
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0316AL333_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL333_5-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V     225      G     220           -
LGA    D     226      R     221           -
LGA    G     227      -       -           -
LGA    R     228      -       -           -
LGA    D     229      -       -           -
LGA    M     230      M     222           #
LGA    G     231      M     223          4.980
LGA    E     232      T     224           -
LGA    -       -      V     225           -
LGA    H     233      D     226          3.176
LGA    A     234      G     227          2.545
LGA    G     235      R     228          1.854
LGA    L     236      D     229          3.058
LGA    -       -      M     230           -
LGA    M     237      G     231          5.186
LGA    Y     239      -       -           -
LGA    T     240      E     232          3.860
LGA    I     241      H     233          2.869
LGA    G     242      A     234           #
LGA    Q     243      -       -           -
LGA    R     244      -       -           -
LGA    G     245      G     235           #
LGA    G     246      L     236          3.501
LGA    L     247      M     237          2.351
LGA    G     248      Y     238          1.505
LGA    I     249      Y     239           #
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    G     250      L     247          2.556
LGA    G     251      G     248          2.039
LGA    Q     252      I     249          3.471
LGA    H     253      G     250          2.406
LGA    G     254      G     251          2.293
LGA    G     255      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    D     256      P     259           #
LGA    N     257      W     260          1.400
LGA    A     258      F     261          5.156
LGA    P     259      V     262          3.325
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    W     260      G     275           #
LGA    F     261      Q     276          2.620
LGA    V     262      G     277           #
LGA    V     263      F     278           #
LGA    G     264      Y     279          3.252
LGA    K     265      H     280          1.244
LGA    D     266      D     281          2.416
LGA    -       -      S     282           -
LGA    L     267      L     283          2.561
LGA    S     268      -       -           -
LGA    K     269      -       -           -
LGA    N     270      -       -           -
LGA    I     271      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   60    5.0     24    3.09    16.67     24.716     0.753

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.157615 * X  +   0.167965 * Y  +   0.973111 * Z  + -12.716877
  Y_new =   0.895072 * X  +   0.440561 * Y  +   0.068931 * Z  + -38.087021
  Z_new =  -0.417137 * X  +   0.881870 * Y  +  -0.219780 * Z  + -57.634636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.815041   -1.326552  [ DEG:   103.9942    -76.0058 ]
  Theta =   0.430292    2.711300  [ DEG:    24.6539    155.3461 ]
  Phi   =   1.745101   -1.396492  [ DEG:    99.9869    -80.0131 ]
 
# 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: T0316AL333_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   60   5.0   24   3.09   16.67  24.716
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_5-D2
REMARK Aligment from pdb entry: 1kqp_A
ATOM    677  N   VAL   225      38.904   2.463 -36.316  1.00  0.00              
ATOM    678  CA  VAL   225      39.573   3.712 -36.008  1.00  0.00              
ATOM    679  C   VAL   225      40.390   3.519 -34.738  1.00  0.00              
