
#######################################################
#                                                     #
#                        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 (  171),  selected   21 , name T0320TS675_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS675_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      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    N     228      H     235          3.468
LGA    N     229      L     236          2.587
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    S     230      P     243          4.435
LGA    L     231      A     244          2.402
LGA    P     232      L     245          1.485
LGA    -       -      H     246           -
LGA    N     233      F     247          4.352
LGA    P     234      E     248          1.596
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    H     235      I     251          1.002
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    L     236      A     254          2.137
LGA    R     237      F     255          3.877
LGA    K     238      G     256          4.135
LGA    D     239      K     257          3.269
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    S     240      A     266          4.080
LGA    N     241      I     267          4.285
LGA    N     242      N     268           -
LGA    P     243      -       -           -
LGA    A     244      -       -           -
LGA    L     245      T     269           #
LGA    H     246      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    -       -      Y     288           -
LGA    F     247      P     289          2.574
LGA    E     248      G     290          1.875
LGA    -       -      W     291           -
LGA    -       -      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)   21   73    5.0     16    3.18     0.00     13.682     0.488

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.845068 * X  +   0.473476 * Y  +  -0.248356 * Z  +   2.842885
  Y_new =   0.062915 * X  +   0.373223 * Y  +   0.925606 * Z  + -59.628906
  Z_new =   0.530944 * X  +  -0.797825 * Y  +   0.285610 * Z  + -35.427982 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.227025    1.914567  [ DEG:   -70.3034    109.6966 ]
  Theta =  -0.559714   -2.581878  [ DEG:   -32.0693   -147.9307 ]
  Phi   =   0.074313   -3.067280  [ DEG:     4.2578   -175.7422 ]
 
# 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: T0320TS675_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS675_2-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   16   3.18    0.00  13.682
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS675_2-D2
PFRMAT TS
TARGET T0320
MODEL  2  REFINED
PARENT 1SUR
ATOM   1865  N   ASN   228      15.275  11.897   4.538  1.00  0.00
ATOM   1866  CA  ASN   228      14.374  12.969   4.229  1.00  0.00
ATOM   1867  C   ASN   228      12.903  12.529   3.893  1.00  0.00
ATOM   1868  O   ASN   228      12.203  12.005   4.765  1.00  0.00
ATOM   1869  CB  ASN   228      15.125  13.824   3.187  1.00  0.00
ATOM   1870  CG  ASN   228      15.397  13.179   1.867  1.00  0.00
ATOM   1871  OD1 ASN   228      16.380  13.524   1.164  1.00  0.00
ATOM   1872  ND2 ASN   228      14.536  12.264   1.420  1.00  0.00
ATOM   1873  N   ASN   229      12.396  13.287   2.933  1.00  0.00
ATOM   1874  CA  ASN   229      11.112  13.226   2.235  1.00  0.00
ATOM   1875  C   ASN   229       9.901  13.862   3.010  1.00  0.00
ATOM   1876  O   ASN   229      10.121  14.565   4.015  1.00  0.00
ATOM   1877  CB  ASN   229      10.838  11.716   1.916  1.00  0.00
