
#######################################################
#                                                     #
#                        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 T0347AL381_3-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL381_3-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     170      D     134           -
LGA    R     171      P     135           -
LGA    D     172      F     136           -
LGA    L     173      R     137           -
LGA    L     174      S     138           -
LGA    S     175      L     139           -
LGA    D     176      A     140           -
LGA    S     177      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    -       -      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    F     178      L     174           #
LGA    D     179      S     175          3.597
LGA    D     180      D     176          4.711
LGA    A     181      -       -           -
LGA    L     182      S     177          2.038
LGA    A     183      F     178          1.824
LGA    E     184      D     179          1.397
LGA    A     185      D     180          0.722
LGA    M     186      A     181          0.922
LGA    K     187      L     182          0.769
LGA    L     188      A     183          0.494
LGA    A     189      E     184          0.322
LGA    K     190      A     185          0.532
LGA    S     191      M     186          0.774
LGA    R     192      K     187          0.643
LGA    E     193      L     188          0.479
LGA    A     194      A     189          0.340
LGA    R     195      K     190          0.384
LGA    H     196      S     191          0.506
LGA    L     197      R     192          3.541
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    P     198      R     195          2.857
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    G     199      W     200          5.001
LGA    W     200      C     201          1.699
LGA    C     201      G     202          2.133
LGA    G     202      V     203           #
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   71    5.0     22    2.15     9.09     27.941     0.976

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.429976 * X  +   0.506561 * Y  +   0.747340 * Z  + -79.238594
  Y_new =  -0.662088 * X  +   0.739684 * Y  +  -0.120445 * Z  +  87.851669
  Z_new =  -0.613808 * X  +  -0.443017 * Y  +   0.653434 * Z  + -28.076111 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.595796    2.545797  [ DEG:   -34.1366    145.8634 ]
  Theta =   0.660875    2.480718  [ DEG:    37.8654    142.1346 ]
  Phi   =  -0.994827    2.146766  [ DEG:   -56.9994    123.0006 ]
 
# 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: T0347AL381_3-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_3-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   22   2.15    9.09  27.941
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_3-D2
REMARK Aligment from pdb entry: 1fcyA
ATOM      1  N   ASP   170      -4.734  64.123 -15.634  1.00  0.00              
ATOM      2  CA  ASP   170      -3.703  63.122 -15.783  1.00  0.00              
ATOM      3  C   ASP   170      -2.354  63.607 -15.237  1.00  0.00              
ATOM      4  O   ASP   170      -1.718  62.881 -14.470  1.00  0.00              
ATOM      5  N   ARG   171      -1.961  64.810 -15.623  1.00  0.00              
ATOM      6  CA  ARG   171      -0.706  65.411 -15.185  1.00  0.00              
ATOM      7  C   ARG   171      -0.727  66.914 -15.478  1.00  0.00              
ATOM      8  O   ARG   171      -1.042  67.313 -16.580  1.00  0.00              
ATOM      9  N   ASP   172      -0.384  67.726 -14.498  1.00  0.00              
ATOM     10  CA  ASP   172      -0.182  69.164 -14.710  1.00  0.00              
ATOM     11  C   ASP   172       1.320  69.378 -14.786  1.00  0.00              
ATOM     12  O   ASP   172       2.086  69.160 -13.840  1.00  0.00              
ATOM     13  N   LEU   173       1.792  69.770 -15.949  1.00  0.00              
ATOM     14  CA  LEU   173       3.230  69.827 -16.171  1.00  0.00              
ATOM     15  C   LEU   173       3.914  70.892 -15.327  1.00  0.00              
ATOM     16  O   LEU   173       5.083  70.664 -14.969  1.00  0.00              
ATOM     17  N   LEU   174       3.228  71.980 -15.011  1.00  0.00              
ATOM     18  CA  LEU   174       3.861  72.985 -14.135  1.00  0.00              
ATOM     19  C   LEU   174       4.041  72.375 -12.733  1.00  0.00              
ATOM     20  O   LEU   174       5.097  72.608 -12.130  1.00  0.00              