ATOM    680  O   VAL   225      40.121   4.135 -33.695  1.00  0.00              
ATOM    681  N   ASP   226      41.373   2.643 -34.804  1.00  0.00              
ATOM    682  CA  ASP   226      42.156   2.334 -33.597  1.00  0.00              
ATOM    683  C   ASP   226      42.916   3.551 -33.114  1.00  0.00              
ATOM    684  O   ASP   226      43.345   4.426 -33.907  1.00  0.00              
ATOM    685  N   GLY   227      43.119   3.634 -31.817  1.00  0.00              
ATOM    686  CA  GLY   227      43.916   4.697 -31.184  1.00  0.00              
ATOM    687  C   GLY   227      43.309   6.044 -31.508  1.00  0.00              
ATOM    688  O   GLY   227      44.024   7.044 -31.480  1.00  0.00              
ATOM    689  N   ARG   228      42.011   6.153 -31.734  1.00  0.00              
ATOM    690  CA  ARG   228      41.418   7.458 -31.965  1.00  0.00              
ATOM    691  C   ARG   228      41.591   8.305 -30.719  1.00  0.00              
ATOM    692  O   ARG   228      41.299   7.887 -29.584  1.00  0.00              
ATOM    693  N   ASP   229      42.008   9.558 -30.892  1.00  0.00              
ATOM    694  CA  ASP   229      42.189  10.385 -29.701  1.00  0.00              
ATOM    695  C   ASP   229      40.839  10.771 -29.116  1.00  0.00              
ATOM    696  O   ASP   229      39.835  10.957 -29.819  1.00  0.00              
ATOM    697  N   MET   230      40.843  10.938 -27.807  1.00  0.00              
ATOM    698  CA  MET   230      39.625  11.406 -27.167  1.00  0.00              
ATOM    699  C   MET   230      39.132  12.724 -27.760  1.00  0.00              
ATOM    700  O   MET   230      37.947  12.931 -27.964  1.00  0.00              
ATOM    701  N   GLY   231      40.076  13.612 -28.011  1.00  0.00              
ATOM    702  CA  GLY   231      39.711  14.922 -28.532  1.00  0.00              
ATOM    703  C   GLY   231      39.048  14.838 -29.893  1.00  0.00              
ATOM    704  O   GLY   231      38.134  15.588 -30.216  1.00  0.00              
ATOM    705  N   GLU   232      39.488  13.913 -30.743  1.00  0.00              
ATOM    706  CA  GLU   232      38.803  13.658 -32.005  1.00  0.00              
ATOM    707  C   GLU   232      37.365  13.269 -31.771  1.00  0.00              
ATOM    708  O   GLU   232      36.450  13.780 -32.470  1.00  0.00              
ATOM    709  N   HIS   233      37.114  12.368 -30.841  1.00  0.00              
ATOM    710  CA  HIS   233      35.738  11.924 -30.602  1.00  0.00              
ATOM    711  C   HIS   233      34.893  13.021 -29.982  1.00  0.00              
ATOM    712  O   HIS   233      33.718  13.171 -30.352  1.00  0.00              
ATOM    713  N   ALA   234      35.443  13.741 -28.997  1.00  0.00              
ATOM    714  CA  ALA   234      34.707  14.700 -28.219  1.00  0.00              
ATOM    715  C   ALA   234      34.478  16.049 -28.896  1.00  0.00              
ATOM    716  O   ALA   234      33.508  16.736 -28.608  1.00  0.00              
ATOM    717  N   GLY   235      35.440  16.450 -29.737  1.00  0.00              
ATOM    718  CA  GLY   235      35.395  17.797 -30.266  1.00  0.00              
ATOM    719  C   GLY   235      35.736  18.859 -29.257  1.00  0.00              
ATOM    720  O   GLY   235      35.322  20.015 -29.437  1.00  0.00              
ATOM    721  N   LEU   236      36.439  18.546 -28.197  1.00  0.00              
ATOM    722  CA  LEU   236      36.865  19.428 -27.134  1.00  0.00              
ATOM    723  C   LEU   236      38.237  18.947 -26.683  1.00  0.00              
ATOM    724  O   LEU   236      38.433  17.729 -26.636  1.00  0.00              
ATOM    725  N   MET   237      39.166  19.856 -26.437  1.00  0.00              