ATOM   1878  CG  ASN   229      11.738  11.156   0.839  1.00  0.00
ATOM   1879  OD1 ASN   229      12.084  11.837  -0.131  1.00  0.00
ATOM   1880  ND2 ASN   229      12.183   9.923   1.042  1.00  0.00
ATOM   1881  N   SER   230       8.649  13.521   2.638  1.00  0.00
ATOM   1882  CA  SER   230       7.455  14.037   3.220  1.00  0.00
ATOM   1883  C   SER   230       6.353  12.987   3.443  1.00  0.00
ATOM   1884  O   SER   230       5.902  12.317   2.489  1.00  0.00
ATOM   1885  CB  SER   230       6.882  15.105   2.277  1.00  0.00
ATOM   1886  OG  SER   230       6.331  14.619   1.043  1.00  0.00
ATOM   1887  N   LEU   231       6.070  12.703   4.736  1.00  0.00
ATOM   1888  CA  LEU   231       5.016  11.761   5.062  1.00  0.00
ATOM   1889  C   LEU   231       3.776  12.470   5.781  1.00  0.00
ATOM   1890  O   LEU   231       2.700  11.946   5.475  1.00  0.00
ATOM   1891  CB  LEU   231       5.589  10.660   5.957  1.00  0.00
ATOM   1892  CG  LEU   231       4.727   9.391   6.096  1.00  0.00
ATOM   1893  CD1 LEU   231       3.980   9.126   4.797  1.00  0.00
ATOM   1894  CD2 LEU   231       5.627   8.217   6.438  1.00  0.00
ATOM   1895  N   PRO   232       3.960  13.340   6.795  1.00  0.00
ATOM   1896  CA  PRO   232       2.789  13.915   7.495  1.00  0.00
ATOM   1897  C   PRO   232       2.039  15.018   6.693  1.00  0.00
ATOM   1898  O   PRO   232       2.563  15.472   5.640  1.00  0.00
ATOM   1899  CB  PRO   232       3.189  14.473   8.908  1.00  0.00
ATOM   1900  CG  PRO   232       4.411  13.488   9.124  1.00  0.00
ATOM   1901  CD  PRO   232       5.081  13.538   7.765  1.00  0.00
ATOM   1902  N   ASN   233       0.862  15.425   7.138  1.00  0.00
ATOM   1903  CA  ASN   233       0.017  16.545   6.609  1.00  0.00
ATOM   1904  C   ASN   233      -0.702  17.479   7.606  1.00  0.00
ATOM   1905  O   ASN   233      -1.437  18.309   7.100  1.00  0.00
ATOM   1906  CB  ASN   233      -1.133  15.932   5.719  1.00  0.00
ATOM   1907  CG  ASN   233      -1.779  16.953   4.809  1.00  0.00
ATOM   1908  OD1 ASN   233      -1.126  17.849   4.257  1.00  0.00
ATOM   1909  ND2 ASN   233      -3.084  16.814   4.622  1.00  0.00
ATOM   1910  N   PRO   234      -0.535  17.478   8.960  1.00  0.00
ATOM   1911  CA  PRO   234      -1.324  18.321   9.805  1.00  0.00
ATOM   1912  C   PRO   234      -1.000  19.872   9.714  1.00  0.00
ATOM   1913  O   PRO   234      -0.417  20.332   8.732  1.00  0.00
ATOM   1914  CB  PRO   234      -1.169  17.893  11.301  1.00  0.00
ATOM   1915  CG  PRO   234       0.264  17.342  11.189  1.00  0.00
ATOM   1916  CD  PRO   234       0.216  16.567   9.903  1.00  0.00
ATOM   1917  N   HIS   235      -1.805  20.684  10.467  1.00  0.00
ATOM   1918  CA  HIS   235      -1.829  22.126  10.525  1.00  0.00
ATOM   1919  C   HIS   235      -1.694  22.766  11.954  1.00  0.00
ATOM   1920  O   HIS   235      -2.289  22.273  12.917  1.00  0.00
ATOM   1921  CB  HIS   235      -3.215  22.539   9.934  1.00  0.00
ATOM   1922  CG  HIS   235      -4.390  22.162  10.761  1.00  0.00
ATOM   1923  ND1 HIS   235      -4.988  20.925  10.644  1.00  0.00
ATOM   1924  CD2 HIS   235      -5.062  22.820  11.744  1.00  0.00
ATOM   1925  CE1 HIS   235      -5.969  20.832  11.530  1.00  0.00
ATOM   1926  NE2 HIS   235      -6.055  21.977  12.183  1.00  0.00
ATOM   1927  N   LEU   236      -1.073  23.982  12.032  1.00  0.00
ATOM   1928  CA  LEU   236      -0.772  24.716  13.278  1.00  0.00
ATOM   1929  C   LEU   236      -0.394  26.224  13.020  1.00  0.00
