
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0316AL044_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_1-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    M     284      L     288           #
LGA    S     285      E     289          1.687
LGA    T     286      A     290          2.977
LGA    S     287      S     291          2.176
LGA    L     288      Q     292          2.246
LGA    E     289      V     293          2.884
LGA    A     290      H     294          5.242
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    S     291      E     327          1.877
LGA    Q     292      K     328          1.116
LGA    V     293      T     329          1.747
LGA    H     294      E     330          2.893
LGA    F     295      V     331          2.707
LGA    T     296      I     332          2.102
LGA    R     297      F     333          1.074
LGA    E     298      A     334          2.064
LGA    M     299      E     335          2.412
LGA    P     300      P     336          3.980
LGA    E     301      Q     337           -
LGA    E     302      R     338           -
LGA    F     303      A     339           -
LGA    L     305      -       -           -
LGA    C     307      -       -           -
LGA    T     308      -       -           -
LGA    A     309      -       -           -
LGA    E     327      -       -           -
LGA    T     329      -       -           -
LGA    E     330      -       -           -
LGA    V     331      -       -           -
LGA    I     332      -       -           -
LGA    F     333      -       -           -
LGA    A     334      -       -           -
LGA    E     335      -       -           -
LGA    P     336      -       -           -
LGA    Q     337      -       -           -
LGA    R     338      -       -           -
LGA    A     339      -       -           -
LGA    I     340      -       -           -
LGA    T     341      -       -           -
LGA    P     342      I     340           #
LGA    G     343      -       -           -
LGA    Q     344      -       -           -
LGA    A     345      T     341          2.041
LGA    V     346      P     342          2.739
LGA    V     347      G     343          3.098
LGA    F     348      Q     344          1.929
LGA    Y     349      A     345          2.783
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    D     350      L     359          3.233
LGA    G     351      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   90    5.0     22    2.66     9.09     16.265     0.798

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.250808 * X  +  -0.508315 * Y  +   0.823839 * Z  +   2.712760
  Y_new =   0.013042 * X  +   0.852738 * Y  +   0.522176 * Z  +  -5.278601
  Z_new =  -0.967949 * X  +  -0.120221 * Y  +   0.220503 * Z  +  25.907270 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.499161    2.642431  [ DEG:   -28.5998    151.4002 ]
  Theta =   1.316931    1.824661  [ DEG:    75.4546    104.5454 ]
  Phi   =   0.051953   -3.089639  [ DEG:     2.9767   -177.0233 ]
 
# 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: T0316AL044_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   90   5.0   22   2.66    9.09  16.265
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_1-D3
REMARK Aligment from pdb entry: 1vl2_A
ATOM    869  N   MET   284      28.768   1.486  -3.380  1.00  0.00              
ATOM    870  CA  MET   284      29.451   1.772  -2.113  1.00  0.00              
ATOM    871  C   MET   284      30.315   2.987  -2.363  1.00  0.00              
ATOM    872  O   MET   284      31.162   3.025  -3.309  1.00  0.00              
ATOM    873  N   SER   285      30.084   3.986  -1.512  1.00  0.00              
ATOM    874  CA  SER   285      30.792   5.265  -1.599  1.00  0.00              
