
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS030_3-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    N     219      K     222          3.701
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    P     220      V     247          3.572
LGA    E     221      A     248          2.258
LGA    K     222      K     249          2.569
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    I     223      E     252          4.849
LGA    R     224      T     253           #
LGA    L     225      Y     254          4.400
LGA    L     226      T     255          1.945
LGA    K     227      G     256          2.691
LGA    E     228      T     257          1.808
LGA    F     229      Y     258          2.069
LGA    M     230      R     259          1.900
LGA    H     231      G     260          1.955
LGA    T     232      A     261          2.126
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    M     233      F     266          1.132
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    K     234      G     277          3.219
LGA    N     235      N     278          2.858
LGA    T     236      I     279          3.780
LGA    G     237      D     280          3.711
LGA    R     238      H     281           #
LGA    N     239      L     282           -
LGA    V     240      P     283           -
LGA    N     241      P     284           -
LGA    D     242      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      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     18    2.98    11.11     14.850     0.585

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.006246 * X  +  -0.803658 * Y  +  -0.595059 * Z  +  40.784397
  Y_new =  -0.678058 * X  +   0.440778 * Y  +  -0.588177 * Z  +  45.877567
  Z_new =   0.734982 * X  +   0.399811 * Y  +  -0.547679 * Z  +  63.052158 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.511009   -0.630584  [ DEG:   143.8702    -36.1298 ]
  Theta =  -0.825640   -2.315953  [ DEG:   -47.3057   -132.6943 ]
  Phi   =  -1.580007    1.561585  [ DEG:   -90.5277     89.4723 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS030_3-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   18   2.98   11.11  14.850
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS030_3-D2
PFRMAT TS
TARGET T0386
MODEL 3 
PARENT 2g03A
ATOM   1761  N   ASN   219       6.566  56.221  78.270  1.00  1.00          
ATOM   1762  CA  ASN   219       6.682  54.829  77.851  1.00  1.00          
ATOM   1763  CB  ASN   219       6.367  54.686  76.360  1.00  1.00          
ATOM   1764  CG  ASN   219       6.262  53.210  75.989  1.00  1.00          
ATOM   1765  OD1 ASN   219       6.544  52.833  74.852  1.00  1.00          
ATOM   1766  ND2 ASN   219       5.873  52.348  76.887  1.00  1.00          
ATOM   1767  C   ASN   219       8.071  54.276  78.151  1.00  1.00          
ATOM   1768  O   ASN   219       8.220  53.324  78.916  1.00  1.00          
ATOM   1769  N   PRO   220       9.080  54.857  77.562  1.00  1.00          
ATOM   1770  CA  PRO   220      10.491  54.420  77.763  1.00  1.00          
ATOM   1771  CB  PRO   220      11.298  55.572  77.159  1.00  1.00          
ATOM   1772  CG  PRO   220      10.408  56.142  76.106  1.00  1.00          
ATOM   1773  CD  PRO   220       8.980  55.997  76.635  1.00  1.00          
ATOM   1774  C   PRO   220      10.828  54.263  79.242  1.00  1.00          
ATOM   1775  O   PRO   220      10.108  54.760  80.108  1.00  1.00          
ATOM   1776  N   GLU   221      11.927  53.571  79.524  1.00  1.00          
