
#######################################################
#                                                     #
#                        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 (  177),  selected   21 , name T0386TS022_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS022_4-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    K     222      N     219          0.944
LGA    I     223      P     220          1.699
LGA    R     224      E     221          1.792
LGA    L     225      K     222          1.087
LGA    L     226      I     223          0.495
LGA    K     227      R     224          0.560
LGA    E     228      L     225          0.987
LGA    F     229      L     226          1.497
LGA    M     230      K     227          1.276
LGA    H     231      E     228          0.624
LGA    T     232      F     229          0.875
LGA    M     233      M     230          1.166
LGA    K     234      H     231          0.841
LGA    N     235      T     232          1.050
LGA    T     236      M     233          1.216
LGA    G     237      K     234          1.253
LGA    R     238      N     235          1.672
LGA    N     239      T     236          2.091
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    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
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    -       -      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)   21   81    5.0     18    1.25     5.56     21.269     1.333

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.021799 * X  +  -0.853680 * Y  +  -0.520341 * Z  + -32.160015
  Y_new =  -0.905280 * X  +   0.237718 * Y  +  -0.352078 * Z  + 103.911980
  Z_new =   0.424256 * X  +   0.463379 * Y  +  -0.778002 * Z  +  64.079857 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.604414   -0.537179  [ DEG:   149.2219    -30.7781 ]
  Theta =  -0.438140   -2.703453  [ DEG:   -25.1036   -154.8964 ]
  Phi   =  -1.594872    1.546721  [ DEG:   -91.3794     88.6206 ]
 
# 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: T0386TS022_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS022_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   81   5.0   18   1.25    5.56  21.269
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS022_4-D2
PFRMAT TS
TARGET T0386
MODEL  4
PARENT 1vfg_A
ATOM   1669  N   ASN   219      -2.344  52.986  74.826  1.00  0.00
ATOM   1670  CA  ASN   219      -0.930  52.814  74.759  1.00  0.00
ATOM   1671  C   ASN   219      -0.347  53.632  75.858  1.00  0.00
ATOM   1672  O   ASN   219       0.407  54.575  75.627  1.00  0.00
ATOM   1673  CB  ASN   219      -0.396  53.284  73.405  1.00  0.00
ATOM   1674  CG  ASN   219       1.028  52.830  73.150  1.00  0.00
ATOM   1675  OD1 ASN   219       1.758  52.491  74.081  1.00  0.00
ATOM   1676  ND2 ASN   219       1.428  52.822  71.884  1.00  0.00
ATOM   1677  N   PRO   220      -0.676  53.264  77.061  1.00  0.00
ATOM   1678  CA  PRO   220      -0.217  53.984  78.210  1.00  0.00
ATOM   1679  C   PRO   220       1.275  54.029  78.194  1.00  0.00
ATOM   1680  O   PRO   220       1.842  55.029  78.633  1.00  0.00
ATOM   1681  CB  PRO   220      -0.761  53.181  79.392  1.00  0.00
ATOM   1682  CG  PRO   220      -1.991  52.522  78.863  1.00  0.00
ATOM   1683  CD  PRO   220      -1.676  52.130  77.447  1.00  0.00
ATOM   1684  N   GLU   221       1.935  52.957  77.713  1.00  0.00
ATOM   1685  CA  GLU   221       3.369  52.940  77.738  1.00  0.00
ATOM   1686  C   GLU   221       3.856  54.021  76.834  1.00  0.00
ATOM   1687  O   GLU   221       4.818  54.721  77.144  1.00  0.00
ATOM   1688  CB  GLU   221       3.896  51.587  77.257  1.00  0.00
ATOM   1689  CG  GLU   221       3.651  50.444  78.230  1.00  0.00
ATOM   1690  CD  GLU   221       4.076  49.101  77.668  1.00  0.00
ATOM   1691  OE1 GLU   221       4.493  49.054  76.492  1.00  0.00
ATOM   1692  OE2 GLU   221       3.991  48.096  78.405  1.00  0.00