ATOM    875  C   SER   285      31.652   5.483  -0.350  1.00  0.00              
ATOM    876  O   SER   285      31.332   4.991   0.714  1.00  0.00              
ATOM    877  N   THR   286      32.718   6.253  -0.516  1.00  0.00              
ATOM    878  CA  THR   286      33.541   6.635   0.600  1.00  0.00              
ATOM    879  C   THR   286      33.000   7.893   1.183  1.00  0.00              
ATOM    880  O   THR   286      32.801   8.847   0.473  1.00  0.00              
ATOM    881  N   SER   287      32.714   7.879   2.473  1.00  0.00              
ATOM    882  CA  SER   287      32.148   9.029   3.154  1.00  0.00              
ATOM    883  C   SER   287      33.225  10.038   3.485  1.00  0.00              
ATOM    884  O   SER   287      34.408   9.744   3.448  1.00  0.00              
ATOM    885  N   LEU   288      32.817  11.252   3.858  1.00  0.00              
ATOM    886  CA  LEU   288      33.795  12.231   4.339  1.00  0.00              
ATOM    887  C   LEU   288      34.033  11.963   5.863  1.00  0.00              
ATOM    888  O   LEU   288      35.140  11.933   6.283  1.00  0.00              
ATOM    889  N   GLU   289      32.950  11.795   6.630  1.00  0.00              
ATOM    890  CA  GLU   289      32.996  11.350   8.033  1.00  0.00              
ATOM    891  C   GLU   289      32.601   9.895   8.019  1.00  0.00              
ATOM    892  O   GLU   289      31.481   9.532   7.670  1.00  0.00              
ATOM    893  N   ALA   290      33.547   9.061   8.390  1.00  0.00              
ATOM    894  CA  ALA   290      33.391   7.630   8.273  1.00  0.00              
ATOM    895  C   ALA   290      34.165   7.068   7.075  1.00  0.00              
ATOM    896  O   ALA   290      34.940   7.775   6.419  1.00  0.00              
ATOM    897  N   SER   291      33.919   5.784   6.818  1.00  0.00              
ATOM    898  CA  SER   291      34.692   5.053   5.878  1.00  0.00              
ATOM    899  C   SER   291      33.946   4.868   4.553  1.00  0.00              
ATOM    900  O   SER   291      34.240   5.599   3.555  1.00  0.00              
ATOM    901  N   GLN   292      33.129   3.812   4.526  1.00  0.00              
ATOM    902  CA  GLN   292      32.347   3.438   3.335  1.00  0.00              
ATOM    903  C   GLN   292      30.899   3.219   3.712  1.00  0.00              
ATOM    904  O   GLN   292      30.603   2.837   4.859  1.00  0.00              
ATOM    905  N   VAL   293      29.975   3.433   2.757  1.00  0.00              
ATOM    906  CA  VAL   293      28.553   3.222   2.961  1.00  0.00              
ATOM    907  C   VAL   293      27.908   2.762   1.663  1.00  0.00              
ATOM    908  O   VAL   293      28.259   3.274   0.597  1.00  0.00              
ATOM    909  N   HIS   294      26.993   1.793   1.746  1.00  0.00              
ATOM    910  CA  HIS   294      26.259   1.319   0.573  1.00  0.00              
ATOM    911  C   HIS   294      24.972   2.122   0.457  1.00  0.00              
ATOM    912  O   HIS   294      24.204   2.171   1.425  1.00  0.00              
ATOM    913  N   PHE   295      24.726   2.657  -0.745  1.00  0.00              
ATOM    914  CA  PHE   295      23.542   3.424  -1.037  1.00  0.00              
ATOM    915  C   PHE   295      22.857   3.022  -2.310  1.00  0.00              
ATOM    916  O   PHE   295      23.507   2.518  -3.228  1.00  0.00              
ATOM    917  N   THR   296      21.513   3.189  -2.322  1.00  0.00              
ATOM    918  CA  THR   296      20.754   2.973  -3.511  1.00  0.00              
ATOM    919  C   THR   296      20.095   4.326  -3.798  1.00  0.00              
ATOM    920  O   THR   296      19.421   4.883  -2.930  1.00  0.00              
