
#######################################################
#                                                     #
#                        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   24 (  200),  selected   24 , name T0386TS030_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS030_1-D2.T0386_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     219      N     219           -
LGA    P     220      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    E     221      M     230           #
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    K     222      M     233          4.069
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    I     223      V     240          0.831
LGA    R     224      N     241          4.640
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    L     225      P     244          2.474
LGA    L     226      V     245          3.126
LGA    K     227      M     246          1.787
LGA    E     228      V     247          3.247
LGA    F     229      A     248          2.122
LGA    M     230      K     249          1.583
LGA    -       -      E     250           -
LGA    H     231      G     251          3.801
LGA    T     232      E     252          1.951
LGA    M     233      T     253          3.328
LGA    K     234      Y     254          1.901
LGA    N     235      T     255          2.612
LGA    T     236      G     256          2.426
LGA    G     237      T     257          3.499
LGA    R     238      Y     258          1.895
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    N     239      L     290          3.882
LGA    V     240      K     291          2.918
LGA    N     241      P     292          5.171
LGA    D     242      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   81    5.0     20    3.06     0.00     15.032     0.633

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.971694 * X  +   0.226087 * Y  +  -0.068522 * Z  +  11.230358
  Y_new =  -0.055117 * X  +   0.065085 * Y  +   0.996356 * Z  +  74.909439
  Z_new =   0.229723 * X  +   0.971930 * Y  +  -0.050782 * Z  +  40.693661 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.622997   -1.518596  [ DEG:    92.9909    -87.0091 ]
  Theta =  -0.231793   -2.909799  [ DEG:   -13.2808   -166.7192 ]
  Phi   =  -3.084931    0.056662  [ DEG:  -176.7535      3.2465 ]
 
# 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: T0386TS030_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS030_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   81   5.0   20   3.06    0.00  15.032
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS030_1-D2
PFRMAT TS
TARGET T0386
MODEL 1 
PARENT 2g03A
ATOM   1761  N   ASN   219      22.699  62.685  79.932  1.00  1.00          
ATOM   1762  CA  ASN   219      21.664  63.695  80.119  1.00  1.00          
ATOM   1763  CB  ASN   219      20.282  63.041  80.173  1.00  1.00          
ATOM   1764  CG  ASN   219      19.705  63.146  81.581  1.00  1.00          
ATOM   1765  OD1 ASN   219      20.333  62.702  82.543  1.00  1.00          
ATOM   1766  ND2 ASN   219      18.541  63.710  81.759  1.00  1.00          
ATOM   1767  C   ASN   219      21.708  64.741  79.011  1.00  1.00          
ATOM   1768  O   ASN   219      21.954  65.919  79.264  1.00  1.00          
ATOM   1769  N   PRO   220      21.472  64.327  77.796  1.00  1.00          
ATOM   1770  CA  PRO   220      21.481  65.238  76.618  1.00  1.00          
ATOM   1771  CB  PRO   220      20.832  64.391  75.521  1.00  1.00          
ATOM   1772  CG  PRO   220      21.162  62.983  75.889  1.00  1.00          