ATOM   1777  CA  GLU   221      12.361  53.348  80.897  1.00  1.00          
ATOM   1778  CB  GLU   221      12.724  54.675  81.567  1.00  1.00          
ATOM   1779  CG  GLU   221      14.236  54.737  81.792  1.00  1.00          
ATOM   1780  CD  GLU   221      14.824  55.946  81.072  1.00  1.00          
ATOM   1781  OE1 GLU   221      15.408  55.756  80.018  1.00  1.00          
ATOM   1782  OE2 GLU   221      14.680  57.044  81.585  1.00  1.00          
ATOM   1783  C   GLU   221      13.547  52.391  80.954  1.00  1.00          
ATOM   1784  O   GLU   221      13.796  51.756  81.978  1.00  1.00          
ATOM   1785  N   LYS   222      14.275  52.294  79.846  1.00  1.00          
ATOM   1786  CA  LYS   222      15.436  51.415  79.767  1.00  1.00          
ATOM   1787  CB  LYS   222      15.600  50.868  78.347  1.00  1.00          
ATOM   1788  CG  LYS   222      15.804  52.031  77.374  1.00  1.00          
ATOM   1789  CD  LYS   222      16.044  51.480  75.966  1.00  1.00          
ATOM   1790  CE  LYS   222      16.678  50.092  76.061  1.00  1.00          
ATOM   1791  NZ  LYS   222      17.564  49.869  74.884  1.00  1.00          
ATOM   1792  C   LYS   222      16.707  52.139  80.201  1.00  1.00          
ATOM   1793  O   LYS   222      16.841  53.346  80.005  1.00  1.00          
ATOM   1794  N   ILE   223      17.636  51.392  80.789  1.00  1.00          
ATOM   1795  CA  ILE   223      18.896  51.961  81.252  1.00  1.00          
ATOM   1796  CB  ILE   223      19.497  51.100  82.364  1.00  1.00          
ATOM   1797  CG1 ILE   223      18.761  51.375  83.677  1.00  1.00          
ATOM   1798  CG2 ILE   223      20.980  51.440  82.529  1.00  1.00          
ATOM   1799  CD1 ILE   223      17.503  52.199  83.394  1.00  1.00          
ATOM   1800  C   ILE   223      19.889  52.104  80.103  1.00  1.00          
ATOM   1801  O   ILE   223      20.040  51.198  79.284  1.00  1.00          
ATOM   1802  N   ARG   224      20.566  53.246  80.051  1.00  1.00          
ATOM   1803  CA  ARG   224      21.547  53.509  79.005  1.00  1.00          
ATOM   1804  CB  ARG   224      21.817  55.011  78.889  1.00  1.00          
ATOM   1805  CG  ARG   224      22.876  55.257  77.812  1.00  1.00          
ATOM   1806  CD  ARG   224      23.254  56.740  77.798  1.00  1.00          
ATOM   1807  NE  ARG   224      22.882  57.349  76.527  1.00  1.00          
ATOM   1808  CZ  ARG   224      23.765  57.513  75.547  1.00  1.00          
ATOM   1809  NH1 ARG   224      23.654  56.821  74.446  1.00  1.00          
ATOM   1810  NH2 ARG   224      24.741  58.367  75.685  1.00  1.00          
ATOM   1811  C   ARG   224      22.849  52.761  79.270  1.00  1.00          
ATOM   1812  O   ARG   224      23.163  51.783  78.591  1.00  1.00          
ATOM   1813  N   LEU   225      23.603  53.228  80.258  1.00  1.00          
ATOM   1814  CA  LEU   225      24.873  52.605  80.614  1.00  1.00          
ATOM   1815  CB  LEU   225      26.045  53.475  80.154  1.00  1.00          
ATOM   1816  CG  LEU   225      25.607  54.334  78.966  1.00  1.00          
ATOM   1817  CD1 LEU   225      26.659  55.413  78.702  1.00  1.00          
ATOM   1818  CD2 LEU   225      25.459  53.452  77.724  1.00  1.00          
ATOM   1819  C   LEU   225      24.963  52.355  82.116  1.00  1.00          
ATOM   1820  O   LEU   225      24.590  51.287  82.600  1.00  1.00          
ATOM   1821  N   LEU   226      25.461  53.347  82.846  1.00  1.00          
ATOM   1822  CA  LEU   226      25.601  53.236  84.293  1.00  1.00          