ATOM    726  CA  MET   237      40.493  19.449 -25.987  1.00  0.00              
ATOM    727  C   MET   237      40.577  19.359 -24.456  1.00  0.00              
ATOM    728  O   MET   237      39.782  19.966 -23.738  1.00  0.00              
ATOM    729  N   TYR   239      41.583  18.637 -23.990  1.00  0.00              
ATOM    730  CA  TYR   239      41.784  18.571 -22.533  1.00  0.00              
ATOM    731  C   TYR   239      42.232  19.915 -21.984  1.00  0.00              
ATOM    732  O   TYR   239      41.935  20.176 -20.812  1.00  0.00              
ATOM    733  N   THR   240      42.916  20.781 -22.761  1.00  0.00              
ATOM    734  CA  THR   240      43.215  22.081 -22.194  1.00  0.00              
ATOM    735  C   THR   240      41.932  22.887 -21.971  1.00  0.00              
ATOM    736  O   THR   240      41.849  23.616 -21.009  1.00  0.00              
ATOM    737  N   ILE   241      40.941  22.757 -22.855  1.00  0.00              
ATOM    738  CA  ILE   241      39.649  23.425 -22.687  1.00  0.00              
ATOM    739  C   ILE   241      38.920  22.844 -21.467  1.00  0.00              
ATOM    740  O   ILE   241      38.371  23.575 -20.619  1.00  0.00              
ATOM    741  N   GLY   242      38.850  21.503 -21.376  1.00  0.00              
ATOM    742  CA  GLY   242      38.227  20.846 -20.245  1.00  0.00              
ATOM    743  C   GLY   242      38.856  21.292 -18.929  1.00  0.00              
ATOM    744  O   GLY   242      38.154  21.632 -17.982  1.00  0.00              
ATOM    745  N   GLN   243      40.177  21.255 -18.878  1.00  0.00              
ATOM    746  CA  GLN   243      40.895  21.564 -17.659  1.00  0.00              
ATOM    747  C   GLN   243      40.722  23.023 -17.279  1.00  0.00              
ATOM    748  O   GLN   243      40.561  23.350 -16.123  1.00  0.00              
ATOM    749  N   ARG   244      40.771  23.926 -18.280  1.00  0.00              
ATOM    750  CA  ARG   244      40.558  25.333 -17.971  1.00  0.00              
ATOM    751  C   ARG   244      39.172  25.541 -17.367  1.00  0.00              
ATOM    752  O   ARG   244      39.020  26.295 -16.402  1.00  0.00              
ATOM    753  N   GLY   245      38.182  24.884 -17.937  1.00  0.00              
ATOM    754  CA  GLY   245      36.821  24.970 -17.388  1.00  0.00              
ATOM    755  C   GLY   245      36.788  24.486 -15.949  1.00  0.00              
ATOM    756  O   GLY   245      36.280  25.120 -15.038  1.00  0.00              
ATOM    757  N   GLY   246      37.281  23.262 -15.747  1.00  0.00              
ATOM    758  CA  GLY   246      37.204  22.635 -14.450  1.00  0.00              
ATOM    759  C   GLY   246      38.031  23.352 -13.369  1.00  0.00              
ATOM    760  O   GLY   246      37.689  23.310 -12.202  1.00  0.00              
ATOM    761  N   LEU   247      39.102  24.021 -13.772  1.00  0.00              
ATOM    762  CA  LEU   247      39.970  24.750 -12.817  1.00  0.00              
ATOM    763  C   LEU   247      39.461  26.139 -12.551  1.00  0.00              
ATOM    764  O   LEU   247      40.131  26.895 -11.799  1.00  0.00              
ATOM    765  N   GLY   248      38.314  26.518 -13.097  1.00  0.00              
ATOM    766  CA  GLY   248      37.686  27.783 -12.771  1.00  0.00              
ATOM    767  C   GLY   248      38.280  28.944 -13.550  1.00  0.00              
ATOM    768  O   GLY   248      38.103  30.103 -13.129  1.00  0.00              
ATOM    769  N   ILE   249      39.024  28.735 -14.607  1.00  0.00              
ATOM    770  CA  ILE   249      39.469  29.828 -15.486  1.00  0.00              
