
#######################################################
#                                                     #
#                        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   21 (  203),  selected   21 , name T0320TS277_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS277_1-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     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    N     228      N     242          4.543
LGA    N     229      P     243          0.590
LGA    S     230      A     244          3.384
LGA    L     231      L     245          1.888
LGA    P     232      H     246          2.440
LGA    N     233      F     247          2.464
LGA    P     234      E     248          2.920
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    H     235      I     252          1.384
LGA    L     236      H     253          2.337
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    R     237      K     257          4.485
LGA    K     238      D     258          3.800
LGA    D     239      R     263          3.998
LGA    S     240      S     264          4.810
LGA    N     241      S     265          3.737
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    N     242      N     268           #
LGA    P     243      T     269           -
LGA    A     244      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    L     245      Y     288          4.647
LGA    H     246      P     289          2.699
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    F     247      Y     292          2.608
LGA    E     248      L     293          2.420
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)   21   73    5.0     18    3.28    16.67     15.363     0.533

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.612224 * X  +   0.161265 * Y  +  -0.774064 * Z  +  87.811737
  Y_new =  -0.723104 * X  +  -0.510211 * Y  +   0.465624 * Z  +  -2.552282
  Z_new =  -0.319847 * X  +   0.844795 * Y  +   0.428975 * Z  + -18.124088 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.100940   -2.040653  [ DEG:    63.0792   -116.9208 ]
  Theta =   0.325568    2.816025  [ DEG:    18.6537    161.3463 ]
  Phi   =  -2.273349    0.868244  [ DEG:  -130.2533     49.7467 ]
 
# 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: T0320TS277_1-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS277_1-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   73   5.0   18   3.28   16.67  15.363
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS277_1-D2
PFRMAT TS 
TARGET T0320
MODEL 1
PARENT 1SUR
ATOM   4297  H   ASN   228       7.958   5.310   1.409  1.00  0.00                              
ATOM   4299  N   ASN   228       7.365   5.008   2.075  1.00  0.00                              
ATOM   4301  CA  ASN   228       6.216   5.826   2.452  1.00  0.00                              
ATOM   4303  CB  ASN   228       5.835   5.540   3.919  1.00  0.00                              
ATOM   4305  C   ASN   228       6.468   7.305   2.274  1.00  0.00                              
ATOM   4307  O   ASN   228       6.172   7.875   1.224  1.00  0.00                              
ATOM   4309  CG  ASN   228       4.581   6.274   4.363  1.00  0.00                              
ATOM   4311  ND2 ASN   228       4.625   6.870   5.549  1.00  0.00                              
ATOM   4313 HD21 ASN   228       5.417   6.805   6.057  1.00  0.00                              
ATOM   4315 HD22 ASN   228       3.865   7.328   5.867  1.00  0.00                              
ATOM   4317  OD1 ASN   228       3.565   6.276   3.658  1.00  0.00                              
ATOM   4319  H   ASN   229       7.260   7.428   4.065  1.00  0.00                              
ATOM   4321  N   ASN   229       6.986   7.936   3.322  1.00  0.00                              
ATOM   4323  CA  ASN   229       7.188   9.363   3.360  1.00  0.00                              
ATOM   4325  CB  ASN   229       7.074   9.987   1.965  1.00  0.00                              
ATOM   4327  C   ASN   229       6.177   9.983   4.331  1.00  0.00                              
ATOM   4329  O   ASN   229       4.986  10.064   4.029  1.00  0.00                              
ATOM   4331  CG  ASN   229       8.338   9.790   1.141  1.00  0.00                              
ATOM   4333  ND2 ASN   229       8.316  10.250  -0.101  1.00  0.00                              
