
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0320AL044_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_5-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    N     233      N     229          2.048
LGA    -       -      S     230           -
LGA    P     234      L     231          4.040
LGA    H     235      P     232          4.894
LGA    L     236      N     233           -
LGA    R     237      P     234           -
LGA    K     238      H     235           -
LGA    D     239      L     236           -
LGA    S     240      R     237           -
LGA    N     241      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    N     242      N     268           #
LGA    P     243      T     269          3.499
LGA    A     244      S     270          1.919
LGA    L     245      P     271          2.262
LGA    H     246      I     272          3.079
LGA    F     247      S     273          1.915
LGA    E     248      V     274          1.111
LGA    W     249      V     275          1.077
LGA    E     250      D     276          1.485
LGA    I     251      K     277          2.491
LGA    G     256      E     278          2.733
LGA    A     259      R     279          2.571
LGA    E     260      F     280          3.408
LGA    -       -      S     281           -
LGA    G     261      K     282          4.573
LGA    E     262      Y     283          3.868
LGA    R     263      H     284          2.974
LGA    S     264      D     285          3.245
LGA    A     266      N     286          2.834
LGA    N     268      Y     287           #
LGA    T     269      -       -           -
LGA    S     270      -       -           -
LGA    P     271      Y     288           #
LGA    V     274      P     289           -
LGA    V     275      G     290           -
LGA    D     276      W     291           -
LGA    F     280      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   73    5.0     20    2.99     5.00     19.967     0.648

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.492358 * X  +   0.556711 * Y  +   0.669071 * Z  +   9.445708
  Y_new =   0.096457 * X  +  -0.729066 * Y  +   0.677612 * Z  +  29.923218
  Z_new =   0.865031 * X  +   0.398165 * Y  +   0.305263 * Z  + -61.820293 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.916708   -2.224885  [ DEG:    52.5235   -127.4765 ]
  Theta =  -1.045213   -2.096380  [ DEG:   -59.8863   -120.1137 ]
  Phi   =   2.948135   -0.193458  [ DEG:   168.9157    -11.0843 ]
 
# 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: T0320AL044_5-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_5-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   73   5.0   20   2.99    5.00  19.967
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_5-D2
REMARK Aligment from pdb entry: 1wxe_A
ATOM    697  N   ASN   233      27.424  17.845   8.122  1.00  0.00              
ATOM    698  CA  ASN   233      28.028  18.124   6.824  1.00  0.00              
ATOM    699  C   ASN   233      27.204  17.305   5.841  1.00  0.00              
ATOM    700  O   ASN   233      26.579  16.318   6.235  1.00  0.00              
ATOM    701  N   PRO   234      27.220  17.690   4.567  1.00  0.00              
ATOM    702  CA  PRO   234      26.380  17.039   3.567  1.00  0.00              
ATOM    703  C   PRO   234      25.097  17.682   4.058  1.00  0.00              
ATOM    704  O   PRO   234      24.440  17.178   4.969  1.00  0.00              
ATOM    705  N   HIS   235      24.784  18.823   3.455  1.00  0.00              
ATOM    706  CA  HIS   235      23.660  19.675   3.825  1.00  0.00              
ATOM    707  C   HIS   235      24.417  20.687   4.663  1.00  0.00              
ATOM    708  O   HIS   235      24.292  20.708   5.886  1.00  0.00              
ATOM    709  N   LEU   236      25.243  21.490   4.000  1.00  0.00              
ATOM    710  CA  LEU   236      26.029  22.492   4.700  1.00  0.00              
ATOM    711  C   LEU   236      25.157  23.509   5.403  1.00  0.00              
ATOM    712  O   LEU   236      25.453  24.702   5.397  1.00  0.00              
ATOM    713  N   ARG   237      24.081  23.023   6.011  1.00  0.00              
ATOM    714  CA  ARG   237      23.124  23.854   6.730  1.00  0.00              
ATOM    715  C   ARG   237      22.596  23.068   7.931  1.00  0.00              
ATOM    716  O   ARG   237      22.661  21.842   7.948  1.00  0.00              
ATOM    717  N   LYS   238      22.079  23.774   8.931  1.00  0.00              
ATOM    718  CA  LYS   238      21.537  23.116  10.119  1.00  0.00              
ATOM    719  C   LYS   238      20.046  22.892   9.934  1.00  0.00              
ATOM    720  O   LYS   238      19.444  23.423   9.000  1.00  0.00              