ATOM   1773  CD  PRO   220      21.170  62.935  77.419  1.00  1.00          
ATOM   1774  C   PRO   220      20.657  66.496  76.866  1.00  1.00          
ATOM   1775  O   PRO   220      19.430  66.436  76.962  1.00  1.00          
ATOM   1776  N   GLU   221      21.336  67.633  76.973  1.00  1.00          
ATOM   1777  CA  GLU   221      20.667  68.906  77.211  1.00  1.00          
ATOM   1778  CB  GLU   221      19.712  68.795  78.402  1.00  1.00          
ATOM   1779  CG  GLU   221      20.491  68.997  79.702  1.00  1.00          
ATOM   1780  CD  GLU   221      20.103  70.324  80.345  1.00  1.00          
ATOM   1781  OE1 GLU   221      20.813  71.295  80.132  1.00  1.00          
ATOM   1782  OE2 GLU   221      19.101  70.353  81.040  1.00  1.00          
ATOM   1783  C   GLU   221      19.908  69.371  75.973  1.00  1.00          
ATOM   1784  O   GLU   221      18.703  69.620  76.027  1.00  1.00          
ATOM   1785  N   LYS   222      20.620  69.484  74.856  1.00  1.00          
ATOM   1786  CA  LYS   222      20.016  69.919  73.602  1.00  1.00          
ATOM   1787  CB  LYS   222      20.050  71.445  73.491  1.00  1.00          
ATOM   1788  CG  LYS   222      18.887  71.918  72.617  1.00  1.00          
ATOM   1789  CD  LYS   222      17.935  72.774  73.455  1.00  1.00          
ATOM   1790  CE  LYS   222      18.604  73.132  74.783  1.00  1.00          
ATOM   1791  NZ  LYS   222      19.795  73.989  74.524  1.00  1.00          
ATOM   1792  C   LYS   222      20.718  69.290  72.404  1.00  1.00          
ATOM   1793  O   LYS   222      21.300  69.989  71.576  1.00  1.00          
ATOM   1794  N   ILE   223      20.659  67.965  72.320  1.00  1.00          
ATOM   1795  CA  ILE   223      21.289  67.238  71.223  1.00  1.00          
ATOM   1796  CB  ILE   223      22.629  66.647  71.671  1.00  1.00          
ATOM   1797  CG1 ILE   223      22.588  65.126  71.527  1.00  1.00          
ATOM   1798  CG2 ILE   223      22.886  67.016  73.134  1.00  1.00          
ATOM   1799  CD1 ILE   223      23.673  64.677  70.544  1.00  1.00          
ATOM   1800  C   ILE   223      20.379  66.133  70.698  1.00  1.00          
ATOM   1801  O   ILE   223      20.340  65.864  69.498  1.00  1.00          
ATOM   1802  N   ARG   224      19.646  65.496  71.607  1.00  1.00          
ATOM   1803  CA  ARG   224      18.736  64.419  71.238  1.00  1.00          
ATOM   1804  CB  ARG   224      17.355  64.650  71.857  1.00  1.00          
ATOM   1805  CG  ARG   224      16.354  65.005  70.756  1.00  1.00          
ATOM   1806  CD  ARG   224      15.682  63.728  70.247  1.00  1.00          
ATOM   1807  NE  ARG   224      16.584  62.591  70.376  1.00  1.00          
ATOM   1808  CZ  ARG   224      17.528  62.341  69.476  1.00  1.00          
ATOM   1809  NH1 ARG   224      18.286  61.286  69.599  1.00  1.00          
ATOM   1810  NH2 ARG   224      17.697  63.152  68.466  1.00  1.00          
ATOM   1811  C   ARG   224      19.282  63.063  71.668  1.00  1.00          
ATOM   1812  O   ARG   224      20.486  62.816  71.593  1.00  1.00          
ATOM   1813  N   LEU   225      18.390  62.186  72.117  1.00  1.00          
ATOM   1814  CA  LEU   225      18.782  60.853  72.561  1.00  1.00          
ATOM   1815  CB  LEU   225      19.495  60.927  73.912  1.00  1.00          
ATOM   1816  CG  LEU   225      19.167  59.675  74.731  1.00  1.00          
ATOM   1817  CD1 LEU   225      20.447  59.132  75.370  1.00  1.00          
ATOM   1818  CD2 LEU   225      18.161  60.032  75.827  1.00  1.00          
ATOM   1819  C   LEU   225      17.575  59.926  72.654  1.00  1.00          