ATOM   4335 HD21 ASN   229       7.533  10.671  -0.411  1.00  0.00                              
ATOM   4337 HD22 ASN   229       9.081  10.157  -0.644  1.00  0.00                              
ATOM   4339  OD1 ASN   229       9.320   9.188   1.613  1.00  0.00                              
ATOM   4341  H   SER   230       7.551  10.239   5.751  1.00  0.00                              
ATOM   4343  N   SER   230       6.644  10.350   5.543  1.00  0.00                              
ATOM   4345  CA  SER   230       5.747  10.907   6.574  1.00  0.00                              
ATOM   4347  CB  SER   230       6.255  10.533   7.989  1.00  0.00                              
ATOM   4349  C   SER   230       5.631  12.435   6.461  1.00  0.00                              
ATOM   4351  O   SER   230       6.614  13.151   6.657  1.00  0.00                              
ATOM   4353  OG  SER   230       5.506  11.198   8.985  1.00  0.00                              
ATOM   4355  H   LEU   231       3.700  12.332   6.061  1.00  0.00                              
ATOM   4357  N   LEU   231       4.422  12.926   6.194  1.00  0.00                              
ATOM   4359  CA  LEU   231       4.180  14.366   6.123  1.00  0.00                              
ATOM   4361  CB  LEU   231       4.530  14.901   4.729  1.00  0.00                              
ATOM   4363  C   LEU   231       2.728  14.683   6.447  1.00  0.00                              
ATOM   4365  O   LEU   231       2.021  15.276   5.630  1.00  0.00                              
ATOM   4367  CG  LEU   231       3.704  14.354   3.564  1.00  0.00                              
ATOM   4369  CD1 LEU   231       3.752  15.306   2.411  1.00  0.00                              
ATOM   4371  CD2 LEU   231       4.241  12.994   3.144  1.00  0.00                              
ATOM   4373  N   PRO   232       2.247  14.252   7.624  1.00  0.00                              
ATOM   4375  CA  PRO   232       0.867  14.506   8.025  1.00  0.00                              
ATOM   4377  CB  PRO   232       0.594  13.405   9.024  1.00  0.00                              
ATOM   4379  C   PRO   232       0.670  15.883   8.659  1.00  0.00                              
ATOM   4381  O   PRO   232       1.638  16.591   8.945  1.00  0.00                              
ATOM   4383  CG  PRO   232       1.914  13.238   9.729  1.00  0.00                              
ATOM   4385  CD  PRO   232       2.966  13.449   8.643  1.00  0.00                              
ATOM   4387  H   ASN   233      -1.283  15.683   8.624  1.00  0.00                              
ATOM   4389  N   ASN   233      -0.580  16.249   8.891  1.00  0.00                              
ATOM   4391  CA  ASN   233      -0.909  17.527   9.553  1.00  0.00                              
ATOM   4393  CB  ASN   233       0.321  18.450   9.576  1.00  0.00                              
ATOM   4395  C   ASN   233      -2.080  18.228   8.855  1.00  0.00                              
ATOM   4397  O   ASN   233      -1.965  18.631   7.695  1.00  0.00                              
ATOM   4399  CG  ASN   233       0.169  19.611  10.542  1.00  0.00                              
ATOM   4401  ND2 ASN   233       0.712  20.770  10.174  1.00  0.00                              
ATOM   4403 HD21 ASN   233       1.166  20.813   9.349  1.00  0.00                              
ATOM   4405 HD22 ASN   233       0.648  21.516  10.746  1.00  0.00                              
ATOM   4407  OD1 ASN   233      -0.405  19.462  11.623  1.00  0.00                              
ATOM   4409  N   PRO   234      -3.228  18.393   9.550  1.00  0.00                              
ATOM   4411  CA  PRO   234      -4.393  19.048   8.964  1.00  0.00                              
ATOM   4413  CB  PRO   234      -5.525  18.670   9.914  1.00  0.00                              
ATOM   4415  C   PRO   234      -4.219  20.555   8.881  1.00  0.00                              
ATOM   4417  O   PRO   234      -3.368  21.128   9.578  1.00  0.00                              
ATOM   4419  CG  PRO   234      -4.855  18.636  11.248  1.00  0.00                              
ATOM   4421  CD  PRO   234      -3.485  18.001  10.961  1.00  0.00                              
ATOM   4423  H   HIS   235      -5.659  20.716   7.534  1.00  0.00                              
ATOM   4425  N   HIS   235      -5.024  21.206   8.037  1.00  0.00                              