ATOM   1823  CB  LEU   226      27.008  53.651  84.728  1.00  1.00          
ATOM   1824  CG  LEU   226      27.762  54.236  83.532  1.00  1.00          
ATOM   1825  CD1 LEU   226      28.885  55.146  84.032  1.00  1.00          
ATOM   1826  CD2 LEU   226      28.357  53.101  82.698  1.00  1.00          
ATOM   1827  C   LEU   226      24.559  54.085  85.015  1.00  1.00          
ATOM   1828  O   LEU   226      23.590  53.562  85.564  1.00  1.00          
ATOM   1829  N   LYS   227      24.765  55.399  85.009  1.00  1.00          
ATOM   1830  CA  LYS   227      23.846  56.321  85.662  1.00  1.00          
ATOM   1831  CB  LYS   227      24.184  56.453  87.148  1.00  1.00          
ATOM   1832  CG  LYS   227      23.320  55.481  87.956  1.00  1.00          
ATOM   1833  CD  LYS   227      22.891  56.147  89.265  1.00  1.00          
ATOM   1834  CE  LYS   227      21.712  57.085  88.998  1.00  1.00          
ATOM   1835  NZ  LYS   227      21.937  58.380  89.703  1.00  1.00          
ATOM   1836  C   LYS   227      23.874  57.692  84.995  1.00  1.00          
ATOM   1837  O   LYS   227      23.190  57.923  83.998  1.00  1.00          
ATOM   1838  N   GLU   228      24.670  58.600  85.552  1.00  1.00          
ATOM   1839  CA  GLU   228      24.789  59.950  85.013  1.00  1.00          
ATOM   1840  CB  GLU   228      24.930  59.907  83.490  1.00  1.00          
ATOM   1841  CG  GLU   228      26.383  59.605  83.120  1.00  1.00          
ATOM   1842  CD  GLU   228      26.606  58.098  83.063  1.00  1.00          
ATOM   1843  OE1 GLU   228      27.756  57.688  83.074  1.00  1.00          
ATOM   1844  OE2 GLU   228      25.625  57.374  83.009  1.00  1.00          
ATOM   1845  C   GLU   228      23.590  60.807  85.404  1.00  1.00          
ATOM   1846  O   GLU   228      23.051  60.672  86.503  1.00  1.00          
ATOM   1847  N   PHE   229      23.179  61.689  84.499  1.00  1.00          
ATOM   1848  CA  PHE   229      22.044  62.570  84.748  1.00  1.00          
ATOM   1849  CB  PHE   229      20.832  61.763  85.218  1.00  1.00          
ATOM   1850  CG  PHE   229      20.269  60.978  84.058  1.00  1.00          
ATOM   1851  CD1 PHE   229      18.995  60.404  84.153  1.00  1.00          
ATOM   1852  CD2 PHE   229      21.019  60.824  82.885  1.00  1.00          
ATOM   1853  CE1 PHE   229      18.472  59.676  83.078  1.00  1.00          
ATOM   1854  CE2 PHE   229      20.496  60.097  81.810  1.00  1.00          
ATOM   1855  CZ  PHE   229      19.222  59.523  81.906  1.00  1.00          
ATOM   1856  C   PHE   229      22.392  63.640  85.778  1.00  1.00          
ATOM   1857  O   PHE   229      22.684  63.332  86.933  1.00  1.00          
ATOM   1858  N   MET   230      22.360  64.898  85.351  1.00  1.00          
ATOM   1859  CA  MET   230      22.672  66.015  86.234  1.00  1.00          
ATOM   1860  CB  MET   230      22.589  67.339  85.473  1.00  1.00          
ATOM   1861  CG  MET   230      22.276  67.064  84.001  1.00  1.00          
ATOM   1862  SD  MET   230      22.398  68.604  83.058  1.00  1.00          
ATOM   1863  CE  MET   230      22.358  69.737  84.469  1.00  1.00          
ATOM   1864  C   MET   230      21.736  66.044  87.438  1.00  1.00          
ATOM   1865  O   MET   230      21.878  65.247  88.366  1.00  1.00          
ATOM   1866  N   HIS   231      20.779  66.966  87.416  1.00  1.00          
ATOM   1867  CA  HIS   231      19.819  67.100  88.506  1.00  1.00          
ATOM   1868  CB  HIS   231      20.018  68.430  89.234  1.00  1.00          
