
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0323AL242_4-D1
# Molecule2: number of CA atoms  101 (  777),  selected  101 , name T0323_D1.pdb
# PARAMETERS: T0323AL242_4-D1.T0323_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      20      M       1           -
LGA    -       -      R       2           -
LGA    -       -      Y       3           -
LGA    -       -      F       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      S       8           -
LGA    L      21      P       9          5.551
LGA    F      22      E      10          1.172
LGA    Q      23      V      11          2.865
LGA    -       -      K      12           -
LGA    -       -      T      13           -
LGA    F      24      I      14          1.766
LGA    I      25      V      15          1.439
LGA    -       -      A      16           -
LGA    -       -      Q      17           -
LGA    E      26      D      18          1.521
LGA    I      27      S      19          2.645
LGA    A      28      R      20          1.501
LGA    G      29      L      21          3.626
LGA    -       -      F      22           -
LGA    -       -      Q      23           -
LGA    E      30      F      24          2.400
LGA    V      31      I      25          3.850
LGA    -       -      E      26           -
LGA    -       -      I      27           -
LGA    Q      32      A      28          4.289
LGA    L      33      G      29           #
LGA    -       -      E      30           -
LGA    -       -      V      31           -
LGA    -       -      Q      32           -
LGA    -       -      L      33           -
LGA    -       -      L     150           -
LGA    L     150      D     151           #
LGA    D     151      V     152          2.448
LGA    V     152      L     153          3.347
LGA    L     153      S     154          2.537
LGA    S     154      V     155          3.093
LGA    -       -      G     156           -
LGA    -       -      D     157           -
LGA    -       -      V     158           -
LGA    -       -      G     159           -
LGA    V     155      L     160          1.377
LGA    G     156      Q     161          2.249
LGA    D     157      R     162          1.424
LGA    -       -      G     163           -
LGA    V     158      A     164          3.302
LGA    G     159      K     165          4.241
LGA    L     160      W     166           #
LGA    Q     161      L     167           #
LGA    R     162      Y     168          3.707
LGA    G     163      G     169           -
LGA    -       -      N     170           -
LGA    -       -      G     171           -
LGA    -       -      E     172           -
LGA    -       -      G     173           -
LGA    -       -      D     174           -
LGA    -       -      G     175           -
LGA    -       -      K     176           -
LGA    -       -      K     177           -
LGA    -       -      L     178           -
LGA    A     164      L     179          4.162
LGA    K     165      I     180          3.727
LGA    W     166      Y     181          4.768
LGA    L     167      H     182          4.408
LGA    Y     168      G     183          2.915
LGA    G     169      K     184          2.922
LGA    N     170      A     185          3.300
LGA    G     171      -       -           -
LGA    E     172      -       -           -
LGA    G     173      -       -           -
LGA    D     174      -       -           -
LGA    G     175      -       -           -
LGA    K     176      W     186           #
LGA    -       -      A     187           -
LGA    K     177      P     188          1.965
LGA    -       -      Y     189           -
LGA    -       -      E     190           -
LGA    -       -      T     191           -
LGA    -       -      V     192           -
LGA    -       -      A     193           -
LGA    -       -      C     194           -
LGA    -       -      L     195           -