ATOM    921  N   ARG   297      20.285   4.810  -5.013  1.00  0.00              
ATOM    922  CA  ARG   297      19.806   6.167  -5.415  1.00  0.00              
ATOM    923  C   ARG   297      18.942   6.104  -6.637  1.00  0.00              
ATOM    924  O   ARG   297      19.182   5.353  -7.573  1.00  0.00              
ATOM    925  N   GLU   298      17.897   6.940  -6.651  1.00  0.00              
ATOM    926  CA  GLU   298      17.004   7.100  -7.802  1.00  0.00              
ATOM    927  C   GLU   298      17.021   8.542  -8.249  1.00  0.00              
ATOM    928  O   GLU   298      16.570   9.426  -7.492  1.00  0.00              
ATOM    929  N   MET   299      17.603   8.807  -9.416  1.00  0.00              
ATOM    930  CA  MET   299      17.817  10.161  -9.914  1.00  0.00              
ATOM    931  C   MET   299      17.350  10.255 -11.371  1.00  0.00              
ATOM    932  O   MET   299      18.138  10.433 -12.279  1.00  0.00              
ATOM    933  N   PRO   300      16.047  10.177 -11.584  1.00  0.00              
ATOM    934  CA  PRO   300      15.509  10.047 -12.971  1.00  0.00              
ATOM    935  C   PRO   300      15.822  11.218 -13.903  1.00  0.00              
ATOM    936  O   PRO   300      16.427  11.061 -14.992  1.00  0.00              
ATOM    937  N   GLU   301      22.716  14.039 -21.628  1.00  0.00              
ATOM    938  CA  GLU   301      22.488  14.937 -22.725  1.00  0.00              
ATOM    939  C   GLU   301      23.539  16.069 -22.784  1.00  0.00              
ATOM    940  O   GLU   301      24.060  16.394 -23.827  1.00  0.00              
ATOM    941  N   GLU   302      23.861  16.604 -21.632  1.00  0.00              
ATOM    942  CA  GLU   302      24.805  17.706 -21.542  1.00  0.00              
ATOM    943  C   GLU   302      26.203  17.277 -22.026  1.00  0.00              
ATOM    944  O   GLU   302      26.837  17.969 -22.853  1.00  0.00              
ATOM    945  N   PHE   303      26.682  16.120 -21.560  1.00  0.00              
ATOM    946  CA  PHE   303      27.994  15.610 -22.007  1.00  0.00              
ATOM    947  C   PHE   303      27.949  15.385 -23.533  1.00  0.00              
ATOM    948  O   PHE   303      28.916  15.696 -24.241  1.00  0.00              
ATOM    949  N   LEU   305      26.834  14.876 -24.052  1.00  0.00              
ATOM    950  CA  LEU   305      26.769  14.684 -25.503  1.00  0.00              
ATOM    951  C   LEU   305      26.924  16.003 -26.282  1.00  0.00              
ATOM    952  O   LEU   305      27.676  16.079 -27.274  1.00  0.00              
ATOM    953  N   CYS   307      26.259  17.057 -25.822  1.00  0.00              
ATOM    954  CA  CYS   307      26.397  18.366 -26.463  1.00  0.00              
ATOM    955  C   CYS   307      27.836  18.891 -26.356  1.00  0.00              
ATOM    956  O   CYS   307      28.330  19.523 -27.301  1.00  0.00              
ATOM    957  N   THR   308      28.495  18.664 -25.207  1.00  0.00              
ATOM    958  CA  THR   308      29.882  19.057 -25.060  1.00  0.00              
ATOM    959  C   THR   308      30.798  18.429 -26.112  1.00  0.00              
ATOM    960  O   THR   308      31.775  19.056 -26.568  1.00  0.00              
ATOM    961  N   ALA   309      30.463  17.213 -26.555  1.00  0.00              
ATOM    962  CA  ALA   309      31.209  16.563 -27.619  1.00  0.00              
ATOM    963  C   ALA   309      31.345  17.367 -28.885  1.00  0.00              
ATOM    964  O   ALA   309      32.398  17.287 -29.571  1.00  0.00              
ATOM    965  N   GLU   327      30.278  18.091 -29.276  1.00  0.00              
ATOM    966  CA  GLU   327      30.315  18.851 -30.502  1.00  0.00              
ATOM    967  C   GLU   327      30.703  20.315 -30.349  1.00  0.00              