ATOM   4427  CA  HIS   235      -4.942  22.658   7.856  1.00  0.00                              
ATOM   4429  CB  HIS   235      -5.893  23.096   6.732  1.00  0.00                              
ATOM   4431  C   HIS   235      -5.291  23.397   9.143  1.00  0.00                              
ATOM   4433  O   HIS   235      -4.402  23.935   9.818  1.00  0.00                              
ATOM   4435  CG  HIS   235      -5.960  24.583   6.530  1.00  0.00                              
ATOM   4437  ND1 HIS   235      -7.049  25.342   6.906  1.00  0.00                              
ATOM   4439  HD1 HIS   235      -7.848  25.014   7.311  1.00  0.00                              
ATOM   4441  CE1 HIS   235      -6.845  26.599   6.549  1.00  0.00                              
ATOM   4443  NE2 HIS   235      -5.621  26.699   6.053  1.00  0.00                              
ATOM   4445  HE2 HIS   235      -5.217  27.511   5.764  1.00  0.00                              
ATOM   4447  CD2 HIS   235      -5.029  25.459   6.070  1.00  0.00                              
ATOM   4449  H   LEU   236      -7.233  23.093   8.878  1.00  0.00                              
ATOM   4451  N   LEU   236      -6.589  23.464   9.463  1.00  0.00                              
ATOM   4453  CA  LEU   236      -7.039  24.092  10.707  1.00  0.00                              
ATOM   4455  CB  LEU   236      -5.880  24.182  11.712  1.00  0.00                              
ATOM   4457  C   LEU   236      -7.599  25.494  10.457  1.00  0.00                              
ATOM   4459  O   LEU   236      -8.207  25.755   9.416  1.00  0.00                              
ATOM   4461  CG  LEU   236      -6.206  24.836  13.066  1.00  0.00                              
ATOM   4463  CD1 LEU   236      -7.048  23.886  13.916  1.00  0.00                              
ATOM   4465  CD2 LEU   236      -4.928  25.208  13.794  1.00  0.00                              
ATOM   4467  H   ARG   237      -6.851  26.142  12.169  1.00  0.00                              
ATOM   4469  N   ARG   237      -7.369  26.396  11.411  1.00  0.00                              
ATOM   4471  CA  ARG   237      -7.871  27.772  11.322  1.00  0.00                              
ATOM   4473  CB  ARG   237      -8.534  28.163  12.637  1.00  0.00                              
ATOM   4475  C   ARG   237      -6.727  28.763  11.018  1.00  0.00                              
ATOM   4477  O   ARG   237      -6.923  29.740  10.293  1.00  0.00                              
ATOM   4479  CG  ARG   237      -9.671  27.223  13.055  1.00  0.00                              
ATOM   4481  CD  ARG   237     -10.356  27.681  14.357  1.00  0.00                              
ATOM   4483  NE  ARG   237     -11.510  26.821  14.691  1.00  0.00                              
ATOM   4485  HE  ARG   237     -11.727  26.126  14.079  1.00  0.00                              
ATOM   4487  CZ  ARG   237     -12.276  26.932  15.799  1.00  0.00                              
ATOM   4489  NH1 ARG   237     -12.025  27.878  16.710  1.00  0.00                              
ATOM   4491  NH2 ARG   237     -13.286  26.090  15.993  1.00  0.00                              
ATOM   4493  H   LYS   238      -5.421  27.707  12.079  1.00  0.00                              
ATOM   4495  N   LYS   238      -5.538  28.503  11.575  1.00  0.00                              
ATOM   4497  CA  LYS   238      -4.385  29.415  11.404  1.00  0.00                              
ATOM   4499  CB  LYS   238      -3.252  29.039  12.380  1.00  0.00                              
ATOM   4501  C   LYS   238      -3.851  29.389   9.959  1.00  0.00                              
ATOM   4503  O   LYS   238      -3.459  30.427   9.417  1.00  0.00                              
ATOM   4505  CG  LYS   238      -3.588  29.268  13.854  1.00  0.00                              
ATOM   4507  CD  LYS   238      -2.429  28.862  14.757  1.00  0.00                              
ATOM   4509  CE  LYS   238      -2.752  29.099  16.227  1.00  0.00                              
ATOM   4511  NZ  LYS   238      -1.626  28.687  17.115  1.00  0.00                              
ATOM   4513  H   ASP   239      -4.114  27.442   9.818  1.00  0.00                              
ATOM   4515  N   ASP   239      -3.808  28.207   9.357  1.00  0.00                              
ATOM   4517  CA  ASP   239      -3.318  28.053   7.981  1.00  0.00                              
