
#######################################################
#                                                     #
#                        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 T0316AL380_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_1-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      -       -           -
LGA    R     221      -       -           -
LGA    M     222      -       -           -
LGA    M     223      -       -           -
LGA    T     224      G     220          4.470
LGA    V     225      R     221          4.854
LGA    D     226      M     222          2.360
LGA    G     227      M     223          3.354
LGA    R     228      T     224           #
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    D     229      D     229          2.696
LGA    M     230      M     230          2.801
LGA    G     231      G     231          1.891
LGA    E     232      E     232          2.127
LGA    H     233      H     233          2.746
LGA    A     234      A     234          2.023
LGA    G     235      G     235          1.646
LGA    L     236      L     236           -
LGA    -       -      M     237           -
LGA    M     237      Y     238           #
LGA    Y     238      Y     239          4.580
LGA    Y     239      T     240          5.844
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    T     240      G     245          1.416
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    I     241      W     260          3.041
LGA    G     242      F     261          1.231
LGA    Q     243      V     262           #
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    R     244      G     275           #
LGA    G     245      Q     276          1.736
LGA    G     246      G     277          2.118
LGA    L     247      F     278          3.258
LGA    G     248      Y     279           #
LGA    I     249      H     280           -
LGA    G     250      D     281           -
LGA    G     251      S     282           -
LGA    Q     252      L     283           -
LGA    H     253      -       -           -
LGA    G     254      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   60    5.0     19    3.11    47.37     21.372     0.592

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.471324 * X  +   0.834738 * Y  +   0.284723 * Z  +  -5.067082
  Y_new =  -0.722174 * X  +   0.550586 * Y  +  -0.418713 * Z  +  49.117981
  Z_new =  -0.506280 * X  +  -0.008270 * Y  +   0.862330 * Z  +  -2.489052 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.009590    3.132003  [ DEG:    -0.5495    179.4505 ]
  Theta =   0.530865    2.610728  [ DEG:    30.4163    149.5837 ]
  Phi   =  -0.992564    2.149029  [ DEG:   -56.8697    123.1303 ]
 
# 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: T0316AL380_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_1-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   60   5.0   19   3.11   47.37  21.372
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_1-D2
REMARK Aligment from pdb entry: 1vl2A
ATOM    737  N   GLY   220      43.739  12.632  -7.865  1.00  0.00              
ATOM    738  CA  GLY   220      42.332  12.866  -7.704  1.00  0.00              
ATOM    739  C   GLY   220      41.893  14.304  -7.828  1.00  0.00              
ATOM    740  O   GLY   220      40.687  14.602  -7.665  1.00  0.00              
ATOM    741  N   ARG   221      42.829  15.201  -8.132  1.00  0.00              
ATOM    742  CA  ARG   221      42.525  16.640  -8.267  1.00  0.00              
ATOM    743  C   ARG   221      42.548  17.010  -9.727  1.00  0.00              
ATOM    744  O   ARG   221      43.522  16.694 -10.381  1.00  0.00              
ATOM    745  N   MET   222      41.510  17.677 -10.259  1.00  0.00              
ATOM    746  CA  MET   222      41.487  18.127 -11.638  1.00  0.00              
ATOM    747  C   MET   222      42.585  19.148 -11.861  1.00  0.00              
ATOM    748  O   MET   222      42.733  20.107 -11.031  1.00  0.00              
ATOM    749  N   MET   223      43.361  18.948 -12.924  1.00  0.00              
ATOM    750  CA  MET   223      44.488  19.861 -13.224  1.00  0.00              
ATOM    751  C   MET   223      44.510  20.419 -14.648  1.00  0.00              
ATOM    752  O   MET   223      45.364  21.286 -14.967  1.00  0.00              
ATOM    753  N   THR   224      43.673  19.895 -15.552  1.00  0.00              
ATOM    754  CA  THR   224      43.581  20.439 -16.911  1.00  0.00              
ATOM    755  C   THR   224      42.247  20.023 -17.528  1.00  0.00              
ATOM    756  O   THR   224      41.794  18.898 -17.293  1.00  0.00              
ATOM    757  N   VAL   225      41.632  20.935 -18.289  1.00  0.00              
ATOM    758  CA  VAL   225      40.542  20.564 -19.200  1.00  0.00              