ATOM   1869  CG  HIS   231      20.315  68.168  90.685  1.00  1.00          
ATOM   1870  ND1 HIS   231      21.554  68.438  91.245  1.00  1.00          
ATOM   1871  CD2 HIS   231      19.545  67.660  91.703  1.00  1.00          
ATOM   1872  CE1 HIS   231      21.494  68.095  92.544  1.00  1.00          
ATOM   1873  NE2 HIS   231      20.293  67.615  92.876  1.00  1.00          
ATOM   1874  C   HIS   231      18.387  66.991  87.993  1.00  1.00          
ATOM   1875  O   HIS   231      17.865  67.920  87.378  1.00  1.00          
ATOM   1876  N   THR   232      17.756  65.849  88.252  1.00  1.00          
ATOM   1877  CA  THR   232      16.384  65.617  87.818  1.00  1.00          
ATOM   1878  CB  THR   232      15.540  66.878  88.012  1.00  1.00          
ATOM   1879  OG1 THR   232      16.074  67.647  89.080  1.00  1.00          
ATOM   1880  CG2 THR   232      14.098  66.482  88.340  1.00  1.00          
ATOM   1881  C   THR   232      16.334  65.173  86.360  1.00  1.00          
ATOM   1882  O   THR   232      16.887  65.834  85.480  1.00  1.00          
ATOM   1883  N   MET   233      15.670  64.049  86.110  1.00  1.00          
ATOM   1884  CA  MET   233      15.547  63.516  84.759  1.00  1.00          
ATOM   1885  CB  MET   233      16.907  63.034  84.248  1.00  1.00          
ATOM   1886  CG  MET   233      17.597  64.170  83.489  1.00  1.00          
ATOM   1887  SD  MET   233      17.980  63.626  81.805  1.00  1.00          
ATOM   1888  CE  MET   233      18.889  65.104  81.291  1.00  1.00          
ATOM   1889  C   MET   233      14.535  62.376  84.706  1.00  1.00          
ATOM   1890  O   MET   233      14.737  61.326  85.316  1.00  1.00          
ATOM   1891  N   LYS   234      13.445  62.590  83.974  1.00  1.00          
ATOM   1892  CA  LYS   234      12.404  61.578  83.845  1.00  1.00          
ATOM   1893  CB  LYS   234      12.836  60.503  82.845  1.00  1.00          
ATOM   1894  CG  LYS   234      13.417  61.171  81.596  1.00  1.00          
ATOM   1895  CD  LYS   234      14.594  60.344  81.077  1.00  1.00          
ATOM   1896  CE  LYS   234      15.743  61.279  80.690  1.00  1.00          
ATOM   1897  NZ  LYS   234      15.529  61.782  79.304  1.00  1.00          
ATOM   1898  C   LYS   234      12.104  60.943  85.194  1.00  1.00          
ATOM   1899  O   LYS   234      12.789  60.007  85.609  1.00  1.00          
ATOM   1900  N   ASN   235      11.088  61.452  85.888  1.00  1.00          
ATOM   1901  CA  ASN   235      10.745  60.905  87.197  1.00  1.00          
ATOM   1902  CB  ASN   235      11.780  61.334  88.233  1.00  1.00          
ATOM   1903  CG  ASN   235      12.962  60.371  88.229  1.00  1.00          
ATOM   1904  OD1 ASN   235      12.775  59.154  88.222  1.00  1.00          
ATOM   1905  ND2 ASN   235      14.178  60.846  88.244  1.00  1.00          
ATOM   1906  C   ASN   235       9.338  61.276  87.678  1.00  1.00          
ATOM   1907  O   ASN   235       9.149  61.569  88.857  1.00  1.00          
ATOM   1908  N   THR   236       8.351  61.248  86.788  1.00  1.00          
ATOM   1909  CA  THR   236       6.983  61.565  87.175  1.00  1.00          
ATOM   1910  CB  THR   236       6.023  61.322  86.008  1.00  1.00          
ATOM   1911  OG1 THR   236       5.595  59.968  86.020  1.00  1.00          
ATOM   1912  CG2 THR   236       6.737  61.621  84.688  1.00  1.00          
ATOM   1913  C   THR   236       6.571  60.724  88.380  1.00  1.00          
ATOM   1914  O   THR   236       7.388  59.996  88.943  1.00  1.00          