ATOM   4519  CB  ASP   239      -3.380  29.387   7.233  1.00  0.00                              
ATOM   4521  C   ASP   239      -1.889  27.500   7.950  1.00  0.00                              
ATOM   4523  O   ASP   239      -0.967  28.177   7.488  1.00  0.00                              
ATOM   4525  CG  ASP   239      -2.857  29.291   5.814  1.00  0.00                              
ATOM   4527  OD1 ASP   239      -2.958  28.203   5.209  1.00  0.00                              
ATOM   4529  OD2 ASP   239      -2.312  30.292   5.306  1.00  0.00                              
ATOM   4531  H   SER   240      -2.439  25.774   8.734  1.00  0.00                              
ATOM   4533  N   SER   240      -1.708  26.264   8.419  1.00  0.00                              
ATOM   4535  CA  SER   240      -0.371  25.662   8.480  1.00  0.00                              
ATOM   4537  CB  SER   240      -0.350  24.486   9.462  1.00  0.00                              
ATOM   4539  C   SER   240       0.121  25.197   7.091  1.00  0.00                              
ATOM   4541  O   SER   240      -0.569  24.444   6.401  1.00  0.00                              
ATOM   4543  OG  SER   240       0.945  23.891   9.502  1.00  0.00                              
ATOM   4545  H   ASN   241       1.858  26.133   7.312  1.00  0.00                              
ATOM   4547  N   ASN   241       1.348  25.612   6.715  1.00  0.00                              
ATOM   4549  CA  ASN   241       1.908  25.282   5.389  1.00  0.00                              
ATOM   4551  CB  ASN   241       2.033  26.545   4.542  1.00  0.00                              
ATOM   4553  C   ASN   241       3.276  24.617   5.503  1.00  0.00                              
ATOM   4555  O   ASN   241       4.292  25.306   5.599  1.00  0.00                              
ATOM   4557  CG  ASN   241       0.694  27.215   4.295  1.00  0.00                              
ATOM   4559  ND2 ASN   241       0.516  28.415   4.839  1.00  0.00                              
ATOM   4561 HD21 ASN   241       1.214  28.784   5.355  1.00  0.00                              
ATOM   4563 HD22 ASN   241      -0.301  28.868   4.710  1.00  0.00                              
ATOM   4565  OD1 ASN   241      -0.186  26.648   3.644  1.00  0.00                              
ATOM   4567  H   ASN   242       2.504  22.800   5.354  1.00  0.00                              
ATOM   4569  N   ASN   242       3.309  23.277   5.441  1.00  0.00                              
ATOM   4571  CA  ASN   242       4.572  22.530   5.504  1.00  0.00                              
ATOM   4573  CB  ASN   242       5.016  22.360   6.976  1.00  0.00                              
ATOM   4575  C   ASN   242       4.423  21.147   4.874  1.00  0.00                              
ATOM   4577  O   ASN   242       5.212  20.760   4.032  1.00  0.00                              
ATOM   4579  CG  ASN   242       5.047  23.663   7.753  1.00  0.00                              
ATOM   4581  ND2 ASN   242       3.993  23.924   8.525  1.00  0.00                              
ATOM   4583 HD21 ASN   242       3.288  23.300   8.550  1.00  0.00                              
ATOM   4585 HD22 ASN   242       3.980  24.712   9.042  1.00  0.00                              
ATOM   4587  OD1 ASN   242       6.030  24.413   7.695  1.00  0.00                              
ATOM   4589  N   PRO   243       3.360  20.417   5.252  1.00  0.00                              
ATOM   4591  CA  PRO   243       3.080  19.074   4.748  1.00  0.00                              
ATOM   4593  CB  PRO   243       1.578  19.059   4.698  1.00  0.00                              
ATOM   4595  C   PRO   243       3.699  18.731   3.385  1.00  0.00                              
ATOM   4597  O   PRO   243       4.746  18.072   3.321  1.00  0.00                              
ATOM   4599  CG  PRO   243       1.183  19.793   5.961  1.00  0.00                              
ATOM   4601  CD  PRO   243       2.283  20.856   6.169  1.00  0.00                              
ATOM   4603  H   ALA   244       2.265  19.654   2.413  1.00  0.00                              
ATOM   4605  N   ALA   244       3.029  19.128   2.307  1.00  0.00                              
ATOM   4607  CA  ALA   244       3.464  18.775   0.941  1.00  0.00                              
ATOM   4609  CB  ALA   244       2.737  19.641  -0.084  1.00  0.00                              