ATOM    759  C   VAL   225      40.919  21.046 -20.605  1.00  0.00              
ATOM    760  O   VAL   225      41.416  22.158 -20.777  1.00  0.00              
ATOM    761  N   ASP   226      40.708  20.178 -21.574  1.00  0.00              
ATOM    762  CA  ASP   226      40.988  20.471 -22.986  1.00  0.00              
ATOM    763  C   ASP   226      39.737  20.142 -23.802  1.00  0.00              
ATOM    764  O   ASP   226      39.173  19.043 -23.697  1.00  0.00              
ATOM    765  N   GLY   227      39.304  21.094 -24.623  1.00  0.00              
ATOM    766  CA  GLY   227      38.206  20.858 -25.553  1.00  0.00              
ATOM    767  C   GLY   227      38.875  20.323 -26.820  1.00  0.00              
ATOM    768  O   GLY   227      39.752  21.004 -27.435  1.00  0.00              
ATOM    769  N   ARG   228      38.538  19.080 -27.189  1.00  0.00              
ATOM    770  CA  ARG   228      39.251  18.390 -28.294  1.00  0.00              
ATOM    771  C   ARG   228      38.782  18.865 -29.668  1.00  0.00              
ATOM    772  O   ARG   228      39.435  18.582 -30.698  1.00  0.00              
ATOM    773  N   ASP   229      37.689  19.607 -29.685  1.00  0.00              
ATOM    774  CA  ASP   229      37.126  20.172 -30.925  1.00  0.00              
ATOM    775  C   ASP   229      37.698  21.556 -31.175  1.00  0.00              
ATOM    776  O   ASP   229      38.202  21.832 -32.275  1.00  0.00              
ATOM    777  N   MET   230      37.634  22.426 -30.162  1.00  0.00              
ATOM    778  CA  MET   230      37.946  23.854 -30.383  1.00  0.00              
ATOM    779  C   MET   230      39.218  24.347 -29.757  1.00  0.00              
ATOM    780  O   MET   230      39.588  25.523 -29.929  1.00  0.00              
ATOM    781  N   GLY   231      39.914  23.438 -29.070  1.00  0.00              
ATOM    782  CA  GLY   231      41.221  23.691 -28.540  1.00  0.00              
ATOM    783  C   GLY   231      41.344  24.436 -27.223  1.00  0.00              
ATOM    784  O   GLY   231      42.472  24.604 -26.731  1.00  0.00              
ATOM    785  N   GLU   232      40.232  24.934 -26.669  1.00  0.00              
ATOM    786  CA  GLU   232      40.262  25.588 -25.383  1.00  0.00              
ATOM    787  C   GLU   232      41.011  24.709 -24.381  1.00  0.00              
ATOM    788  O   GLU   232      40.750  23.498 -24.334  1.00  0.00              
ATOM    789  N   HIS   233      41.905  25.304 -23.585  1.00  0.00              
ATOM    790  CA  HIS   233      42.605  24.589 -22.500  1.00  0.00              
ATOM    791  C   HIS   233      42.593  25.465 -21.280  1.00  0.00              
ATOM    792  O   HIS   233      42.874  26.669 -21.370  1.00  0.00              
ATOM    793  N   ALA   234      42.361  24.856 -20.127  1.00  0.00              
ATOM    794  CA  ALA   234      42.333  25.566 -18.845  1.00  0.00              
ATOM    795  C   ALA   234      43.052  24.673 -17.852  1.00  0.00              
ATOM    796  O   ALA   234      42.783  23.444 -17.822  1.00  0.00              
ATOM    797  N   GLY   235      43.965  25.247 -17.074  1.00  0.00              
ATOM    798  CA  GLY   235      44.642  24.560 -15.964  1.00  0.00              
ATOM    799  C   GLY   235      44.374  25.139 -14.567  1.00  0.00              
ATOM    800  O   GLY   235      44.446  24.405 -13.553  1.00  0.00              
ATOM    801  N   LEU   236      34.892  26.722 -13.916  1.00  0.00              
ATOM    802  CA  LEU   236      33.972  27.623 -14.622  1.00  0.00              
ATOM    803  C   LEU   236      33.732  27.201 -16.074  1.00  0.00              
ATOM    804  O   LEU   236      32.602  27.248 -16.567  1.00  0.00              
ATOM    805  N   MET   237      34.780  26.729 -16.724  1.00  0.00              
ATOM    806  CA  MET   237      34.649  26.211 -18.072  1.00  0.00              
ATOM    807  C   MET   237      33.765  24.969 -18.120  1.00  0.00              
ATOM    808  O   MET   237      32.901  24.895 -19.005  1.00  0.00              
ATOM    809  N   TYR   238      33.953  24.032 -17.179  1.00  0.00              
ATOM    810  CA  TYR   238      33.060  22.854 -17.099  1.00  0.00              
ATOM    811  C   TYR   238      31.608  23.310 -16.875  1.00  0.00              
ATOM    812  O   TYR   238      30.684  22.727 -17.459  1.00  0.00              
ATOM    813  N   TYR   239      31.398  24.348 -16.048  1.00  0.00              
ATOM    814  CA  TYR   239      30.057  24.924 -15.832  1.00  0.00              
ATOM    815  C   TYR   239      29.478  25.410 -17.157  1.00  0.00              
ATOM    816  O   TYR   239      28.333  25.132 -17.487  1.00  0.00              
ATOM    817  N   THR   240      30.295  26.145 -17.912  1.00  0.00              