ATOM   1915  N   GLY   237       5.307  60.825  88.777  1.00  1.00          
ATOM   1916  CA  GLY   237       4.820  60.065  89.921  1.00  1.00          
ATOM   1917  C   GLY   237       3.685  59.121  89.528  1.00  1.00          
ATOM   1918  O   GLY   237       2.745  59.528  88.846  1.00  1.00          
ATOM   1919  N   ARG   238       3.785  57.865  89.974  1.00  1.00          
ATOM   1920  CA  ARG   238       2.787  56.822  89.696  1.00  1.00          
ATOM   1921  CB  ARG   238       1.968  57.129  88.440  1.00  1.00          
ATOM   1922  CG  ARG   238       2.853  56.984  87.203  1.00  1.00          
ATOM   1923  CD  ARG   238       2.354  55.814  86.352  1.00  1.00          
ATOM   1924  NE  ARG   238       1.606  54.868  87.172  1.00  1.00          
ATOM   1925  CZ  ARG   238       1.752  53.555  87.032  1.00  1.00          
ATOM   1926  NH1 ARG   238       2.770  53.077  86.370  1.00  1.00          
ATOM   1927  NH2 ARG   238       0.877  52.742  87.558  1.00  1.00          
ATOM   1928  C   ARG   238       1.860  56.584  90.888  1.00  1.00          
ATOM   1929  O   ARG   238       1.516  55.443  91.196  1.00  1.00          
ATOM   1930  N   ASN   239       1.462  57.661  91.557  1.00  1.00          
ATOM   1931  CA  ASN   239       0.583  57.561  92.711  1.00  1.00          
ATOM   1932  CB  ASN   239       1.169  58.318  93.905  1.00  1.00          
ATOM   1933  CG  ASN   239       0.886  57.555  95.194  1.00  1.00          
ATOM   1934  OD1 ASN   239       1.746  56.826  95.687  1.00  1.00          
ATOM   1935  ND2 ASN   239      -0.279  57.674  95.769  1.00  1.00          
ATOM   1936  C   ASN   239      -0.818  58.070  92.400  1.00  1.00          
ATOM   1937  O   ASN   239      -1.328  58.950  93.089  1.00  1.00          
ATOM   1938  N   VAL   240      -1.439  57.510  91.365  1.00  1.00          
ATOM   1939  CA  VAL   240      -2.785  57.917  90.989  1.00  1.00          
ATOM   1940  CB  VAL   240      -2.766  59.234  90.208  1.00  1.00          
ATOM   1941  CG1 VAL   240      -2.217  60.357  91.091  1.00  1.00          
ATOM   1942  CG2 VAL   240      -4.188  59.584  89.763  1.00  1.00          
ATOM   1943  C   VAL   240      -3.682  58.032  92.223  1.00  1.00          
ATOM   1944  O   VAL   240      -4.660  58.776  92.222  1.00  1.00          
ATOM   1945  N   ASN   241      -3.329  57.282  93.272  1.00  1.00          
ATOM   1946  CA  ASN   241      -4.066  57.253  94.544  1.00  1.00          
ATOM   1947  CB  ASN   241      -5.518  57.709  94.384  1.00  1.00          
ATOM   1948  CG  ASN   241      -5.651  59.188  94.739  1.00  1.00          
ATOM   1949  OD1 ASN   241      -4.951  60.033  94.181  1.00  1.00          
ATOM   1950  ND2 ASN   241      -6.513  59.552  95.650  1.00  1.00          
ATOM   1951  C   ASN   241      -3.368  58.085  95.619  1.00  1.00          
ATOM   1952  O   ASN   241      -3.348  57.710  96.793  1.00  1.00          
ATOM   1953  N   ASP   242      -2.796  59.213  95.210  1.00  1.00          
ATOM   1954  CA  ASP   242      -2.093  60.103  96.128  1.00  1.00          
ATOM   1955  CB  ASP   242      -0.941  60.802  95.411  1.00  1.00          
ATOM   1956  CG  ASP   242       0.216  61.053  96.370  1.00  1.00          
ATOM   1957  OD1 ASP   242       0.034  60.852  97.561  1.00  1.00          
ATOM   1958  OD2 ASP   242       1.270  61.446  95.899  1.00  1.00          
ATOM   1959  C   ASP   242      -3.042  61.130  96.734  1.00  1.00          
ATOM   1960  O   ASP   242      -3.884  61.694  96.052  1.00  1.00          
TER     
END