ATOM    771  C   ILE   249      38.288  30.403 -16.245  1.00  0.00              
ATOM    772  O   ILE   249      37.244  29.783 -16.401  1.00  0.00              
ATOM    773  N   GLY   250      38.445  31.648 -16.729  1.00  0.00              
ATOM    774  CA  GLY   250      37.381  32.262 -17.542  1.00  0.00              
ATOM    775  C   GLY   250      37.520  31.804 -18.965  1.00  0.00              
ATOM    776  O   GLY   250      38.317  32.291 -19.732  1.00  0.00              
ATOM    777  N   GLY   251      36.754  30.819 -19.382  1.00  0.00              
ATOM    778  CA  GLY   251      36.912  30.154 -20.642  1.00  0.00              
ATOM    779  C   GLY   251      35.895  30.738 -21.641  1.00  0.00              
ATOM    780  O   GLY   251      34.941  31.412 -21.279  1.00  0.00              
ATOM    781  N   GLN   252      36.174  30.463 -22.906  1.00  0.00              
ATOM    782  CA  GLN   252      35.265  30.863 -23.971  1.00  0.00              
ATOM    783  C   GLN   252      33.901  30.225 -23.752  1.00  0.00              
ATOM    784  O   GLN   252      33.755  29.097 -23.268  1.00  0.00              
ATOM    785  N   HIS   253      32.852  30.931 -24.184  1.00  0.00              
ATOM    786  CA  HIS   253      31.486  30.486 -24.008  1.00  0.00              
ATOM    787  C   HIS   253      31.227  29.195 -24.735  1.00  0.00              
ATOM    788  O   HIS   253      30.425  28.371 -24.251  1.00  0.00              
ATOM    789  N   GLY   254      31.889  28.931 -25.861  1.00  0.00              
ATOM    790  CA  GLY   254      31.665  27.709 -26.585  1.00  0.00              
ATOM    791  C   GLY   254      32.033  26.497 -25.724  1.00  0.00              
ATOM    792  O   GLY   254      31.437  25.406 -25.864  1.00  0.00              
ATOM    793  N   GLY   255      33.077  26.607 -24.930  1.00  0.00              
ATOM    794  CA  GLY   255      33.546  25.514 -24.067  1.00  0.00              
ATOM    795  C   GLY   255      32.497  25.271 -22.988  1.00  0.00              
ATOM    796  O   GLY   255      32.125  24.114 -22.708  1.00  0.00              
ATOM    797  N   ASP   256      32.028  26.307 -22.306  1.00  0.00              
ATOM    798  CA  ASP   256      31.018  26.129 -21.269  1.00  0.00              
ATOM    799  C   ASP   256      29.753  25.540 -21.844  1.00  0.00              
ATOM    800  O   ASP   256      29.140  24.652 -21.237  1.00  0.00              
ATOM    801  N   ASN   257      29.332  25.952 -23.031  1.00  0.00              
ATOM    802  CA  ASN   257      28.110  25.426 -23.658  1.00  0.00              
ATOM    803  C   ASN   257      28.293  23.934 -23.872  1.00  0.00              
ATOM    804  O   ASN   257      27.435  23.104 -23.508  1.00  0.00              
ATOM    805  N   ALA   258      29.391  23.536 -24.479  1.00  0.00              
ATOM    806  CA  ALA   258      29.638  22.151 -24.839  1.00  0.00              
ATOM    807  C   ALA   258      29.711  21.257 -23.584  1.00  0.00              
ATOM    808  O   ALA   258      29.105  20.191 -23.560  1.00  0.00              
ATOM    809  N   PRO   259      30.448  21.684 -22.609  1.00  0.00              
ATOM    810  CA  PRO   259      30.638  20.880 -21.420  1.00  0.00              
ATOM    811  C   PRO   259      29.400  20.817 -20.559  1.00  0.00              
ATOM    812  O   PRO   259      29.079  19.757 -20.001  1.00  0.00              
ATOM    813  N   TRP   260      28.658  21.900 -20.435  1.00  0.00              
ATOM    814  CA  TRP   260      27.451  21.859 -19.597  1.00  0.00              
ATOM    815  C   TRP   260      26.424  20.944 -20.225  1.00  0.00              