ATOM    721  N   ASP   239      19.450  22.099  10.818  1.00  0.00              
ATOM    722  CA  ASP   239      18.019  21.851  10.740  1.00  0.00              
ATOM    723  C   ASP   239      17.238  23.136  10.986  1.00  0.00              
ATOM    724  O   ASP   239      16.131  23.298  10.474  1.00  0.00              
ATOM    725  N   SER   240      13.516  27.104   9.165  1.00  0.00              
ATOM    726  CA  SER   240      13.234  28.519   8.910  1.00  0.00              
ATOM    727  C   SER   240      12.867  28.720   7.442  1.00  0.00              
ATOM    728  O   SER   240      11.897  29.406   7.114  1.00  0.00              
ATOM    729  N   ASN   241      13.649  28.108   6.556  1.00  0.00              
ATOM    730  CA  ASN   241      13.401  28.213   5.120  1.00  0.00              
ATOM    731  C   ASN   241      11.992  27.710   4.814  1.00  0.00              
ATOM    732  O   ASN   241      11.221  28.375   4.109  1.00  0.00              
ATOM    733  N   ASN   242      11.665  26.535   5.349  1.00  0.00              
ATOM    734  CA  ASN   242      10.355  25.928   5.138  1.00  0.00              
ATOM    735  C   ASN   242       9.212  26.761   5.706  1.00  0.00              
ATOM    736  O   ASN   242       8.082  26.654   5.239  1.00  0.00              
ATOM    737  N   PRO   243       9.083  29.923   5.503  1.00  0.00              
ATOM    738  CA  PRO   243       9.016  31.137   4.703  1.00  0.00              
ATOM    739  C   PRO   243       9.810  32.319   5.223  1.00  0.00              
ATOM    740  O   PRO   243       9.598  33.458   4.796  1.00  0.00              
ATOM    741  N   ALA   244      10.733  32.054   6.139  1.00  0.00              
ATOM    742  CA  ALA   244      11.544  33.111   6.719  1.00  0.00              
ATOM    743  C   ALA   244      12.689  33.538   5.819  1.00  0.00              
ATOM    744  O   ALA   244      13.103  32.812   4.916  1.00  0.00              
ATOM    745  N   LEU   245      13.188  34.738   6.076  1.00  0.00              
ATOM    746  CA  LEU   245      14.293  35.298   5.321  1.00  0.00              
ATOM    747  C   LEU   245      15.576  34.724   5.913  1.00  0.00              
ATOM    748  O   LEU   245      15.876  34.941   7.085  1.00  0.00              
ATOM    749  N   HIS   246      16.317  33.967   5.114  1.00  0.00              
ATOM    750  CA  HIS   246      17.562  33.375   5.583  1.00  0.00              
ATOM    751  C   HIS   246      18.707  33.912   4.735  1.00  0.00              
ATOM    752  O   HIS   246      18.480  34.492   3.671  1.00  0.00              
ATOM    753  N   PHE   247      19.954  33.753   5.204  1.00  0.00              
ATOM    754  CA  PHE   247      21.089  34.247   4.416  1.00  0.00              
ATOM    755  C   PHE   247      21.002  33.659   3.003  1.00  0.00              
ATOM    756  O   PHE   247      20.629  32.500   2.830  1.00  0.00              
ATOM    757  N   GLU   248      21.336  34.455   1.994  1.00  0.00              
ATOM    758  CA  GLU   248      21.247  33.986   0.616  1.00  0.00              
ATOM    759  C   GLU   248      22.092  32.750   0.328  1.00  0.00              
ATOM    760  O   GLU   248      21.672  31.874  -0.429  1.00  0.00              
ATOM    761  N   TRP   249      23.278  32.671   0.924  1.00  0.00              
ATOM    762  CA  TRP   249      24.148  31.515   0.704  1.00  0.00              
ATOM    763  C   TRP   249      23.472  30.255   1.240  1.00  0.00              
ATOM    764  O   TRP   249      23.630  29.167   0.686  1.00  0.00              
ATOM    765  N   GLU   250      22.714  30.414   2.321  1.00  0.00              
ATOM    766  CA  GLU   250      21.994  29.302   2.937  1.00  0.00              
ATOM    767  C   GLU   250      20.846  28.868   2.028  1.00  0.00              
ATOM    768  O   GLU   250      20.615  27.672   1.825  1.00  0.00              
ATOM    769  N   ILE   251      20.128  29.846   1.482  1.00  0.00              
ATOM    770  CA  ILE   251      19.023  29.562   0.575  1.00  0.00              
ATOM    771  C   ILE   251      19.529  28.818  -0.663  1.00  0.00              
ATOM    772  O   ILE   251      18.897  27.867  -1.119  1.00  0.00              
ATOM    773  N   GLY   256      20.670  29.249  -1.200  1.00  0.00              
ATOM    774  CA  GLY   256      21.235  28.607  -2.386  1.00  0.00              
ATOM    775  C   GLY   256      21.610  27.152  -2.123  1.00  0.00              
ATOM    776  O   GLY   256      21.414  26.291  -2.977  1.00  0.00              
ATOM    777  N   ALA   259      22.155  26.879  -0.943  1.00  0.00              
ATOM    778  CA  ALA   259      22.554  25.520  -0.589  1.00  0.00              
