
#######################################################
#                                                     #
#                        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   18 (  147),  selected   18 , name T0347TS389_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS389_2-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    A     140      -       -           -
LGA    G     141      -       -           -
LGA    G     148      -       -           -
LGA    Y     149      -       -           -
LGA    A     150      D     134          1.606
LGA    K     151      P     135          2.039
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    V     152      S     138          3.408
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    S     157      A     146          3.248
LGA    -       -      G     147           -
LGA    W     161      G     148          2.662
LGA    A     162      Y     149          3.571
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    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    D     163      M     186          5.762
LGA    F     164      K     187          3.517
LGA    -       -      L     188           -
LGA    L     165      A     189          1.235
LGA    R     166      K     190          3.483
LGA    R     167      S     191          0.927
LGA    -       -      R     192           -
LGA    R     168      E     193          3.401
LGA    I     169      A     194          1.033
LGA    D     170      R     195          3.948
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   71    5.0     14    3.13     0.00     13.161     0.434

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.899659 * X  +   0.025575 * Y  +  -0.435844 * Z  +  30.389313
  Y_new =   0.222525 * X  +   0.832023 * Y  +   0.508154 * Z  +  39.349113
  Z_new =   0.375628 * X  +  -0.554151 * Y  +   0.742846 * Z  +  -1.135240 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.640926    2.500666  [ DEG:   -36.7224    143.2776 ]
  Theta =  -0.385074   -2.756518  [ DEG:   -22.0631   -157.9369 ]
  Phi   =   0.242477   -2.899116  [ DEG:    13.8929   -166.1071 ]
 
# 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: T0347TS389_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS389_2-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   71   5.0   14   3.13    0.00  13.161
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS389_2-D2
PFRMAT TS
TARGET T0347
MODEL  2
PARENT N/A
ATOM    732  N   ALA   140      11.209  53.061 -10.913  1.00  0.00
ATOM    733  CA  ALA   140      12.528  53.235 -10.316  1.00  0.00
ATOM    734  CB  ALA   140      12.435  54.097  -9.066  1.00  0.00
ATOM    735  O   ALA   140      14.342  51.692 -10.163  1.00  0.00
ATOM    736  C   ALA   140      13.175  51.909  -9.906  1.00  0.00
ATOM    737  N   GLY   141      12.427  51.024  -9.266  1.00  0.00
ATOM    738  CA  GLY   141      13.006  49.771  -8.785  1.00  0.00
ATOM    739  O   GLY   141      14.628  48.378  -9.898  1.00  0.00
ATOM    740  C   GLY   141      13.532  48.923  -9.954  1.00  0.00
ATOM    744  N   GLY   148      20.534  51.000 -14.300  1.00  0.00
ATOM    745  CA  GLY   148      20.331  52.222 -15.093  1.00  0.00
ATOM    746  O   GLY   148      20.545  54.553 -14.831  1.00  0.00
ATOM    747  C   GLY   148      20.369  53.495 -14.283  1.00  0.00
ATOM    748  N   TYR   149      20.142  53.373 -12.976  1.00  0.00
ATOM    749  CA  TYR   149      20.193  54.500 -12.053  1.00  0.00
ATOM    750  CB  TYR   149      18.781  54.908 -11.627  1.00  0.00
ATOM    751  CG  TYR   149      17.891  55.325 -12.776  1.00  0.00
ATOM    752  CD1 TYR   149      16.939  54.453 -13.291  1.00  0.00
ATOM    753  CD2 TYR   149      18.005  56.588 -13.342  1.00  0.00
ATOM    754  CE1 TYR   149      16.122  54.826 -14.341  1.00  0.00
ATOM    755  CE2 TYR   149      17.196  56.977 -14.392  1.00  0.00
ATOM    756  CZ  TYR   149      16.250  56.083 -14.891  1.00  0.00
ATOM    757  OH  TYR   149      15.437  56.456 -15.936  1.00  0.00
ATOM    758  O   TYR   149      21.260  52.885 -10.682  1.00  0.00
ATOM    759  C   TYR   149      20.986  54.065 -10.851  1.00  0.00