ATOM   1820  O   LEU   225      16.436  60.383  72.742  1.00  1.00          
ATOM   1821  N   LEU   226      17.833  58.623  72.634  1.00  1.00          
ATOM   1822  CA  LEU   226      16.769  57.629  72.718  1.00  1.00          
ATOM   1823  CB  LEU   226      17.352  56.215  72.678  1.00  1.00          
ATOM   1824  CG  LEU   226      18.666  56.224  71.896  1.00  1.00          
ATOM   1825  CD1 LEU   226      18.380  56.537  70.424  1.00  1.00          
ATOM   1826  CD2 LEU   226      19.336  54.854  72.004  1.00  1.00          
ATOM   1827  C   LEU   226      15.934  57.819  73.980  1.00  1.00          
ATOM   1828  O   LEU   226      16.174  57.169  74.996  1.00  1.00          
ATOM   1829  N   LYS   227      14.954  58.713  73.907  1.00  1.00          
ATOM   1830  CA  LYS   227      14.083  58.989  75.043  1.00  1.00          
ATOM   1831  CB  LYS   227      13.049  60.057  74.678  1.00  1.00          
ATOM   1832  CG  LYS   227      12.156  60.336  75.889  1.00  1.00          
ATOM   1833  CD  LYS   227      10.690  60.140  75.498  1.00  1.00          
ATOM   1834  CE  LYS   227       9.880  61.365  75.924  1.00  1.00          
ATOM   1835  NZ  LYS   227       8.748  60.935  76.793  1.00  1.00          
ATOM   1836  C   LYS   227      13.383  57.722  75.521  1.00  1.00          
ATOM   1837  O   LYS   227      13.149  57.545  76.717  1.00  1.00          
ATOM   1838  N   GLU   228      13.053  56.843  74.581  1.00  1.00          
ATOM   1839  CA  GLU   228      12.381  55.591  74.904  1.00  1.00          
ATOM   1840  CB  GLU   228      10.884  55.827  75.119  1.00  1.00          
ATOM   1841  CG  GLU   228      10.286  56.488  73.874  1.00  1.00          
ATOM   1842  CD  GLU   228       9.324  57.598  74.281  1.00  1.00          
ATOM   1843  OE1 GLU   228       9.263  57.900  75.462  1.00  1.00          
ATOM   1844  OE2 GLU   228       8.662  58.133  73.406  1.00  1.00          
ATOM   1845  C   GLU   228      12.991  54.939  76.140  1.00  1.00          
ATOM   1846  O   GLU   228      13.934  54.155  76.039  1.00  1.00          
ATOM   1847  N   PHE   229      12.446  55.269  77.307  1.00  1.00          
ATOM   1848  CA  PHE   229      12.937  54.718  78.565  1.00  1.00          
ATOM   1849  CB  PHE   229      11.911  54.933  79.679  1.00  1.00          
ATOM   1850  CG  PHE   229      10.622  54.233  79.320  1.00  1.00          
ATOM   1851  CD1 PHE   229       9.940  54.579  78.148  1.00  1.00          
ATOM   1852  CD2 PHE   229      10.109  53.238  80.161  1.00  1.00          
ATOM   1853  CE1 PHE   229       8.745  53.929  77.815  1.00  1.00          
ATOM   1854  CE2 PHE   229       8.914  52.589  79.829  1.00  1.00          
ATOM   1855  CZ  PHE   229       8.232  52.934  78.655  1.00  1.00          
ATOM   1856  C   PHE   229      13.256  53.233  78.427  1.00  1.00          
ATOM   1857  O   PHE   229      12.760  52.563  77.521  1.00  1.00          
ATOM   1858  N   MET   230      14.087  52.725  79.331  1.00  1.00          
ATOM   1859  CA  MET   230      14.474  51.319  79.313  1.00  1.00          
ATOM   1860  CB  MET   230      15.321  51.013  78.076  1.00  1.00          
ATOM   1861  CG  MET   230      15.539  49.504  77.967  1.00  1.00          
ATOM   1862  SD  MET   230      17.003  49.034  78.924  1.00  1.00          
ATOM   1863  CE  MET   230      17.963  50.539  78.621  1.00  1.00          
ATOM   1864  C   MET   230      15.237  50.941  80.577  1.00  1.00          
ATOM   1865  O   MET   230      16.379  51.356  80.773  1.00  1.00          
ATOM   1866  N   HIS   231      14.598  50.149  81.432  1.00  1.00          