ATOM    816  O   TRP   260      25.693  20.218 -19.527  1.00  0.00              
ATOM    817  N   PHE   261      26.313  20.920 -21.560  1.00  0.00              
ATOM    818  CA  PHE   261      25.389  19.993 -22.223  1.00  0.00              
ATOM    819  C   PHE   261      25.833  18.572 -21.991  1.00  0.00              
ATOM    820  O   PHE   261      25.010  17.726 -21.603  1.00  0.00              
ATOM    821  N   VAL   262      27.107  18.257 -22.194  1.00  0.00              
ATOM    822  CA  VAL   262      27.572  16.892 -21.963  1.00  0.00              
ATOM    823  C   VAL   262      27.410  16.466 -20.534  1.00  0.00              
ATOM    824  O   VAL   262      27.011  15.323 -20.268  1.00  0.00              
ATOM    825  N   VAL   263      27.695  17.342 -19.600  1.00  0.00              
ATOM    826  CA  VAL   263      27.558  16.986 -18.173  1.00  0.00              
ATOM    827  C   VAL   263      26.106  16.654 -17.868  1.00  0.00              
ATOM    828  O   VAL   263      25.809  15.650 -17.192  1.00  0.00              
ATOM    829  N   GLY   264      25.178  17.487 -18.314  1.00  0.00              
ATOM    830  CA  GLY   264      23.764  17.213 -18.049  1.00  0.00              
ATOM    831  C   GLY   264      23.326  15.899 -18.646  1.00  0.00              
ATOM    832  O   GLY   264      22.630  15.090 -18.036  1.00  0.00              
ATOM    833  N   LYS   265      23.706  15.642 -19.897  1.00  0.00              
ATOM    834  CA  LYS   265      23.281  14.435 -20.607  1.00  0.00              
ATOM    835  C   LYS   265      23.830  13.159 -20.030  1.00  0.00              
ATOM    836  O   LYS   265      23.224  12.100 -20.219  1.00  0.00              
ATOM    837  N   ASP   266      24.949  13.240 -19.336  1.00  0.00              
ATOM    838  CA  ASP   266      25.615  12.038 -18.791  1.00  0.00              
ATOM    839  C   ASP   266      25.471  11.907 -17.285  1.00  0.00              
ATOM    840  O   ASP   266      26.148  11.055 -16.699  1.00  0.00              
ATOM    841  N   LEU   267      24.565  12.652 -16.652  1.00  0.00              
ATOM    842  CA  LEU   267      24.396  12.524 -15.190  1.00  0.00              
ATOM    843  C   LEU   267      24.091  11.083 -14.779  1.00  0.00              
ATOM    844  O   LEU   267      24.553  10.642 -13.738  1.00  0.00              
ATOM    845  N   SER   268      23.326  10.355 -15.605  1.00  0.00              
ATOM    846  CA  SER   268      23.007   8.977 -15.302  1.00  0.00              
ATOM    847  C   SER   268      24.244   8.136 -15.077  1.00  0.00              
ATOM    848  O   SER   268      24.202   7.135 -14.347  1.00  0.00              
ATOM    849  N   LYS   269      25.377   8.494 -15.691  1.00  0.00              
ATOM    850  CA  LYS   269      26.587   7.695 -15.537  1.00  0.00              
ATOM    851  C   LYS   269      27.261   7.953 -14.193  1.00  0.00              
ATOM    852  O   LYS   269      28.162   7.192 -13.796  1.00  0.00              
ATOM    853  N   ASN   270      26.887   9.039 -13.501  1.00  0.00              
ATOM    854  CA  ASN   270      27.502   9.418 -12.262  1.00  0.00              
ATOM    855  C   ASN   270      26.549   9.240 -11.082  1.00  0.00              
ATOM    856  O   ASN   270      26.802   9.719  -9.983  1.00  0.00              
ATOM    857  N   ILE   271      25.454   8.491 -11.282  1.00  0.00              
ATOM    858  CA  ILE   271      24.484   8.184 -10.250  1.00  0.00              
ATOM    859  C   ILE   271      24.262   6.672 -10.280  1.00  0.00              
ATOM    860  O   ILE   271      24.412   6.034 -11.324  1.00  0.00              
END