ATOM    818  CA  THR   240      29.857  26.690 -19.199  1.00  0.00              
ATOM    819  C   THR   240      29.475  25.581 -20.180  1.00  0.00              
ATOM    820  O   THR   240      28.412  25.633 -20.824  1.00  0.00              
ATOM    821  N   ILE   241      30.375  24.620 -20.364  1.00  0.00              
ATOM    822  CA  ILE   241      30.124  23.519 -21.298  1.00  0.00              
ATOM    823  C   ILE   241      28.895  22.741 -20.866  1.00  0.00              
ATOM    824  O   ILE   241      28.022  22.391 -21.660  1.00  0.00              
ATOM    825  N   GLY   242      28.829  22.434 -19.582  1.00  0.00              
ATOM    826  CA  GLY   242      27.673  21.706 -19.091  1.00  0.00              
ATOM    827  C   GLY   242      26.352  22.406 -19.303  1.00  0.00              
ATOM    828  O   GLY   242      25.346  21.796 -19.757  1.00  0.00              
ATOM    829  N   GLN   243      26.303  23.680 -18.941  1.00  0.00              
ATOM    830  CA  GLN   243      25.086  24.449 -19.006  1.00  0.00              
ATOM    831  C   GLN   243      24.618  24.530 -20.457  1.00  0.00              
ATOM    832  O   GLN   243      23.462  24.369 -20.700  1.00  0.00              
ATOM    833  N   ARG   244      25.545  24.785 -21.378  1.00  0.00              
ATOM    834  CA  ARG   244      25.216  24.937 -22.812  1.00  0.00              
ATOM    835  C   ARG   244      24.637  23.627 -23.383  1.00  0.00              
ATOM    836  O   ARG   244      23.784  23.657 -24.321  1.00  0.00              
ATOM    837  N   GLY   245      25.120  22.485 -22.846  1.00  0.00              
ATOM    838  CA  GLY   245      24.769  21.168 -23.360  1.00  0.00              
ATOM    839  C   GLY   245      23.729  20.434 -22.513  1.00  0.00              
ATOM    840  O   GLY   245      23.467  19.252 -22.774  1.00  0.00              
ATOM    841  N   GLY   246      23.063  21.120 -21.615  1.00  0.00              
ATOM    842  CA  GLY   246      21.891  20.579 -20.890  1.00  0.00              
ATOM    843  C   GLY   246      22.232  19.579 -19.764  1.00  0.00              
ATOM    844  O   GLY   246      21.396  18.746 -19.394  1.00  0.00              
ATOM    845  N   LEU   247      23.467  19.687 -19.250  1.00  0.00              
ATOM    846  CA  LEU   247      23.993  18.736 -18.281  1.00  0.00              
ATOM    847  C   LEU   247      23.707  19.193 -16.865  1.00  0.00              
ATOM    848  O   LEU   247      23.839  20.331 -16.538  1.00  0.00              
ATOM    849  N   GLY   248      23.297  18.261 -16.014  1.00  0.00              
ATOM    850  CA  GLY   248      23.303  18.513 -14.576  1.00  0.00              
ATOM    851  C   GLY   248      21.997  18.807 -13.888  1.00  0.00              
ATOM    852  O   GLY   248      21.999  19.267 -12.740  1.00  0.00              
ATOM    853  N   ILE   249      20.870  18.475 -14.527  1.00  0.00              
ATOM    854  CA  ILE   249      19.573  18.649 -13.899  1.00  0.00              
ATOM    855  C   ILE   249      19.233  17.425 -13.049  1.00  0.00              
ATOM    856  O   ILE   249      19.533  16.272 -13.441  1.00  0.00              
ATOM    857  N   GLY   250      18.634  17.713 -11.891  1.00  0.00              
ATOM    858  CA  GLY   250      18.226  16.695 -10.894  1.00  0.00              
ATOM    859  C   GLY   250      16.931  17.155 -10.246  1.00  0.00              
ATOM    860  O   GLY   250      16.791  18.287  -9.792  1.00  0.00              
ATOM    861  N   GLY   251      15.994  16.226 -10.180  1.00  0.00              
ATOM    862  CA  GLY   251      14.714  16.429  -9.488  1.00  0.00              
ATOM    863  C   GLY   251      14.543  15.257  -8.533  1.00  0.00              
ATOM    864  O   GLY   251      14.491  14.110  -8.963  1.00  0.00              
ATOM    865  N   GLN   252      14.579  15.524  -7.241  1.00  0.00              
ATOM    866  CA  GLN   252      14.490  14.462  -6.239  1.00  0.00              
ATOM    867  C   GLN   252      13.808  14.909  -4.975  1.00  0.00              
ATOM    868  O   GLN   252      13.634  16.091  -4.724  1.00  0.00              
ATOM    869  N   HIS   253      13.393  13.922  -4.175  1.00  0.00              
ATOM    870  CA  HIS   253      12.967  14.126  -2.785  1.00  0.00              
ATOM    871  C   HIS   253      14.081  13.587  -1.917  1.00  0.00              
ATOM    872  O   HIS   253      14.520  12.403  -2.047  1.00  0.00              
ATOM    873  N   GLY   254      14.543  14.475  -1.037  1.00  0.00              
ATOM    874  CA  GLY   254      15.644  14.166  -0.122  1.00  0.00              
ATOM    875  C   GLY   254      15.154  14.200   1.330  1.00  0.00              
ATOM    876  O   GLY   254      14.226  14.914   1.651  1.00  0.00              
END