LGA    -       -      Y     196           -
LGA    -       -      L     197           -
LGA    -       -      W     198           -
LGA    -       -      K     199           -
LGA    -       -      A     200           -
LGA    -       -      A     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      F     204           -
LGA    -       -      A     205           -
LGA    -       -      E     206           -
LGA    -       -      E     207           -
LGA    -       -      Y     208           -
LGA    -       -      R     209           -
LGA    -       -      S     210           -
LGA    -       -      L     211           -
LGA    -       -      E     212           -
LGA    -       -      E     213           -
LGA    -       -      L     214           -
LGA    -       -      L     215           -
LGA    -       -      H     216           -
LGA    -       -      H     217           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42  101    5.0     30    3.16     0.00     17.602     0.921

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.414771 * X  +   0.793535 * Y  +  -0.445272 * Z  +   5.443825
  Y_new =  -0.793516 * X  +   0.075959 * Y  +  -0.603790 * Z  +  61.794651
  Z_new =  -0.445306 * X  +   0.603765 * Y  +   0.661188 * Z  + -15.172064 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.740034   -2.401559  [ DEG:    42.4008   -137.5992 ]
  Theta =   0.461516    2.680076  [ DEG:    26.4429    153.5571 ]
  Phi   =  -1.089154    2.052439  [ DEG:   -62.4039    117.5961 ]
 
# 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: T0323AL242_4-D1                               
REMARK     2: T0323_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323AL242_4-D1.T0323_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42  101   5.0   30   3.16    0.00  17.602
REMARK  ---------------------------------------------------------- 
MOLECULE T0323AL242_4-D1
REMARK Aligment from pdb entry: 1ngn_A
ATOM      1  N   ARG    20      32.176  29.912   6.441  1.00  0.00              
ATOM      2  CA  ARG    20      33.282  30.794   6.767  1.00  0.00              
ATOM      3  C   ARG    20      32.895  31.754   7.884  1.00  0.00              
ATOM      4  O   ARG    20      33.744  32.256   8.636  1.00  0.00              
ATOM      5  N   LEU    21      31.593  32.015   7.992  1.00  0.00              
ATOM      6  CA  LEU    21      31.077  32.897   9.030  1.00  0.00              
ATOM      7  C   LEU    21      30.980  32.142  10.351  1.00  0.00              
ATOM      8  O   LEU    21      30.272  31.138  10.460  1.00  0.00              
ATOM      9  N   PHE    22      31.711  32.620  11.347  1.00  0.00              
ATOM     10  CA  PHE    22      31.676  32.004  12.655  1.00  0.00              
ATOM     11  C   PHE    22      31.156  33.046  13.627  1.00  0.00              
ATOM     12  O   PHE    22      31.817  34.054  13.884  1.00  0.00              
ATOM     13  N   GLN    23      29.945  32.830  14.160  1.00  0.00              
ATOM     14  CA  GLN    23      29.377  33.793  15.108  1.00  0.00              
ATOM     15  C   GLN    23      30.253  33.830  16.349  1.00  0.00              
ATOM     16  O   GLN    23      30.544  32.788  16.932  1.00  0.00              
ATOM     17  N   PHE    24      30.702  35.024  16.763  1.00  0.00              
ATOM     18  CA  PHE    24      31.553  35.115  17.957  1.00  0.00              
ATOM     19  C   PHE    24      30.848  34.643  19.220  1.00  0.00              
ATOM     20  O   PHE    24      29.626  34.663  19.290  1.00  0.00              
ATOM     21  N   ILE    25      31.618  34.212  20.216  1.00  0.00              
ATOM     22  CA  ILE    25      31.035  33.760  21.476  1.00  0.00              
ATOM     23  C   ILE    25      30.727  34.983  22.326  1.00  0.00              
ATOM     24  O   ILE    25      31.579  35.853  22.513  1.00  0.00              