ATOM    760  N   ALA   150       6.349  54.397   0.598  1.00  0.00
ATOM    761  CA  ALA   150       4.998  54.830   0.206  1.00  0.00
ATOM    762  CB  ALA   150       4.514  55.947   1.117  1.00  0.00
ATOM    763  O   ALA   150       4.082  55.035  -2.003  1.00  0.00
ATOM    764  C   ALA   150       5.007  55.340  -1.226  1.00  0.00
ATOM    765  N   LYS   151       6.053  56.107  -1.572  1.00  0.00
ATOM    766  CA  LYS   151       6.295  56.570  -2.925  1.00  0.00
ATOM    767  CB  LYS   151       6.553  58.078  -2.938  1.00  0.00
ATOM    768  CG  LYS   151       5.396  58.910  -2.405  1.00  0.00
ATOM    769  CD  LYS   151       5.690  60.398  -2.514  1.00  0.00
ATOM    770  CE  LYS   151       4.499  61.229  -2.068  1.00  0.00
ATOM    771  NZ  LYS   151       4.772  62.690  -2.169  1.00  0.00
ATOM    772  O   LYS   151       8.285  55.167  -2.789  1.00  0.00
ATOM    773  C   LYS   151       7.532  55.848  -3.510  1.00  0.00
ATOM    774  N   VAL   152       7.746  56.013  -4.811  1.00  0.00
ATOM    775  CA  VAL   152       8.848  55.369  -5.515  1.00  0.00
ATOM    776  CB  VAL   152       8.338  54.340  -6.541  1.00  0.00
ATOM    777  CG1 VAL   152       7.776  53.116  -5.833  1.00  0.00
ATOM    778  CG2 VAL   152       7.238  54.943  -7.400  1.00  0.00
ATOM    779  O   VAL   152       9.077  57.142  -7.092  1.00  0.00
ATOM    780  C   VAL   152       9.627  56.444  -6.231  1.00  0.00
ATOM    784  N   SER   157      27.272  58.565  -7.774  1.00  0.00
ATOM    785  CA  SER   157      26.024  58.941  -7.136  1.00  0.00
ATOM    786  CB  SER   157      24.877  58.923  -8.149  1.00  0.00
ATOM    787  OG  SER   157      25.085  59.880  -9.172  1.00  0.00
ATOM    788  O   SER   157      25.159  58.396  -4.964  1.00  0.00
ATOM    789  C   SER   157      25.673  57.975  -6.003  1.00  0.00
ATOM    793  N   TRP   161      24.917  59.144  -2.137  1.00  0.00
ATOM    794  CA  TRP   161      23.782  58.677  -1.350  1.00  0.00
ATOM    795  CB  TRP   161      22.997  57.612  -2.118  1.00  0.00
ATOM    796  CG  TRP   161      21.805  57.093  -1.374  1.00  0.00
ATOM    797  CD1 TRP   161      20.555  57.638  -1.348  1.00  0.00
ATOM    798  CD2 TRP   161      21.750  55.923  -0.549  1.00  0.00
ATOM    799  CE2 TRP   161      20.435  55.822  -0.055  1.00  0.00
ATOM    800  CE3 TRP   161      22.684  54.950  -0.179  1.00  0.00
ATOM    801  NE1 TRP   161      19.724  56.882  -0.558  1.00  0.00
ATOM    802  CZ2 TRP   161      20.030  54.789   0.789  1.00  0.00
ATOM    803  CZ3 TRP   161      22.280  53.928   0.657  1.00  0.00
ATOM    804  CH2 TRP   161      20.966  53.852   1.134  1.00  0.00
ATOM    805  O   TRP   161      23.787  58.415   1.039  1.00  0.00
ATOM    806  C   TRP   161      24.275  58.073  -0.040  1.00  0.00
ATOM    807  N   ALA   162      25.254  57.182  -0.123  1.00  0.00
ATOM    808  CA  ALA   162      25.755  56.494   1.059  1.00  0.00
ATOM    809  CB  ALA   162      26.805  55.464   0.667  1.00  0.00
ATOM    810  O   ALA   162      26.259  57.238   3.258  1.00  0.00
ATOM    811  C   ALA   162      26.398  57.435   2.062  1.00  0.00
ATOM    812  N   ASP   163      27.087  58.463   1.584  1.00  0.00
ATOM    813  CA  ASP   163      27.691  59.474   2.453  1.00  0.00
ATOM    814  CB  ASP   163      28.461  60.504   1.624  1.00  0.00
ATOM    815  CG  ASP   163      29.749  59.948   1.051  1.00  0.00
ATOM    816  OD1 ASP   163      30.168  58.855   1.486  1.00  0.00
ATOM    817  OD2 ASP   163      30.341  60.605   0.170  1.00  0.00
ATOM    818  O   ASP   163      26.725  60.383   4.460  1.00  0.00
ATOM    819  C   ASP   163      26.603  60.203   3.254  1.00  0.00
ATOM    820  N   PHE   164      25.539  60.615   2.580  1.00  0.00
ATOM    821  CA  PHE   164      24.410  61.265   3.250  1.00  0.00
ATOM    822  CB  PHE   164      23.318  61.616   2.238  1.00  0.00
ATOM    823  CG  PHE   164      22.105  62.251   2.855  1.00  0.00
ATOM    824  CD1 PHE   164      22.105  63.594   3.196  1.00  0.00
ATOM    825  CD2 PHE   164      20.963  61.507   3.096  1.00  0.00
ATOM    826  CE1 PHE   164      20.989  64.179   3.763  1.00  0.00