ATOM   1930  O   LEU   236      -0.950  26.804  12.088  1.00  0.00
ATOM   1931  CB  LEU   236       0.233  23.901  14.115  1.00  0.00
ATOM   1932  CG  LEU   236       0.679  24.631  15.435  1.00  0.00
ATOM   1933  CD1 LEU   236      -0.496  24.645  16.413  1.00  0.00
ATOM   1934  CD2 LEU   236       1.869  23.896  16.037  1.00  0.00
ATOM   1935  N   ARG   237      -0.200  26.895  14.151  1.00  0.00
ATOM   1936  CA  ARG   237       0.134  28.290  14.279  1.00  0.00
ATOM   1937  C   ARG   237      -1.000  29.106  13.667  1.00  0.00
ATOM   1938  O   ARG   237      -2.112  28.986  14.197  1.00  0.00
ATOM   1939  CB  ARG   237       1.481  28.496  13.672  1.00  0.00
ATOM   1940  CG  ARG   237       2.667  28.026  14.449  1.00  0.00
ATOM   1941  CD  ARG   237       3.998  28.408  13.810  1.00  0.00
ATOM   1942  NE  ARG   237       5.135  27.939  14.598  1.00  0.00
ATOM   1943  CZ  ARG   237       5.786  26.794  14.392  1.00  0.00
ATOM   1944  NH1 ARG   237       5.398  25.965  13.416  1.00  0.00
ATOM   1945  NH2 ARG   237       6.839  26.481  15.143  1.00  0.00
ATOM   1946  N   LYS   238      -0.750  30.108  12.832  1.00  0.00
ATOM   1947  CA  LYS   238      -1.852  30.769  12.208  1.00  0.00
ATOM   1948  C   LYS   238      -1.943  30.197  10.774  1.00  0.00
ATOM   1949  O   LYS   238      -1.509  30.830   9.812  1.00  0.00
ATOM   1950  CB  LYS   238      -1.662  32.284  12.228  1.00  0.00
ATOM   1951  CG  LYS   238      -1.629  32.897  13.594  1.00  0.00
ATOM   1952  CD  LYS   238      -1.438  34.411  13.523  1.00  0.00
ATOM   1953  CE  LYS   238      -1.429  35.048  14.911  1.00  0.00
ATOM   1954  NZ  LYS   238      -1.238  36.527  14.842  1.00  0.00
ATOM   1955  N   ASP   239      -2.914  29.281  10.675  1.00  0.00
ATOM   1956  CA  ASP   239      -3.341  28.578   9.454  1.00  0.00
ATOM   1957  C   ASP   239      -2.276  27.694   8.693  1.00  0.00
ATOM   1958  O   ASP   239      -2.594  27.275   7.561  1.00  0.00
ATOM   1959  CB  ASP   239      -3.913  29.676   8.502  1.00  0.00
ATOM   1960  CG  ASP   239      -4.470  29.041   7.201  1.00  0.00
ATOM   1961  OD1 ASP   239      -5.349  28.156   7.295  1.00  0.00
ATOM   1962  OD2 ASP   239      -4.067  29.476   6.094  1.00  0.00
ATOM   1963  N   SER   240      -1.244  27.195   9.308  1.00  0.00
ATOM   1964  CA  SER   240      -0.348  26.296   8.571  1.00  0.00
ATOM   1965  C   SER   240       0.686  25.736   9.548  1.00  0.00
ATOM   1966  O   SER   240       1.248  26.543  10.327  1.00  0.00
ATOM   1967  CB  SER   240       0.328  27.062   7.420  1.00  0.00
ATOM   1968  OG  SER   240       1.297  26.399   6.657  1.00  0.00
ATOM   1969  N   ASN   241       1.247  24.557   9.244  1.00  0.00
ATOM   1970  CA  ASN   241       2.308  24.071  10.110  1.00  0.00
ATOM   1971  C   ASN   241       3.499  23.473   9.353  1.00  0.00
ATOM   1972  O   ASN   241       4.416  24.228   8.973  1.00  0.00
ATOM   1973  CB  ASN   241       1.759  22.940  11.008  1.00  0.00
ATOM   1974  CG  ASN   241       2.692  22.595  12.181  1.00  0.00
ATOM   1975  OD1 ASN   241       3.888  22.900  12.123  1.00  0.00
ATOM   1976  ND2 ASN   241       2.159  21.977  13.242  1.00  0.00
ATOM   1977  N   ASN   242       3.321  22.215   8.893  1.00  0.00
ATOM   1978  CA  ASN   242       4.334  21.613   8.131  1.00  0.00
ATOM   1979  C   ASN   242       3.823  21.104   6.795  1.00  0.00
ATOM   1980  O   ASN   242       4.650  20.432   6.117  1.00  0.00
ATOM   1981  CB  ASN   242       4.882  20.468   8.979  1.00  0.00
ATOM   1982  CG  ASN   242       3.871  19.384   9.377  1.00  0.00