ATOM     25  N   GLU    26      29.498  35.039  22.826  1.00  0.00              
ATOM     26  CA  GLU    26      29.034  36.140  23.659  1.00  0.00              
ATOM     27  C   GLU    26      29.011  35.720  25.128  1.00  0.00              
ATOM     28  O   GLU    26      29.073  34.531  25.441  1.00  0.00              
ATOM     29  N   ILE    27      28.958  36.692  26.050  1.00  0.00              
ATOM     30  CA  ILE    27      28.923  36.324  27.467  1.00  0.00              
ATOM     31  C   ILE    27      27.521  35.874  27.883  1.00  0.00              
ATOM     32  O   ILE    27      27.235  35.719  29.069  1.00  0.00              
ATOM     33  N   ALA    28      26.652  35.655  26.903  1.00  0.00              
ATOM     34  CA  ALA    28      25.284  35.242  27.188  1.00  0.00              
ATOM     35  C   ALA    28      25.010  33.760  26.948  1.00  0.00              
ATOM     36  O   ALA    28      23.942  33.257  27.283  1.00  0.00              
ATOM     37  N   GLY    29      25.986  33.073  26.370  1.00  0.00              
ATOM     38  CA  GLY    29      25.881  31.648  26.090  1.00  0.00              
ATOM     39  C   GLY    29      24.528  31.192  25.549  1.00  0.00              
ATOM     40  O   GLY    29      23.919  30.270  26.087  1.00  0.00              
ATOM     41  N   GLU    30      24.059  31.836  24.485  1.00  0.00              
ATOM     42  CA  GLU    30      22.794  31.448  23.873  1.00  0.00              
ATOM     43  C   GLU    30      22.998  30.031  23.360  1.00  0.00              
ATOM     44  O   GLU    30      24.110  29.664  22.972  1.00  0.00              
ATOM     45  N   VAL    31      21.937  29.234  23.355  1.00  0.00              
ATOM     46  CA  VAL    31      22.050  27.864  22.877  1.00  0.00              
ATOM     47  C   VAL    31      22.406  27.837  21.381  1.00  0.00              
ATOM     48  O   VAL    31      23.030  26.890  20.900  1.00  0.00              
ATOM     49  N   GLN    32      22.026  28.890  20.654  1.00  0.00              
ATOM     50  CA  GLN    32      22.325  29.004  19.224  1.00  0.00              
ATOM     51  C   GLN    32      23.830  29.037  18.966  1.00  0.00              
ATOM     52  O   GLN    32      24.292  28.681  17.880  1.00  0.00              
ATOM     53  N   LEU    33      24.588  29.484  19.962  1.00  0.00              
ATOM     54  CA  LEU    33      26.038  29.575  19.837  1.00  0.00              
ATOM     55  C   LEU    33      26.700  28.199  19.850  1.00  0.00              
ATOM     56  O   LEU    33      27.796  28.021  19.318  1.00  0.00              
ATOM    465  N   LEU   150      23.542  39.067  10.090  1.00  0.00              
ATOM    466  CA  LEU   150      23.162  39.645  11.367  1.00  0.00              
ATOM    467  C   LEU   150      22.854  41.125  11.300  1.00  0.00              
ATOM    468  O   LEU   150      21.948  41.604  11.975  1.00  0.00              
ATOM    469  N   ASP   151      23.600  41.844  10.472  1.00  0.00              
ATOM    470  CA  ASP   151      23.418  43.279  10.325  1.00  0.00              
ATOM    471  C   ASP   151      22.061  43.644   9.745  1.00  0.00              
ATOM    472  O   ASP   151      21.587  44.758   9.923  1.00  0.00              
ATOM    473  N   VAL   152      21.437  42.700   9.057  1.00  0.00              
ATOM    474  CA  VAL   152      20.125  42.930   8.460  1.00  0.00              
ATOM    475  C   VAL   152      18.980  42.455   9.348  1.00  0.00              
ATOM    476  O   VAL   152      17.824  42.756   9.074  1.00  0.00              
ATOM    477  N   LEU   153      19.312  41.710  10.402  1.00  0.00              
ATOM    478  CA  LEU   153      18.323  41.141  11.316  1.00  0.00              
ATOM    479  C   LEU   153      17.946  42.059  12.464  1.00  0.00              
ATOM    480  O   LEU   153      18.807  42.690  13.076  1.00  0.00              