ATOM     21  N   SER   175       3.050  71.633 -12.218  1.00  0.00              
ATOM     22  CA  SER   175       3.251  71.000 -10.923  1.00  0.00              
ATOM     23  C   SER   175       4.298  69.892 -11.037  1.00  0.00              
ATOM     24  O   SER   175       5.120  69.765 -10.106  1.00  0.00              
ATOM     25  N   ASP   176       4.318  69.117 -12.091  1.00  0.00              
ATOM     26  CA  ASP   176       5.366  68.098 -12.248  1.00  0.00              
ATOM     27  C   ASP   176       6.743  68.732 -12.233  1.00  0.00              
ATOM     28  O   ASP   176       7.642  68.241 -11.592  1.00  0.00              
ATOM     29  N   SER   177       6.937  69.827 -12.947  1.00  0.00              
ATOM     30  CA  SER   177       8.268  70.441 -12.978  1.00  0.00              
ATOM     31  C   SER   177       8.680  70.861 -11.594  1.00  0.00              
ATOM     32  O   SER   177       9.806  70.612 -11.178  1.00  0.00              
ATOM     33  N   PHE   178       7.810  71.485 -10.820  1.00  0.00              
ATOM     34  CA  PHE   178       8.209  71.853  -9.463  1.00  0.00              
ATOM     35  C   PHE   178       8.410  70.649  -8.555  1.00  0.00              
ATOM     36  O   PHE   178       9.371  70.626  -7.780  1.00  0.00              
ATOM     37  N   ASP   179       7.514  69.665  -8.642  1.00  0.00              
ATOM     38  CA  ASP   179       7.593  68.441  -7.808  1.00  0.00              
ATOM     39  C   ASP   179       8.909  67.729  -8.031  1.00  0.00              
ATOM     40  O   ASP   179       9.611  67.296  -7.133  1.00  0.00              
ATOM     41  N   ASP   180       9.241  67.589  -9.322  1.00  0.00              
ATOM     42  CA  ASP   180      10.432  66.830  -9.671  1.00  0.00              
ATOM     43  C   ASP   180      11.681  67.584  -9.283  1.00  0.00              
ATOM     44  O   ASP   180      12.662  66.948  -8.878  1.00  0.00              
ATOM     45  N   ALA   181      11.704  68.908  -9.383  1.00  0.00              
ATOM     46  CA  ALA   181      12.800  69.701  -8.877  1.00  0.00              
ATOM     47  C   ALA   181      12.987  69.543  -7.368  1.00  0.00              
ATOM     48  O   ALA   181      14.114  69.372  -6.865  1.00  0.00              
ATOM     49  N   LEU   182      11.885  69.592  -6.652  1.00  0.00              
ATOM     50  CA  LEU   182      11.936  69.399  -5.207  1.00  0.00              
ATOM     51  C   LEU   182      12.391  67.984  -4.861  1.00  0.00              
ATOM     52  O   LEU   182      13.156  67.790  -3.894  1.00  0.00              
ATOM     53  N   ALA   183      11.973  66.972  -5.613  1.00  0.00              
ATOM     54  CA  ALA   183      12.457  65.604  -5.388  1.00  0.00              
ATOM     55  C   ALA   183      13.967  65.524  -5.574  1.00  0.00              
ATOM     56  O   ALA   183      14.642  64.909  -4.749  1.00  0.00              
ATOM     57  N   GLU   184      14.526  66.071  -6.658  1.00  0.00              
ATOM     58  CA  GLU   184      15.978  66.095  -6.814  1.00  0.00              
ATOM     59  C   GLU   184      16.672  66.682  -5.606  1.00  0.00              
ATOM     60  O   GLU   184      17.662  66.162  -5.078  1.00  0.00              
ATOM     61  N   ALA   185      16.212  67.845  -5.156  1.00  0.00              
ATOM     62  CA  ALA   185      16.847  68.484  -4.016  1.00  0.00              
ATOM     63  C   ALA   185      16.799  67.589  -2.775  1.00  0.00              
ATOM     64  O   ALA   185      17.779  67.515  -2.045  1.00  0.00              
ATOM     65  N   MET   186      15.629  66.953  -2.588  1.00  0.00              
ATOM     66  CA  MET   186      15.550  66.033  -1.414  1.00  0.00              
ATOM     67  C   MET   186      16.405  64.796  -1.526  1.00  0.00              
ATOM     68  O   MET   186      16.950  64.337  -0.558  1.00  0.00              
ATOM     69  N   LYS   187      16.591  64.286  -2.777  1.00  0.00              
ATOM     70  CA  LYS   187      17.528  63.171  -2.955  1.00  0.00              
ATOM     71  C   LYS   187      18.933  63.592  -2.475  1.00  0.00              
ATOM     72  O   LYS   187      19.577  62.812  -1.777  1.00  0.00              
ATOM     73  N   LEU   188      19.385  64.766  -2.843  1.00  0.00              
ATOM     74  CA  LEU   188      20.693  65.238  -2.393  1.00  0.00              
ATOM     75  C   LEU   188      20.696  65.363  -0.890  1.00  0.00              
ATOM     76  O   LEU   188      21.675  64.972  -0.265  1.00  0.00              