ATOM    779  C   ALA   259      21.335  24.609  -0.530  1.00  0.00              
ATOM    780  O   ALA   259      21.320  23.527  -1.121  1.00  0.00              
ATOM    781  N   GLU   260      19.931  24.035  -3.927  1.00  0.00              
ATOM    782  CA  GLU   260      20.796  23.177  -4.732  1.00  0.00              
ATOM    783  C   GLU   260      20.464  21.717  -4.435  1.00  0.00              
ATOM    784  O   GLU   260      20.338  20.897  -5.349  1.00  0.00              
ATOM    785  N   GLY   261      20.323  21.400  -3.150  1.00  0.00              
ATOM    786  CA  GLY   261      19.984  20.047  -2.725  1.00  0.00              
ATOM    787  C   GLY   261      18.619  19.646  -3.271  1.00  0.00              
ATOM    788  O   GLY   261      18.429  18.523  -3.734  1.00  0.00              
ATOM    789  N   GLU   262      17.667  20.569  -3.199  1.00  0.00              
ATOM    790  CA  GLU   262      16.320  20.302  -3.680  1.00  0.00              
ATOM    791  C   GLU   262      16.328  19.932  -5.159  1.00  0.00              
ATOM    792  O   GLU   262      15.756  18.919  -5.555  1.00  0.00              
ATOM    793  N   ARG   263      16.980  20.762  -5.965  1.00  0.00              
ATOM    794  CA  ARG   263      17.061  20.539  -7.403  1.00  0.00              
ATOM    795  C   ARG   263      17.809  19.252  -7.737  1.00  0.00              
ATOM    796  O   ARG   263      17.406  18.491  -8.618  1.00  0.00              
ATOM    797  N   SER   264      18.895  19.011  -7.016  1.00  0.00              
ATOM    798  CA  SER   264      19.717  17.828  -7.230  1.00  0.00              
ATOM    799  C   SER   264      19.000  16.514  -6.928  1.00  0.00              
ATOM    800  O   SER   264      19.306  15.485  -7.530  1.00  0.00              
ATOM    801  N   ALA   266      18.035  16.546  -6.016  1.00  0.00              
ATOM    802  CA  ALA   266      17.342  15.322  -5.628  1.00  0.00              
ATOM    803  C   ALA   266      15.889  15.150  -6.064  1.00  0.00              
ATOM    804  O   ALA   266      15.151  14.375  -5.461  1.00  0.00              
ATOM    805  N   ASN   268      15.477  15.846  -7.118  1.00  0.00              
ATOM    806  CA  ASN   268      14.105  15.714  -7.595  1.00  0.00              
ATOM    807  C   ASN   268      13.809  14.265  -8.016  1.00  0.00              
ATOM    808  O   ASN   268      12.684  13.783  -7.859  1.00  0.00              
ATOM    809  N   THR   269      14.818  13.566  -8.530  1.00  0.00              
ATOM    810  CA  THR   269      14.622  12.179  -8.953  1.00  0.00              
ATOM    811  C   THR   269      14.168  11.267  -7.802  1.00  0.00              
ATOM    812  O   THR   269      13.551  10.227  -8.032  1.00  0.00              
ATOM    813  N   SER   270      14.472  11.649  -6.563  1.00  0.00              
ATOM    814  CA  SER   270      14.079  10.845  -5.403  1.00  0.00              
ATOM    815  C   SER   270      12.615  11.034  -5.009  1.00  0.00              
ATOM    816  O   SER   270      12.037  10.196  -4.314  1.00  0.00              
ATOM    817  N   PRO   271      12.020  12.139  -5.444  1.00  0.00              
ATOM    818  CA  PRO   271      10.638  12.439  -5.093  1.00  0.00              
ATOM    819  C   PRO   271       9.643  12.175  -6.224  1.00  0.00              
ATOM    820  O   PRO   271       8.476  12.550  -6.120  1.00  0.00              
ATOM    821  N   VAL   274      10.109  11.524  -7.288  1.00  0.00              
ATOM    822  CA  VAL   274       9.278  11.203  -8.449  1.00  0.00              
ATOM    823  C   VAL   274       9.487   9.750  -8.876  1.00  0.00              
ATOM    824  O   VAL   274      10.501   9.144  -8.546  1.00  0.00              
ATOM    825  N   VAL   275      12.199   7.827 -14.192  1.00  0.00              
ATOM    826  CA  VAL   275      12.160   8.710 -15.352  1.00  0.00              
ATOM    827  C   VAL   275      11.882   7.994 -16.673  1.00  0.00              
ATOM    828  O   VAL   275      12.472   6.957 -16.964  1.00  0.00              
ATOM    829  N   ASP   276      10.631   8.602 -21.128  1.00  0.00              
ATOM    830  CA  ASP   276      10.792   9.500 -22.269  1.00  0.00              
ATOM    831  C   ASP   276       9.803  10.662 -22.248  1.00  0.00              
ATOM    832  O   ASP   276       9.986  11.643 -22.957  1.00  0.00              
ATOM    833  N   PHE   280       8.766  10.559 -21.421  1.00  0.00              
ATOM    834  CA  PHE   280       7.753  11.609 -21.343  1.00  0.00              
ATOM    835  C   PHE   280       8.088  12.735 -20.368  1.00  0.00              
ATOM    836  O   PHE   280       7.490  13.813 -20.436  1.00  0.00              
END