ATOM    481  N   SER   154      16.645  42.115  12.748  1.00  0.00              
ATOM    482  CA  SER   154      16.090  42.913  13.843  1.00  0.00              
ATOM    483  C   SER   154      15.233  41.969  14.690  1.00  0.00              
ATOM    484  O   SER   154      14.021  41.844  14.492  1.00  0.00              
ATOM    485  N   VAL   155      15.878  41.277  15.643  1.00  0.00              
ATOM    486  CA  VAL   155      15.245  40.308  16.552  1.00  0.00              
ATOM    487  C   VAL   155      14.137  40.833  17.443  1.00  0.00              
ATOM    488  O   VAL   155      14.101  42.006  17.786  1.00  0.00              
ATOM    489  N   GLY   156      13.223  39.946  17.810  1.00  0.00              
ATOM    490  CA  GLY   156      12.140  40.309  18.697  1.00  0.00              
ATOM    491  C   GLY   156      12.209  39.400  19.924  1.00  0.00              
ATOM    492  O   GLY   156      11.372  39.466  20.816  1.00  0.00              
ATOM    493  N   ASP   157      13.226  38.550  19.953  1.00  0.00              
ATOM    494  CA  ASP   157      13.456  37.636  21.059  1.00  0.00              
ATOM    495  C   ASP   157      14.453  38.321  22.005  1.00  0.00              
ATOM    496  O   ASP   157      15.466  38.870  21.563  1.00  0.00              
ATOM    497  N   VAL   158      14.158  38.298  23.301  1.00  0.00              
ATOM    498  CA  VAL   158      15.013  38.931  24.298  1.00  0.00              
ATOM    499  C   VAL   158      16.485  38.513  24.264  1.00  0.00              
ATOM    500  O   VAL   158      17.373  39.360  24.193  1.00  0.00              
ATOM    501  N   GLY   159      16.754  37.217  24.321  1.00  0.00              
ATOM    502  CA  GLY   159      18.138  36.750  24.306  1.00  0.00              
ATOM    503  C   GLY   159      18.833  37.026  22.968  1.00  0.00              
ATOM    504  O   GLY   159      20.039  37.278  22.925  1.00  0.00              
ATOM    505  N   LEU   160      18.073  36.961  21.878  1.00  0.00              
ATOM    506  CA  LEU   160      18.630  37.227  20.560  1.00  0.00              
ATOM    507  C   LEU   160      19.030  38.708  20.522  1.00  0.00              
ATOM    508  O   LEU   160      20.092  39.052  20.013  1.00  0.00              
ATOM    509  N   GLN   161      18.182  39.574  21.080  1.00  0.00              
ATOM    510  CA  GLN   161      18.470  41.003  21.113  1.00  0.00              
ATOM    511  C   GLN   161      19.709  41.289  21.956  1.00  0.00              
ATOM    512  O   GLN   161      20.480  42.190  21.646  1.00  0.00              
ATOM    513  N   ARG   162      19.906  40.512  23.016  1.00  0.00              
ATOM    514  CA  ARG   162      21.065  40.697  23.878  1.00  0.00              
ATOM    515  C   ARG   162      22.310  40.382  23.089  1.00  0.00              
ATOM    516  O   ARG   162      23.279  41.139  23.095  1.00  0.00              
ATOM    517  N   GLY   163      22.268  39.255  22.395  1.00  0.00              
ATOM    518  CA  GLY   163      23.401  38.832  21.594  1.00  0.00              
ATOM    519  C   GLY   163      23.676  39.793  20.435  1.00  0.00              
ATOM    520  O   GLY   163      24.815  40.176  20.193  1.00  0.00              
ATOM    521  N   ALA   164      22.617  40.167  19.732  1.00  0.00              
ATOM    522  CA  ALA   164      22.689  41.055  18.584  1.00  0.00              
ATOM    523  C   ALA   164      23.211  42.451  18.948  1.00  0.00              
ATOM    524  O   ALA   164      24.035  43.015  18.225  1.00  0.00              
ATOM    525  N   LYS   165      22.728  43.005  20.057  1.00  0.00              
ATOM    526  CA  LYS   165      23.165  44.322  20.530  1.00  0.00              
ATOM    527  C   LYS   165      24.662  44.262  20.835  1.00  0.00              
ATOM    528  O   LYS   165      25.423  45.181  20.512  1.00  0.00              