ATOM    968  O   GLU   327      31.055  20.959 -31.317  1.00  0.00              
ATOM    969  N   THR   329      30.689  20.834 -29.110  1.00  0.00              
ATOM    970  CA  THR   329      30.885  22.251 -28.833  1.00  0.00              
ATOM    971  C   THR   329      32.192  22.586 -28.102  1.00  0.00              
ATOM    972  O   THR   329      32.741  23.668 -28.340  1.00  0.00              
ATOM    973  N   GLU   330      32.689  21.696 -27.240  1.00  0.00              
ATOM    974  CA  GLU   330      33.769  22.104 -26.344  1.00  0.00              
ATOM    975  C   GLU   330      35.111  21.861 -27.017  1.00  0.00              
ATOM    976  O   GLU   330      35.325  20.850 -27.699  1.00  0.00              
ATOM    977  N   VAL   331      36.053  22.789 -26.786  1.00  0.00              
ATOM    978  CA  VAL   331      37.434  22.566 -27.200  1.00  0.00              
ATOM    979  C   VAL   331      38.054  21.378 -26.458  1.00  0.00              
ATOM    980  O   VAL   331      37.800  21.163 -25.246  1.00  0.00              
ATOM    981  N   ILE   332      38.839  20.576 -27.183  1.00  0.00              
ATOM    982  CA  ILE   332      39.446  19.375 -26.665  1.00  0.00              
ATOM    983  C   ILE   332      40.284  19.564 -25.415  1.00  0.00              
ATOM    984  O   ILE   332      40.234  18.767 -24.466  1.00  0.00              
ATOM    985  N   PHE   333      41.138  20.609 -25.426  1.00  0.00              
ATOM    986  CA  PHE   333      42.062  20.804 -24.303  1.00  0.00              
ATOM    987  C   PHE   333      41.340  21.359 -23.072  1.00  0.00              
ATOM    988  O   PHE   333      41.649  20.977 -21.943  1.00  0.00              
ATOM    989  N   ALA   334      40.316  22.191 -23.322  1.00  0.00              
ATOM    990  CA  ALA   334      39.410  22.635 -22.258  1.00  0.00              
ATOM    991  C   ALA   334      38.670  21.405 -21.628  1.00  0.00              
ATOM    992  O   ALA   334      38.653  21.236 -20.416  1.00  0.00              
ATOM    993  N   GLU   335      39.578  18.299 -21.692  1.00  0.00              
ATOM    994  CA  GLU   335      40.551  17.500 -20.990  1.00  0.00              
ATOM    995  C   GLU   335      40.882  18.058 -19.595  1.00  0.00              
ATOM    996  O   GLU   335      40.874  17.333 -18.594  1.00  0.00              
ATOM    997  N   PRO   336      41.107  19.371 -19.498  1.00  0.00              
ATOM    998  CA  PRO   336      41.423  19.988 -18.199  1.00  0.00              
ATOM    999  C   PRO   336      40.220  19.904 -17.239  1.00  0.00              
ATOM   1000  O   PRO   336      40.347  19.601 -16.029  1.00  0.00              
ATOM   1001  N   GLN   337      39.050  20.213 -17.778  1.00  0.00              
ATOM   1002  CA  GLN   337      37.829  20.142 -17.009  1.00  0.00              
ATOM   1003  C   GLN   337      37.613  18.751 -16.442  1.00  0.00              
ATOM   1004  O   GLN   337      37.333  18.567 -15.259  1.00  0.00              
ATOM   1005  N   ARG   338      37.791  17.732 -17.285  1.00  0.00              
ATOM   1006  CA  ARG   338      37.607  16.343 -16.845  1.00  0.00              
ATOM   1007  C   ARG   338      38.639  15.905 -15.798  1.00  0.00              
ATOM   1008  O   ARG   338      38.334  15.119 -14.895  1.00  0.00              
ATOM   1009  N   ALA   339      39.851  16.410 -15.907  1.00  0.00              
ATOM   1010  CA  ALA   339      40.872  16.188 -14.861  1.00  0.00              
ATOM   1011  C   ALA   339      40.497  16.750 -13.517  1.00  0.00              
ATOM   1012  O   ALA   339      40.753  16.159 -12.479  1.00  0.00              
ATOM   1013  N   ILE   340      39.764  17.863 -13.531  1.00  0.00              