ATOM   1867  CA  HIS   231      15.215  49.713  82.679  1.00  1.00          
ATOM   1868  CB  HIS   231      14.168  49.098  83.610  1.00  1.00          
ATOM   1869  CG  HIS   231      12.989  50.026  83.720  1.00  1.00          
ATOM   1870  ND1 HIS   231      12.314  50.498  82.607  1.00  1.00          
ATOM   1871  CD2 HIS   231      12.355  50.578  84.807  1.00  1.00          
ATOM   1872  CE1 HIS   231      11.322  51.297  83.042  1.00  1.00          
ATOM   1873  NE2 HIS   231      11.302  51.381  84.375  1.00  1.00          
ATOM   1874  C   HIS   231      16.336  48.711  82.420  1.00  1.00          
ATOM   1875  O   HIS   231      16.350  48.032  81.393  1.00  1.00          
ATOM   1876  N   THR   232      17.276  48.626  83.356  1.00  1.00          
ATOM   1877  CA  THR   232      18.402  47.709  83.231  1.00  1.00          
ATOM   1878  CB  THR   232      18.443  46.744  84.418  1.00  1.00          
ATOM   1879  OG1 THR   232      19.573  45.892  84.297  1.00  1.00          
ATOM   1880  CG2 THR   232      17.167  45.902  84.436  1.00  1.00          
ATOM   1881  C   THR   232      19.722  48.466  83.125  1.00  1.00          
ATOM   1882  O   THR   232      20.081  49.233  84.018  1.00  1.00          
ATOM   1883  N   MET   233      20.438  48.247  82.027  1.00  1.00          
ATOM   1884  CA  MET   233      21.717  48.908  81.802  1.00  1.00          
ATOM   1885  CB  MET   233      22.698  48.574  82.929  1.00  1.00          
ATOM   1886  CG  MET   233      23.895  47.815  82.353  1.00  1.00          
ATOM   1887  SD  MET   233      23.687  46.042  82.654  1.00  1.00          
ATOM   1888  CE  MET   233      25.287  45.757  83.449  1.00  1.00          
ATOM   1889  C   MET   233      21.546  50.419  81.686  1.00  1.00          
ATOM   1890  O   MET   233      20.452  50.910  81.409  1.00  1.00          
ATOM   1891  N   LYS   234      22.635  51.150  81.901  1.00  1.00          
ATOM   1892  CA  LYS   234      22.608  52.606  81.821  1.00  1.00          
ATOM   1893  CB  LYS   234      22.029  53.045  80.469  1.00  1.00          
ATOM   1894  CG  LYS   234      20.576  53.492  80.637  1.00  1.00          
ATOM   1895  CD  LYS   234      19.831  53.316  79.311  1.00  1.00          
ATOM   1896  CE  LYS   234      18.449  53.963  79.412  1.00  1.00          
ATOM   1897  NZ  LYS   234      18.035  54.463  78.071  1.00  1.00          
ATOM   1898  C   LYS   234      21.791  53.177  82.972  1.00  1.00          
ATOM   1899  O   LYS   234      20.624  52.817  83.138  1.00  1.00          
ATOM   1900  N   ASN   235      22.389  54.048  83.798  1.00  1.00          
ATOM   1901  CA  ASN   235      21.607  54.575  84.916  1.00  1.00          
ATOM   1902  CB  ASN   235      21.305  53.466  85.922  1.00  1.00          
ATOM   1903  CG  ASN   235      19.862  52.999  85.772  1.00  1.00          
ATOM   1904  OD1 ASN   235      18.940  53.674  86.232  1.00  1.00          
ATOM   1905  ND2 ASN   235      19.609  51.881  85.148  1.00  1.00          
ATOM   1906  C   ASN   235      22.167  55.808  85.634  1.00  1.00          
ATOM   1907  O   ASN   235      21.530  56.320  86.554  1.00  1.00          
ATOM   1908  N   THR   236      23.340  56.277  85.248  1.00  1.00          
ATOM   1909  CA  THR   236      23.933  57.439  85.911  1.00  1.00          
ATOM   1910  CB  THR   236      24.378  57.084  87.326  1.00  1.00          
ATOM   1911  OG1 THR   236      24.678  55.704  87.403  1.00  1.00          
ATOM   1912  CG2 THR   236      23.243  57.402  88.304  1.00  1.00          
ATOM   1913  C   THR   236      22.955  58.611  85.981  1.00  1.00          