ATOM   1693  N   LYS   222       3.176  54.186  75.687  1.00  0.00
ATOM   1694  CA  LYS   222       3.516  55.185  74.719  1.00  0.00
ATOM   1695  C   LYS   222       3.274  56.520  75.332  1.00  0.00
ATOM   1696  O   LYS   222       3.851  57.517  74.908  1.00  0.00
ATOM   1697  CB  LYS   222       2.654  55.030  73.464  1.00  0.00
ATOM   1698  CG  LYS   222       3.028  55.975  72.333  1.00  0.00
ATOM   1699  CD  LYS   222       4.350  55.577  71.696  1.00  0.00
ATOM   1700  CE  LYS   222       4.679  56.466  70.508  1.00  0.00
ATOM   1701  NZ  LYS   222       5.910  56.016  69.802  1.00  0.00
ATOM   1702  N   ILE   223       2.403  56.567  76.353  1.00  0.00
ATOM   1703  CA  ILE   223       2.040  57.794  76.999  1.00  0.00
ATOM   1704  C   ILE   223       3.189  58.079  77.908  1.00  0.00
ATOM   1705  O   ILE   223       4.033  57.214  78.106  1.00  0.00
ATOM   1706  CB  ILE   223       0.726  57.649  77.789  1.00  0.00
ATOM   1707  CG1 ILE   223      -0.449  57.429  76.834  1.00  0.00
ATOM   1708  CG2 ILE   223       0.454  58.903  78.607  1.00  0.00
ATOM   1709  CD1 ILE   223      -1.733  57.030  77.528  1.00  0.00
ATOM   1710  N   ARG   224       3.334  59.329  78.384  1.00  0.00
ATOM   1711  CA  ARG   224       4.376  59.615  79.331  1.00  0.00
ATOM   1712  C   ARG   224       5.673  59.792  78.615  1.00  0.00
ATOM   1713  O   ARG   224       6.344  60.803  78.800  1.00  0.00
ATOM   1714  CB  ARG   224       4.519  58.469  80.333  1.00  0.00
ATOM   1715  CG  ARG   224       3.321  58.296  81.254  1.00  0.00
ATOM   1716  CD  ARG   224       3.495  57.094  82.168  1.00  0.00
ATOM   1717  NE  ARG   224       2.332  56.886  83.027  1.00  0.00
ATOM   1718  CZ  ARG   224       2.238  55.921  83.936  1.00  0.00
ATOM   1719  NH1 ARG   224       1.140  55.809  84.672  1.00  0.00
ATOM   1720  NH2 ARG   224       3.240  55.070  84.106  1.00  0.00
ATOM   1721  N   LEU   225       6.075  58.810  77.788  1.00  0.00
ATOM   1722  CA  LEU   225       7.325  58.929  77.101  1.00  0.00
ATOM   1723  C   LEU   225       7.201  60.164  76.273  1.00  0.00
ATOM   1724  O   LEU   225       8.088  61.016  76.275  1.00  0.00
ATOM   1725  CB  LEU   225       7.572  57.700  76.223  1.00  0.00
ATOM   1726  CG  LEU   225       7.870  56.391  76.956  1.00  0.00
ATOM   1727  CD1 LEU   225       7.904  55.224  75.982  1.00  0.00
ATOM   1728  CD2 LEU   225       9.218  56.464  77.658  1.00  0.00
ATOM   1729  N   LEU   226       6.072  60.293  75.555  1.00  0.00
ATOM   1730  CA  LEU   226       5.830  61.462  74.763  1.00  0.00
ATOM   1731  C   LEU   226       5.625  62.627  75.676  1.00  0.00
ATOM   1732  O   LEU   226       6.040  63.744  75.372  1.00  0.00
ATOM   1733  CB  LEU   226       4.584  61.274  73.896  1.00  0.00
ATOM   1734  CG  LEU   226       4.218  62.437  72.972  1.00  0.00
ATOM   1735  CD1 LEU   226       5.341  62.712  71.984  1.00  0.00
ATOM   1736  CD2 LEU   226       2.957  62.122  72.183  1.00  0.00
ATOM   1737  N   LYS   227       4.981  62.393  76.834  1.00  0.00
ATOM   1738  CA  LYS   227       4.686  63.476  77.730  1.00  0.00
ATOM   1739  C   LYS   227       5.972  64.126  78.134  1.00  0.00
ATOM   1740  O   LYS   227       6.067  65.350  78.189  1.00  0.00
ATOM   1741  CB  LYS   227       3.966  62.960  78.977  1.00  0.00
ATOM   1742  CG  LYS   227       3.573  64.048  79.963  1.00  0.00
ATOM   1743  CD  LYS   227       2.794  63.475  81.136  1.00  0.00
ATOM   1744  CE  LYS   227       2.427  64.559  82.137  1.00  0.00
ATOM   1745  NZ  LYS   227       1.676  64.010  83.299  1.00  0.00
ATOM   1746  N   GLU   228       6.995  63.305  78.427  1.00  0.00
ATOM   1747  CA  GLU   228       8.290  63.754  78.851  1.00  0.00
ATOM   1748  C   GLU   228       8.956  64.467  77.720  1.00  0.00
ATOM   1749  O   GLU   228       9.700  65.423  77.934  1.00  0.00
ATOM   1750  CB  GLU   228       9.157  62.567  79.275  1.00  0.00