ATOM   4611  C   ALA   244       4.976  18.893   0.746  1.00  0.00                              
ATOM   4613  O   ALA   244       5.519  18.325  -0.185  1.00  0.00                              
ATOM   4615  H   LEU   245       5.182  20.085   2.296  1.00  0.00                              
ATOM   4617  N   LEU   245       5.639  19.670   1.581  1.00  0.00                              
ATOM   4619  CA  LEU   245       7.071  19.886   1.431  1.00  0.00                              
ATOM   4621  CB  LEU   245       7.356  21.368   1.428  1.00  0.00                              
ATOM   4623  C   LEU   245       7.832  19.242   2.568  1.00  0.00                              
ATOM   4625  O   LEU   245       8.943  18.738   2.379  1.00  0.00                              
ATOM   4627  CG  LEU   245       6.387  22.238   0.636  1.00  0.00                              
ATOM   4629  CD1 LEU   245       6.654  23.704   0.919  1.00  0.00                              
ATOM   4631  CD2 LEU   245       6.523  21.951  -0.854  1.00  0.00                              
ATOM   4633  H   HIS   246       6.405  19.686   3.831  1.00  0.00                              
ATOM   4635  N   HIS   246       7.260  19.291   3.752  1.00  0.00                              
ATOM   4637  CA  HIS   246       7.913  18.779   4.924  1.00  0.00                              
ATOM   4639  CB  HIS   246       7.291  19.387   6.183  1.00  0.00                              
ATOM   4641  C   HIS   246       7.822  17.278   4.988  1.00  0.00                              
ATOM   4643  O   HIS   246       7.057  16.731   5.789  1.00  0.00                              
ATOM   4645  CG  HIS   246       8.085  19.119   7.416  1.00  0.00                              
ATOM   4647  ND1 HIS   246       8.348  17.845   7.874  1.00  0.00                              
ATOM   4649  HD1 HIS   246       8.039  17.036   7.480  1.00  0.00                              
ATOM   4651  CE1 HIS   246       9.034  17.922   9.000  1.00  0.00                              
ATOM   4653  NE2 HIS   246       9.244  19.198   9.278  1.00  0.00                              
ATOM   4655  HE2 HIS   246       9.687  19.519  10.054  1.00  0.00                              
ATOM   4657  CD2 HIS   246       8.634  19.970   8.320  1.00  0.00                              
ATOM   4659  H   PHE   247       9.183  17.071   3.591  1.00  0.00                              
ATOM   4661  N   PHE   247       8.616  16.605   4.189  1.00  0.00                              
ATOM   4663  CA  PHE   247       8.658  15.169   4.217  1.00  0.00                              
ATOM   4665  CB  PHE   247       9.177  14.624   2.885  1.00  0.00                              
ATOM   4667  C   PHE   247       9.540  14.688   5.386  1.00  0.00                              
ATOM   4669  O   PHE   247       9.775  15.436   6.333  1.00  0.00                              
ATOM   4671  CG  PHE   247       8.294  14.976   1.703  1.00  0.00                              
ATOM   4673  CD1 PHE   247       8.569  16.104   0.919  1.00  0.00                              
ATOM   4675  CE1 PHE   247       7.776  16.422  -0.160  1.00  0.00                              
ATOM   4677  CZ  PHE   247       6.706  15.593  -0.504  1.00  0.00                              
ATOM   4679  CD2 PHE   247       7.179  14.209   1.401  1.00  0.00                              
ATOM   4681  CE2 PHE   247       6.384  14.512   0.302  1.00  0.00                              
ATOM   4683  H   GLU   248       9.756  12.889   4.596  1.00  0.00                              
ATOM   4685  N   GLU   248       9.988  13.435   5.334  1.00  0.00                              
ATOM   4687  CA  GLU   248      10.792  12.877   6.402  1.00  0.00                              
ATOM   4689  CB  GLU   248      12.287  13.021   6.070  1.00  0.00                              
ATOM   4691  C   GLU   248      10.476  13.561   7.736  1.00  0.00                              
ATOM   4693  O   GLU   248       9.573  13.132   8.463  1.00  0.00                              
ATOM   4695  CG  GLU   248      13.226  12.596   7.196  1.00  0.00                              
ATOM   4697  CD  GLU   248      14.667  12.405   6.730  1.00  0.00                              
ATOM   4699  OE1 GLU   248      14.962  12.723   5.553  1.00  0.00                              
ATOM   4701  OE2 GLU   248      15.503  11.903   7.530  1.00  0.00                              
TER 
END
