.471  1.00  0.00              
ATOM    574  CA  ARG   144      28.667  56.222  -7.871  1.00  0.00              
ATOM    575  C   ARG   144      29.014  57.219  -6.775  1.00  0.00              
ATOM    576  O   ARG   144      30.173  57.357  -6.385  1.00  0.00              
ATOM    577  N   MET   145      27.996  57.916  -6.288  1.00  0.00              
ATOM    578  CA  MET   145      28.179  58.922  -5.252  1.00  0.00              
ATOM    579  C   MET   145      28.317  58.345  -3.852  1.00  0.00              
ATOM    580  O   MET   145      28.823  59.014  -2.956  1.00  0.00              
ATOM    581  N   ALA   146      27.873  57.107  -3.663  1.00  0.00              
ATOM    582  CA  ALA   146      27.922  56.521  -2.338  1.00  0.00              
ATOM    583  C   ALA   146      27.108  57.427  -1.430  1.00  0.00              
ATOM    584  O   ALA   146      27.425  57.604  -0.255  1.00  0.00              
ATOM    585  N   GLY   147      26.054  58.016  -1.995  1.00  0.00              
ATOM    586  CA  GLY   147      25.176  58.924  -1.261  1.00  0.00              
ATOM    587  C   GLY   147      23.712  58.616  -1.559  1.00  0.00              
ATOM    588  O   GLY   147      23.395  57.865  -2.484  1.00  0.00              
ATOM    589  N   GLY   148      22.820  59.204  -0.770  1.00  0.00              
ATOM    590  CA  GLY   148      21.390  59.004  -0.953  1.00  0.00              
ATOM    591  C   GLY   148      20.733  60.289  -1.447  1.00  0.00              
ATOM    592  O   GLY   148      21.033  61.376  -0.956  1.00  0.00              
ATOM    593  N   TYR   149      19.843  60.158  -2.427  1.00  0.00              
ATOM    594  CA  TYR   149      19.138  61.313  -2.980  1.00  0.00              
ATOM    595  C   TYR   149      17.637  61.102  -2.941  1.00  0.00              
ATOM    596  O   TYR   149      17.158  59.966  -2.908  1.00  0.00              
ATOM    597  N   ALA   150      16.895  62.200  -2.952  1.00  0.00              
ATOM    598  CA  ALA   150      15.450  62.104  -2.953  1.00  0.00              
ATOM    599  C   ALA   150      15.012  61.946  -4.410  1.00  0.00              
ATOM    600  O   ALA   150      15.836  62.025  -5.321  1.00  0.00              
ATOM    601  N   LYS   151      13.726  61.716  -4.635  1.00  0.00              
ATOM    602  CA  LYS   151      13.220  61.521  -5.991  1.00  0.00              
ATOM    603  C   LYS   151      13.313  62.754  -6.884  1.00  0.00              
ATOM    604  O   LYS   151      12.844  62.741  -8.022  1.00  0.00              
ATOM    605  N   LEU   165      13.928  63.816  -6.376  1.00  0.00              
ATOM    606  CA  LEU   165      14.064  65.037  -7.154  1.00  0.00              
ATOM    607  C   LEU   165      15.527  65.362  -7.430  1.00  0.00              
ATOM    608  O   LEU   165      15.839  66.396  -8.018  1.00  0.00              
ATOM    609  N   ARG   166      16.424  64.479  -7.003  1.00  0.00              
ATOM    610  CA  ARG   166      17.839  64.709  -7.229  1.00  0.00              
ATOM    611  C   ARG   166      18.555  65.395  -6.079  1.00  0.00              
ATOM    612  O   ARG   166      19.773  65.576  -6.123  1.00  0.00              
ATOM    613  N   ARG   167      17.810  65.776  -5.048  1.00  0.00              
ATOM    614  CA  ARG   167      18.419  66.438  -3.908  1.00  0.00              
ATOM    615  C   ARG   167      18.994  65.451  -2.911  1.00  0.00              
ATOM    616  O   ARG   167      18.323  64.496  -2.517  1.00  0.00              
ATOM    617  N   ARG   168      20.234  65.681  -2.494  1.00  0.00              
ATOM    618  CA  ARG   168      20.902  64.795  -1.543  1.00  0.00              
ATOM    619  C   ARG   168      20.244  64.767  -0.166  1.00  0.00              
ATOM    620  O   ARG   168      19.761  65.782   0.328  1.00  0.00              
ATOM    621  N   ILE   169      20.241  63.592   0.451  1.00  0.00              
ATOM    622  CA  ILE   169      19.655  63.414   1.772  1.00  0.00              
ATOM    623  C   ILE   169      20.723  62.976   2.781  1.00  0.00              
ATOM    624  O   ILE   169      21.338  61.916   2.633  1.00  0.00              
ATOM    625  N   ASP   170      20.947  63.790   3.827  1.00  0.00              
ATOM    626  CA  ASP   170      21.941  63.483   4.859  1.00  0.00              
ATOM    627  C   ASP   170      21.665  62.112   5.452  1.00  0.00              
ATOM    628  O   ASP   170      20.535  61.636   5.424  1.00  0.00              
ATOM    629  N   ARG   171      22.696  61.481   5.994  1.00  0.00              
ATOM    630  CA  ARG   171      22.532  60.162   6.583  1.00  0.00              
ATOM    631  C   ARG   171      21.763  60.206   7.903  1.00  0.00              
ATOM    632  O   ARG   171      21.092  59.238   8.265  1.00  0.00              
ATOM    633  N   ASP   172      21.852  61.330   8.612  1.00  0.00              
ATOM    634  CA  ASP   172      21.170  61.484   9.895  1.00  0.00              