ATOM   1914  O   THR   236      21.786  58.482  85.623  1.00  1.00          
ATOM   1915  N   GLY   237      23.443  59.750  86.468  1.00  1.00          
ATOM   1916  CA  GLY   237      22.619  60.946  86.606  1.00  1.00          
ATOM   1917  C   GLY   237      23.479  62.194  86.814  1.00  1.00          
ATOM   1918  O   GLY   237      24.667  62.089  87.114  1.00  1.00          
ATOM   1919  N   ARG   238      22.860  63.372  86.643  1.00  1.00          
ATOM   1920  CA  ARG   238      23.533  64.672  86.790  1.00  1.00          
ATOM   1921  CB  ARG   238      25.052  64.560  86.626  1.00  1.00          
ATOM   1922  CG  ARG   238      25.373  63.960  85.256  1.00  1.00          
ATOM   1923  CD  ARG   238      24.388  64.502  84.216  1.00  1.00          
ATOM   1924  NE  ARG   238      24.436  65.960  84.181  1.00  1.00          
ATOM   1925  CZ  ARG   238      23.359  66.699  84.423  1.00  1.00          
ATOM   1926  NH1 ARG   238      23.476  67.988  84.587  1.00  1.00          
ATOM   1927  NH2 ARG   238      22.185  66.135  84.501  1.00  1.00          
ATOM   1928  C   ARG   238      23.182  65.391  88.096  1.00  1.00          
ATOM   1929  O   ARG   238      23.627  66.516  88.327  1.00  1.00          
ATOM   1930  N   ASN   239      22.381  64.750  88.940  1.00  1.00          
ATOM   1931  CA  ASN   239      21.972  65.341  90.212  1.00  1.00          
ATOM   1932  CB  ASN   239      21.263  66.677  89.978  1.00  1.00          
ATOM   1933  CG  ASN   239      21.320  67.530  91.240  1.00  1.00          
ATOM   1934  OD1 ASN   239      21.339  66.998  92.350  1.00  1.00          
ATOM   1935  ND2 ASN   239      21.349  68.831  91.135  1.00  1.00          
ATOM   1936  C   ASN   239      23.159  65.534  91.153  1.00  1.00          
ATOM   1937  O   ASN   239      23.099  65.159  92.322  1.00  1.00          
ATOM   1938  N   VAL   240      24.236  66.119  90.636  1.00  1.00          
ATOM   1939  CA  VAL   240      25.432  66.355  91.437  1.00  1.00          
ATOM   1940  CB  VAL   240      26.124  65.035  91.776  1.00  1.00          
ATOM   1941  CG1 VAL   240      25.668  64.558  93.157  1.00  1.00          
ATOM   1942  CG2 VAL   240      27.639  65.242  91.783  1.00  1.00          
ATOM   1943  C   VAL   240      25.106  67.123  92.718  1.00  1.00          
ATOM   1944  O   VAL   240      25.922  67.183  93.634  1.00  1.00          
ATOM   1945  N   ASN   241      23.911  67.708  92.767  1.00  1.00          
ATOM   1946  CA  ASN   241      23.452  68.487  93.922  1.00  1.00          
ATOM   1947  CB  ASN   241      24.613  69.196  94.637  1.00  1.00          
ATOM   1948  CG  ASN   241      25.118  68.375  95.826  1.00  1.00          
ATOM   1949  OD1 ASN   241      24.367  68.109  96.764  1.00  1.00          
ATOM   1950  ND2 ASN   241      26.360  67.973  95.850  1.00  1.00          
ATOM   1951  C   ASN   241      22.628  67.653  94.903  1.00  1.00          
ATOM   1952  O   ASN   241      22.086  68.183  95.872  1.00  1.00          
ATOM   1953  N   ASP   242      22.536  66.351  94.644  1.00  1.00          
ATOM   1954  CA  ASP   242      21.772  65.447  95.503  1.00  1.00          
ATOM   1955  CB  ASP   242      20.492  66.119  96.004  1.00  1.00          
ATOM   1956  CG  ASP   242      19.491  65.061  96.458  1.00  1.00          
ATOM   1957  OD1 ASP   242      19.070  65.123  97.601  1.00  1.00          
ATOM   1958  OD2 ASP   242      19.163  64.202  95.656  1.00  1.00          
ATOM   1959  C   ASP   242      22.603  64.942  96.679  1.00  1.00          
ATOM   1960  O   ASP   242      23.802  64.698  96.544  1.00  1.00          
TER
END