ATOM     77  N   ALA   189      19.656  65.824  -0.234  1.00  0.00              
ATOM     78  CA  ALA   189      19.587  65.905   1.207  1.00  0.00              
ATOM     79  C   ALA   189      19.608  64.507   1.814  1.00  0.00              
ATOM     80  O   ALA   189      20.222  64.354   2.894  1.00  0.00              
ATOM     81  N   LYS   190      18.983  63.503   1.219  1.00  0.00              
ATOM     82  CA  LYS   190      19.022  62.156   1.751  1.00  0.00              
ATOM     83  C   LYS   190      20.431  61.588   1.656  1.00  0.00              
ATOM     84  O   LYS   190      20.901  60.896   2.580  1.00  0.00              
ATOM     85  N   SER   191      21.154  61.835   0.584  1.00  0.00              
ATOM     86  CA  SER   191      22.547  61.462   0.486  1.00  0.00              
ATOM     87  C   SER   191      23.372  62.121   1.596  1.00  0.00              
ATOM     88  O   SER   191      24.175  61.455   2.250  1.00  0.00              
ATOM     89  N   ARG   192      23.134  63.419   1.831  1.00  0.00              
ATOM     90  CA  ARG   192      23.844  64.152   2.895  1.00  0.00              
ATOM     91  C   ARG   192      23.549  63.549   4.259  1.00  0.00              
ATOM     92  O   ARG   192      24.442  63.387   5.104  1.00  0.00              
ATOM     93  N   GLU   193      22.269  63.238   4.484  1.00  0.00              
ATOM     94  CA  GLU   193      21.863  62.560   5.712  1.00  0.00              
ATOM     95  C   GLU   193      22.611  61.230   5.877  1.00  0.00              
ATOM     96  O   GLU   193      23.170  60.948   6.935  1.00  0.00              
ATOM     97  N   ALA   194      22.586  60.449   4.794  1.00  0.00              
ATOM     98  CA  ALA   194      23.235  59.121   4.843  1.00  0.00              
ATOM     99  C   ALA   194      24.696  59.238   5.246  1.00  0.00              
ATOM    100  O   ALA   194      25.188  58.458   6.086  1.00  0.00              
ATOM    101  N   ARG   195      25.383  60.212   4.665  1.00  0.00              
ATOM    102  CA  ARG   195      26.845  60.313   4.952  1.00  0.00              
ATOM    103  C   ARG   195      27.145  60.774   6.356  1.00  0.00              
ATOM    104  O   ARG   195      28.273  60.640   6.796  1.00  0.00              
ATOM    105  N   HIS   196      26.160  61.283   7.077  1.00  0.00              
ATOM    106  CA  HIS   196      26.296  61.619   8.482  1.00  0.00              
ATOM    107  C   HIS   196      25.969  60.479   9.422  1.00  0.00              
ATOM    108  O   HIS   196      26.111  60.612  10.641  1.00  0.00              
ATOM    109  N   LEU   197      25.480  59.348   8.888  1.00  0.00              
ATOM    110  CA  LEU   197      25.177  58.214   9.740  1.00  0.00              
ATOM    111  C   LEU   197      26.455  57.481  10.098  1.00  0.00              
ATOM    112  O   LEU   197      27.205  57.126   9.198  1.00  0.00              
ATOM    113  N   PRO   198      26.702  57.252  11.373  1.00  0.00              
ATOM    114  CA  PRO   198      27.944  56.604  11.737  1.00  0.00              
ATOM    115  C   PRO   198      28.182  55.284  10.974  1.00  0.00              
ATOM    116  O   PRO   198      27.314  54.444  10.830  1.00  0.00              
ATOM    117  N   GLY   199      29.386  55.259  10.373  1.00  0.00              
ATOM    118  CA  GLY   199      29.865  54.130   9.640  1.00  0.00              
ATOM    119  C   GLY   199      29.485  54.069   8.184  1.00  0.00              
ATOM    120  O   GLY   199      30.055  53.294   7.418  1.00  0.00              
ATOM    121  N   TRP   200      28.539  54.886   7.715  1.00  0.00              
ATOM    122  CA  TRP   200      28.066  54.754   6.353  1.00  0.00              
ATOM    123  C   TRP   200      29.187  54.971   5.345  1.00  0.00              
ATOM    124  O   TRP   200      29.334  54.248   4.360  1.00  0.00              
ATOM    125  N   CYS   201      30.036  56.001   5.599  1.00  0.00              
ATOM    126  CA  CYS   201      31.145  56.285   4.672  1.00  0.00              
ATOM    127  C   CYS   201      32.291  55.301   4.787  1.00  0.00              
ATOM    128  O   CYS   201      33.210  55.310   3.963  1.00  0.00              
ATOM    129  N   GLY   202      32.261  54.412   5.773  1.00  0.00              
ATOM    130  CA  GLY   202      33.196  53.306   5.812  1.00  0.00              
ATOM    131  C   GLY   202      32.758  52.097   5.003  1.00  0.00              
ATOM    132  O   GLY   202      33.565  51.163   4.832  1.00  0.00              
END