ATOM    635  C   ASP   172      19.656  61.511   9.751  1.00  0.00              
ATOM    636  O   ASP   172      18.934  61.638  10.738  1.00  0.00              
ATOM    637  N   LEU   173      19.182  61.400   8.515  1.00  0.00              
ATOM    638  CA  LEU   173      17.751  61.384   8.241  1.00  0.00              
ATOM    639  C   LEU   173      17.231  59.951   8.370  1.00  0.00              
ATOM    640  O   LEU   173      16.023  59.710   8.361  1.00  0.00              
ATOM    641  N   LEU   174      18.155  59.004   8.502  1.00  0.00              
ATOM    642  CA  LEU   174      17.795  57.598   8.612  1.00  0.00              
ATOM    643  C   LEU   174      18.112  56.984   9.969  1.00  0.00              
ATOM    644  O   LEU   174      19.101  57.337  10.610  1.00  0.00              
ATOM    645  N   SER   175      17.267  56.051  10.394  1.00  0.00              
ATOM    646  CA  SER   175      17.462  55.371  11.665  1.00  0.00              
ATOM    647  C   SER   175      18.784  54.610  11.608  1.00  0.00              
ATOM    648  O   SER   175      19.314  54.351  10.523  1.00  0.00              
ATOM    649  N   ASP   176      19.313  54.259  12.776  1.00  0.00              
ATOM    650  CA  ASP   176      20.569  53.523  12.866  1.00  0.00              
ATOM    651  C   ASP   176      20.524  52.263  12.006  1.00  0.00              
ATOM    652  O   ASP   176      21.530  51.856  11.431  1.00  0.00              
ATOM    653  N   SER   177      19.347  51.652  11.923  1.00  0.00              
ATOM    654  CA  SER   177      19.158  50.439  11.138  1.00  0.00              
ATOM    655  C   SER   177      19.341  50.715   9.656  1.00  0.00              
ATOM    656  O   SER   177      20.100  50.027   8.978  1.00  0.00              
ATOM    657  N   PHE   178      18.619  51.711   9.155  1.00  0.00              
ATOM    658  CA  PHE   178      18.691  52.080   7.744  1.00  0.00              
ATOM    659  C   PHE   178      20.112  52.502   7.384  1.00  0.00              
ATOM    660  O   PHE   178      20.628  52.162   6.320  1.00  0.00              
ATOM    661  N   ASP   179      20.730  53.252   8.287  1.00  0.00              
ATOM    662  CA  ASP   179      22.092  53.729   8.108  1.00  0.00              
ATOM    663  C   ASP   179      23.031  52.626   7.634  1.00  0.00              
ATOM    664  O   ASP   179      23.713  52.772   6.620  1.00  0.00              
ATOM    665  N   ASP   180      23.067  51.523   8.373  1.00  0.00              
ATOM    666  CA  ASP   180      23.942  50.416   8.019  1.00  0.00              
ATOM    667  C   ASP   180      23.462  49.725   6.754  1.00  0.00              
ATOM    668  O   ASP   180      24.268  49.255   5.951  1.00  0.00              
ATOM    669  N   ALA   181      22.145  49.659   6.579  1.00  0.00              
ATOM    670  CA  ALA   181      21.581  49.033   5.392  1.00  0.00              
ATOM    671  C   ALA   181      22.075  49.792   4.169  1.00  0.00              
ATOM    672  O   ALA   181      22.461  49.195   3.161  1.00  0.00              
ATOM    673  N   LEU   182      22.050  51.118   4.269  1.00  0.00              
ATOM    674  CA  LEU   182      22.505  51.974   3.186  1.00  0.00              
ATOM    675  C   LEU   182      23.983  51.681   2.959  1.00  0.00              
ATOM    676  O   LEU   182      24.411  51.417   1.837  1.00  0.00              
ATOM    677  N   ALA   183      24.752  51.709   4.042  1.00  0.00              
ATOM    678  CA  ALA   183      26.178  51.433   3.970  1.00  0.00              
ATOM    679  C   ALA   183      26.391  50.107   3.252  1.00  0.00              
ATOM    680  O   ALA   183      27.266  49.984   2.397  1.00  0.00              
ATOM    681  N   GLU   184      25.579  49.118   3.602  1.00  0.00              
ATOM    682  CA  GLU   184      25.666  47.799   2.985  1.00  0.00              
ATOM    683  C   GLU   184      25.403  47.845   1.485  1.00  0.00              
ATOM    684  O   GLU   184      26.181  47.314   0.694  1.00  0.00              
ATOM    685  N   ALA   185      24.302  48.475   1.093  1.00  0.00              
ATOM    686  CA  ALA   185      23.942  48.570  -0.318  1.00  0.00              
ATOM    687  C   ALA   185      24.980  49.342  -1.135  1.00  0.00              
ATOM    688  O   ALA   185      25.399  48.897  -2.202  1.00  0.00              
ATOM    689  N   MET   186      25.390  50.495  -0.620  1.00  0.00              
ATOM    690  CA  MET   186      26.362  51.344  -1.293  1.00  0.00              
ATOM    691  C   MET   186      27.781  50.788  -1.226  1.00  0.00              
ATOM    692  O   MET   186      28.742  51.545  -1.094  1.00  0.00              
ATOM    693  N   LYS   187      27.908  49.468  -1.315  1.00  0.00              
ATOM    694  CA  LYS   187      29.215  48.812  -1.275  1.00  0.00              
ATOM    695  C   LYS   187      29.142  47.399  -1.847  1.00  0.00              
ATOM    696  O   LYS   187      29.589  46.461  -1.148  1.00  0.00              
END