ATOM    529  N   TRP   166      25.062  43.170  21.481  1.00  0.00              
ATOM    530  CA  TRP   166      26.447  42.935  21.863  1.00  0.00              
ATOM    531  C   TRP   166      27.342  42.760  20.637  1.00  0.00              
ATOM    532  O   TRP   166      28.509  43.162  20.637  1.00  0.00              
ATOM    533  N   LEU   167      26.793  42.140  19.600  1.00  0.00              
ATOM    534  CA  LEU   167      27.539  41.921  18.370  1.00  0.00              
ATOM    535  C   LEU   167      27.796  43.271  17.706  1.00  0.00              
ATOM    536  O   LEU   167      28.883  43.522  17.189  1.00  0.00              
ATOM    537  N   TYR   168      26.784  44.135  17.732  1.00  0.00              
ATOM    538  CA  TYR   168      26.872  45.477  17.159  1.00  0.00              
ATOM    539  C   TYR   168      27.830  46.332  17.992  1.00  0.00              
ATOM    540  O   TYR   168      28.636  47.090  17.450  1.00  0.00              
ATOM    541  N   GLY   169      27.735  46.193  19.311  1.00  0.00              
ATOM    542  CA  GLY   169      28.572  46.949  20.229  1.00  0.00              
ATOM    543  C   GLY   169      30.053  46.646  20.045  1.00  0.00              
ATOM    544  O   GLY   169      30.882  47.556  20.064  1.00  0.00              
ATOM    545  N   ASN   170      30.375  45.370  19.842  1.00  0.00              
ATOM    546  CA  ASN   170      31.761  44.938  19.723  1.00  0.00              
ATOM    547  C   ASN   170      32.219  44.389  18.391  1.00  0.00              
ATOM    548  O   ASN   170      33.294  43.807  18.313  1.00  0.00              
ATOM    549  N   GLY   171      31.443  44.558  17.335  1.00  0.00              
ATOM    550  CA  GLY   171      31.867  44.018  16.043  1.00  0.00              
ATOM    551  C   GLY   171      33.160  44.662  15.535  1.00  0.00              
ATOM    552  O   GLY   171      33.913  44.034  14.806  1.00  0.00              
ATOM    553  N   GLU   172      33.405  45.911  15.913  1.00  0.00              
ATOM    554  CA  GLU   172      34.620  46.613  15.498  1.00  0.00              
ATOM    555  C   GLU   172      35.803  45.880  16.103  1.00  0.00              
ATOM    556  O   GLU   172      36.750  45.508  15.430  1.00  0.00              
ATOM    557  N   GLY   173      35.730  45.679  17.421  1.00  0.00              
ATOM    558  CA  GLY   173      36.788  45.010  18.174  1.00  0.00              
ATOM    559  C   GLY   173      36.977  43.516  17.875  1.00  0.00              
ATOM    560  O   GLY   173      38.063  42.972  18.088  1.00  0.00              
ATOM    561  N   ASP   174      35.935  42.849  17.407  1.00  0.00              
ATOM    562  CA  ASP   174      36.045  41.438  17.116  1.00  0.00              
ATOM    563  C   ASP   174      36.845  41.274  15.822  1.00  0.00              
ATOM    564  O   ASP   174      38.037  40.931  15.878  1.00  0.00              
ATOM    565  N   GLY   175      36.202  41.542  14.676  1.00  0.00              
ATOM    566  CA  GLY   175      36.846  41.437  13.348  1.00  0.00              
ATOM    567  C   GLY   175      35.841  41.385  12.216  1.00  0.00              
ATOM    568  O   GLY   175      36.222  41.362  11.054  1.00  0.00              
ATOM    569  N   LYS   176      34.569  41.393  12.585  1.00  0.00              
ATOM    570  CA  LYS   176      33.461  41.205  11.674  1.00  0.00              
ATOM    571  C   LYS   176      32.795  42.288  10.893  1.00  0.00              
ATOM    572  O   LYS   176      33.165  43.449  10.947  1.00  0.00              
ATOM    573  N   LYS   177      31.833  41.821  10.104  1.00  0.00              
ATOM    574  CA  LYS   177      30.959  42.587   9.230  1.00  0.00              
ATOM    575  C   LYS   177      30.807  44.096   9.472  1.00  0.00              
ATOM    576  O   LYS   177      31.045  44.561  10.604  1.00  0.00              
END