ATOM    827  CE2 PHE   164      19.846  62.093   3.663  1.00  0.00
ATOM    828  CZ  PHE   164      19.856  63.423   3.996  1.00  0.00
ATOM    829  O   PHE   164      23.589  60.757   5.447  1.00  0.00
ATOM    830  C   PHE   164      23.811  60.338   4.308  1.00  0.00
ATOM    831  N   LEU   165      23.566  59.085   3.944  1.00  0.00
ATOM    832  CA  LEU   165      23.020  58.153   4.906  1.00  0.00
ATOM    833  CB  LEU   165      22.819  56.778   4.264  1.00  0.00
ATOM    834  CG  LEU   165      22.229  55.689   5.164  1.00  0.00
ATOM    835  CD1 LEU   165      20.842  56.085   5.649  1.00  0.00
ATOM    836  CD2 LEU   165      22.113  54.374   4.411  1.00  0.00
ATOM    837  O   LEU   165      23.413  57.886   7.250  1.00  0.00
ATOM    838  C   LEU   165      23.906  57.935   6.132  1.00  0.00
ATOM    839  N   ARG   166      25.209  57.833   5.925  1.00  0.00
ATOM    840  CA  ARG   166      26.147  57.653   7.026  1.00  0.00
ATOM    841  CB  ARG   166      27.570  57.472   6.492  1.00  0.00
ATOM    842  CG  ARG   166      28.606  57.194   7.571  1.00  0.00
ATOM    843  CD  ARG   166      29.998  57.052   6.975  1.00  0.00
ATOM    844  NE  ARG   166      30.462  58.298   6.368  1.00  0.00
ATOM    845  CZ  ARG   166      30.940  59.331   7.054  1.00  0.00
ATOM    846  NH1 ARG   166      31.339  60.422   6.416  1.00  0.00
ATOM    847  NH2 ARG   166      31.018  59.268   8.376  1.00  0.00
ATOM    848  O   ARG   166      26.102  58.773   9.170  1.00  0.00
ATOM    849  C   ARG   166      26.111  58.892   7.945  1.00  0.00
ATOM    850  N   ARG   167      26.087  60.083   7.364  1.00  0.00
ATOM    851  CA  ARG   167      26.011  61.295   8.157  1.00  0.00
ATOM    852  CB  ARG   167      26.055  62.530   7.254  1.00  0.00
ATOM    853  CG  ARG   167      27.410  62.784   6.614  1.00  0.00
ATOM    854  CD  ARG   167      27.362  63.979   5.677  1.00  0.00
ATOM    855  NE  ARG   167      28.651  64.221   5.032  1.00  0.00
ATOM    856  CZ  ARG   167      28.862  65.157   4.115  1.00  0.00
ATOM    857  NH1 ARG   167      30.069  65.305   3.583  1.00  0.00
ATOM    858  NH2 ARG   167      27.867  65.944   3.729  1.00  0.00
ATOM    859  O   ARG   167      24.774  61.719  10.160  1.00  0.00
ATOM    860  C   ARG   167      24.731  61.372   8.974  1.00  0.00
ATOM    861  N   ARG   168      23.602  61.022   8.362  1.00  0.00
ATOM    862  CA  ARG   168      22.325  61.070   9.053  1.00  0.00
ATOM    863  CB  ARG   168      21.174  60.853   8.069  1.00  0.00
ATOM    864  CG  ARG   168      19.792  60.999   8.686  1.00  0.00
ATOM    865  CD  ARG   168      18.706  60.952   7.625  1.00  0.00
ATOM    866  NE  ARG   168      17.370  61.083   8.203  1.00  0.00
ATOM    867  CZ  ARG   168      16.241  60.960   7.512  1.00  0.00
ATOM    868  NH1 ARG   168      15.072  61.094   8.125  1.00  0.00
ATOM    869  NH2 ARG   168      16.285  60.705   6.212  1.00  0.00
ATOM    870  O   ARG   168      21.638  60.204  11.170  1.00  0.00
ATOM    871  C   ARG   168      22.234  59.989  10.130  1.00  0.00
ATOM    872  N   ILE   169      22.856  58.833   9.873  1.00  0.00
ATOM    873  CA  ILE   169      22.991  57.738  10.839  1.00  0.00
ATOM    874  CB  ILE   169      23.745  56.540  10.234  1.00  0.00
ATOM    875  CG1 ILE   169      22.908  55.885   9.131  1.00  0.00
ATOM    876  CG2 ILE   169      24.034  55.496  11.302  1.00  0.00
ATOM    877  CD1 ILE   169      23.672  54.879   8.301  1.00  0.00
ATOM    878  O   ILE   169      23.330  58.104  13.202  1.00  0.00
ATOM    879  C   ILE   169      23.770  58.237  12.063  1.00  0.00
ATOM    880  N   ASP   170      24.925  58.820  11.823  1.00  0.00
ATOM    881  CA  ASP   170      25.761  59.322  12.910  1.00  0.00
ATOM    882  CB  ASP   170      27.057  59.918  12.357  1.00  0.00
ATOM    883  CG  ASP   170      28.063  60.234  13.446  1.00  0.00
ATOM    884  OD1 ASP   170      27.805  59.880  14.616  1.00  0.00
ATOM    885  OD2 ASP   170      29.109  60.836  13.130  1.00  0.00
ATOM    886  O   ASP   170      25.262  60.477  14.945  1.00  0.00
ATOM    887  C   ASP   170      25.077  60.414  13.736  1.00  0.00
TER
END