ATOM   1983  OD1 ASN   242       2.719  19.718   9.655  1.00  0.00
ATOM   1984  ND2 ASN   242       4.181  18.082   9.377  1.00  0.00
ATOM   1985  N   PRO   243       2.505  21.245   6.334  1.00  0.00
ATOM   1986  CA  PRO   243       2.332  20.714   4.954  1.00  0.00
ATOM   1987  C   PRO   243       3.373  21.245   3.880  1.00  0.00
ATOM   1988  O   PRO   243       3.893  20.363   3.143  1.00  0.00
ATOM   1989  CB  PRO   243       0.824  21.097   4.697  1.00  0.00
ATOM   1990  CG  PRO   243       0.261  22.070   5.793  1.00  0.00
ATOM   1991  CD  PRO   243       1.269  22.072   6.920  1.00  0.00
ATOM   1992  N   ALA   244       3.660  22.540   3.668  1.00  0.00
ATOM   1993  CA  ALA   244       4.594  22.859   2.576  1.00  0.00
ATOM   1994  C   ALA   244       6.032  23.335   2.980  1.00  0.00
ATOM   1995  O   ALA   244       6.837  23.439   2.051  1.00  0.00
ATOM   1996  CB  ALA   244       3.883  23.952   1.752  1.00  0.00
ATOM   1997  N   LEU   245       6.248  23.819   4.166  1.00  0.00
ATOM   1998  CA  LEU   245       7.555  24.297   4.625  1.00  0.00
ATOM   1999  C   LEU   245       8.502  23.246   5.282  1.00  0.00
ATOM   2000  O   LEU   245       9.608  23.055   4.765  1.00  0.00
ATOM   2001  CB  LEU   245       7.319  25.495   5.606  1.00  0.00
ATOM   2002  CG  LEU   245       8.260  25.547   6.849  1.00  0.00
ATOM   2003  CD1 LEU   245       9.665  25.948   6.416  1.00  0.00
ATOM   2004  CD2 LEU   245       7.719  26.539   7.868  1.00  0.00
ATOM   2005  N   HIS   246       7.973  22.449   6.145  1.00  0.00
ATOM   2006  CA  HIS   246       8.707  21.483   6.931  1.00  0.00
ATOM   2007  C   HIS   246       8.124  20.095   6.613  1.00  0.00
ATOM   2008  O   HIS   246       7.222  19.589   7.300  1.00  0.00
ATOM   2009  CB  HIS   246       8.629  21.740   8.441  1.00  0.00
ATOM   2010  CG  HIS   246       9.371  22.931   8.857  1.00  0.00
ATOM   2011  ND1 HIS   246      10.717  23.096   8.613  1.00  0.00
ATOM   2012  CD2 HIS   246       8.989  23.993   9.601  1.00  0.00
ATOM   2013  CE1 HIS   246      11.099  24.267   9.079  1.00  0.00
ATOM   2014  NE2 HIS   246      10.074  24.824   9.698  1.00  0.00
ATOM   2015  N   PHE   247       8.819  19.394   5.768  1.00  0.00
ATOM   2016  CA  PHE   247       8.512  18.025   5.400  1.00  0.00
ATOM   2017  C   PHE   247       8.969  17.067   6.525  1.00  0.00
ATOM   2018  O   PHE   247       8.316  16.031   6.671  1.00  0.00
ATOM   2019  CB  PHE   247       9.207  17.607   4.082  1.00  0.00
ATOM   2020  CG  PHE   247       8.679  18.136   2.803  1.00  0.00
ATOM   2021  CD1 PHE   247       7.568  18.957   2.696  1.00  0.00
ATOM   2022  CD2 PHE   247       9.294  17.710   1.626  1.00  0.00
ATOM   2023  CE1 PHE   247       7.098  19.387   1.472  1.00  0.00
ATOM   2024  CE2 PHE   247       8.853  18.137   0.369  1.00  0.00
ATOM   2025  CZ  PHE   247       7.730  18.990   0.307  1.00  0.00
ATOM   2026  N   GLU   248      10.192  17.247   7.051  1.00  0.00
ATOM   2027  CA  GLU   248      10.774  16.512   8.128  1.00  0.00
ATOM   2028  C   GLU   248      10.931  15.050   7.655  1.00  0.00
ATOM   2029  O   GLU   248      10.107  14.155   7.925  1.00  0.00
ATOM   2030  CB  GLU   248       9.976  16.641   9.437  1.00  0.00
ATOM   2031  CG  GLU   248      10.599  15.867  10.612  1.00  0.00
ATOM   2032  CD  GLU   248       9.844  16.098  11.929  1.00  0.00
ATOM   2033  OE1 GLU   248       8.693  16.580  11.881  1.00  0.00
ATOM   2034  OE2 GLU   248      10.419  15.809  13.021  1.00  0.00
ATOM   2035  OXT GLU   248      11.842  14.884   6.837  1.00  0.00
TER
END