ATOM   1014  CA  ILE   340      39.357  18.569 -12.344  1.00  0.00              
ATOM   1015  C   ILE   340      37.966  18.177 -11.833  1.00  0.00              
ATOM   1016  O   ILE   340      37.581  18.535 -10.720  1.00  0.00              
ATOM   1017  N   THR   341      37.235  17.430 -12.634  1.00  0.00              
ATOM   1018  CA  THR   341      35.857  17.127 -12.304  1.00  0.00              
ATOM   1019  C   THR   341      35.763  16.229 -11.039  1.00  0.00              
ATOM   1020  O   THR   341      34.881  16.437 -10.216  1.00  0.00              
ATOM   1021  N   PRO   342      36.660  15.272 -10.796  1.00  0.00              
ATOM   1022  CA  PRO   342      36.635  14.602  -9.505  1.00  0.00              
ATOM   1023  C   PRO   342      36.762  15.512  -8.306  1.00  0.00              
ATOM   1024  O   PRO   342      36.028  15.305  -7.324  1.00  0.00              
ATOM   1025  N   GLY   343      37.645  16.513  -8.356  1.00  0.00              
ATOM   1026  CA  GLY   343      37.774  17.491  -7.306  1.00  0.00              
ATOM   1027  C   GLY   343      36.506  18.290  -7.142  1.00  0.00              
ATOM   1028  O   GLY   343      36.030  18.474  -6.042  1.00  0.00              
ATOM   1029  N   GLN   344      35.915  18.696  -8.247  1.00  0.00              
ATOM   1030  CA  GLN   344      34.628  19.455  -8.186  1.00  0.00              
ATOM   1031  C   GLN   344      33.537  18.660  -7.476  1.00  0.00              
ATOM   1032  O   GLN   344      32.884  19.137  -6.559  1.00  0.00              
ATOM   1033  N   ALA   345      33.413  17.374  -7.825  1.00  0.00              
ATOM   1034  CA  ALA   345      32.444  16.520  -7.185  1.00  0.00              
ATOM   1035  C   ALA   345      32.761  16.290  -5.696  1.00  0.00              
ATOM   1036  O   ALA   345      31.858  16.191  -4.845  1.00  0.00              
ATOM   1037  N   VAL   346      34.053  16.136  -5.384  1.00  0.00              
ATOM   1038  CA  VAL   346      34.507  15.988  -3.976  1.00  0.00              
ATOM   1039  C   VAL   346      34.104  17.173  -3.117  1.00  0.00              
ATOM   1040  O   VAL   346      33.619  17.015  -1.980  1.00  0.00              
ATOM   1041  N   VAL   347      34.326  18.362  -3.655  1.00  0.00              
ATOM   1042  CA  VAL   347      33.992  19.587  -2.964  1.00  0.00              
ATOM   1043  C   VAL   347      32.490  19.610  -2.668  1.00  0.00              
ATOM   1044  O   VAL   347      32.083  19.972  -1.560  1.00  0.00              
ATOM   1045  N   PHE   348      31.646  19.254  -3.648  1.00  0.00              
ATOM   1046  CA  PHE   348      30.199  19.207  -3.406  1.00  0.00              
ATOM   1047  C   PHE   348      29.871  18.159  -2.335  1.00  0.00              
ATOM   1048  O   PHE   348      29.110  18.417  -1.385  1.00  0.00              
ATOM   1049  N   TYR   349      30.404  16.930  -2.497  1.00  0.00              
ATOM   1050  CA  TYR   349      30.126  15.857  -1.565  1.00  0.00              
ATOM   1051  C   TYR   349      30.490  16.222  -0.128  1.00  0.00              
ATOM   1052  O   TYR   349      29.777  15.914   0.801  1.00  0.00              
ATOM   1053  N   ASP   350      31.632  16.853   0.029  1.00  0.00              
ATOM   1054  CA  ASP   350      32.182  17.109   1.358  1.00  0.00              
ATOM   1055  C   ASP   350      31.521  18.292   2.067  1.00  0.00              
ATOM   1056  O   ASP   350      31.714  18.464   3.261  1.00  0.00              
ATOM   1057  N   GLY   351      30.814  19.136   1.343  1.00  0.00              
ATOM   1058  CA  GLY   351      30.209  20.280   1.968  1.00  0.00              
ATOM   1059  C   GLY   351      30.881  21.623   1.737  1.00  0.00              
ATOM   1060  O   GLY   351      30.551  22.606   2.391  1.00  0.00              
END