ATOM   1751  CG  GLU   228       8.712  61.903  80.567  1.00  0.00
ATOM   1752  CD  GLU   228       9.537  60.677  80.907  1.00  0.00
ATOM   1753  OE1 GLU   228      10.415  60.310  80.099  1.00  0.00
ATOM   1754  OE2 GLU   228       9.304  60.083  81.981  1.00  0.00
ATOM   1755  N   PHE   229       8.696  64.023  76.478  1.00  0.00
ATOM   1756  CA  PHE   229       9.366  64.569  75.333  1.00  0.00
ATOM   1757  C   PHE   229       9.122  66.041  75.265  1.00  0.00
ATOM   1758  O   PHE   229      10.057  66.820  75.080  1.00  0.00
ATOM   1759  CB  PHE   229       8.847  63.921  74.048  1.00  0.00
ATOM   1760  CG  PHE   229       9.244  62.480  73.893  1.00  0.00
ATOM   1761  CD1 PHE   229      10.229  61.929  74.693  1.00  0.00
ATOM   1762  CD2 PHE   229       8.632  61.677  72.946  1.00  0.00
ATOM   1763  CE1 PHE   229      10.594  60.604  74.550  1.00  0.00
ATOM   1764  CE2 PHE   229       8.999  60.352  72.804  1.00  0.00
ATOM   1765  CZ  PHE   229       9.975  59.815  73.600  1.00  0.00
ATOM   1766  N   MET   230       7.863  66.474  75.439  1.00  0.00
ATOM   1767  CA  MET   230       7.581  67.872  75.320  1.00  0.00
ATOM   1768  C   MET   230       8.388  68.595  76.347  1.00  0.00
ATOM   1769  O   MET   230       8.966  69.643  76.068  1.00  0.00
ATOM   1770  CB  MET   230       6.092  68.140  75.552  1.00  0.00
ATOM   1771  CG  MET   230       5.189  67.618  74.446  1.00  0.00
ATOM   1772  SD  MET   230       5.534  68.378  72.848  1.00  0.00
ATOM   1773  CE  MET   230       4.975  70.053  73.142  1.00  0.00
ATOM   1774  N   HIS   231       8.452  68.043  77.571  1.00  0.00
ATOM   1775  CA  HIS   231       9.183  68.681  78.625  1.00  0.00
ATOM   1776  C   HIS   231      10.639  68.703  78.274  1.00  0.00
ATOM   1777  O   HIS   231      11.315  69.712  78.468  1.00  0.00
ATOM   1778  CB  HIS   231       8.998  67.922  79.941  1.00  0.00
ATOM   1779  CG  HIS   231       9.707  68.545  81.103  1.00  0.00
ATOM   1780  ND1 HIS   231       9.314  69.743  81.659  1.00  0.00
ATOM   1781  CD2 HIS   231      10.854  68.197  81.929  1.00  0.00
ATOM   1782  CE1 HIS   231      10.136  70.045  82.679  1.00  0.00
ATOM   1783  NE2 HIS   231      11.063  69.120  82.847  1.00  0.00
ATOM   1784  N   THR   232      11.155  67.588  77.725  1.00  0.00
ATOM   1785  CA  THR   232      12.557  67.468  77.445  1.00  0.00
ATOM   1786  C   THR   232      12.962  68.521  76.466  1.00  0.00
ATOM   1787  O   THR   232      13.963  69.211  76.653  1.00  0.00
ATOM   1788  CB  THR   232      12.898  66.091  76.847  1.00  0.00
ATOM   1789  OG1 THR   232      12.570  65.063  77.790  1.00  0.00
ATOM   1790  CG2 THR   232      14.380  66.004  76.521  1.00  0.00
ATOM   1791  N   MET   233      12.170  68.701  75.400  1.00  0.00
ATOM   1792  CA  MET   233      12.525  69.667  74.408  1.00  0.00
ATOM   1793  C   MET   233      12.524  70.996  75.077  1.00  0.00
ATOM   1794  O   MET   233      13.348  71.854  74.775  1.00  0.00
ATOM   1795  CB  MET   233      11.513  69.653  73.260  1.00  0.00
ATOM   1796  CG  MET   233      11.565  68.398  72.403  1.00  0.00
ATOM   1797  SD  MET   233      13.161  68.174  71.594  1.00  0.00
ATOM   1798  CE  MET   233      13.139  69.528  70.421  1.00  0.00
ATOM   1799  N   LYS   234      11.594  71.199  76.021  1.00  0.00
ATOM   1800  CA  LYS   234      11.487  72.469  76.668  1.00  0.00
ATOM   1801  C   LYS   234      12.769  72.773  77.375  1.00  0.00
ATOM   1802  O   LYS   234      13.278  73.889  77.283  1.00  0.00
ATOM   1803  CB  LYS   234      10.345  72.457  77.687  1.00  0.00
ATOM   1804  CG  LYS   234       8.959  72.409  77.065  1.00  0.00
ATOM   1805  CD  LYS   234       7.875  72.401  78.132  1.00  0.00
ATOM   1806  CE  LYS   234       6.490  72.328  77.510  1.00  0.00
ATOM   1807  NZ  LYS   234       5.419  72.286  78.545  1.00  0.00
ATOM   1808  N   ASN   235      13.347  71.784  78.084  1.00  0.00
ATOM   1809  CA  ASN   235      14.531  72.086  78.832  1.00  0.00
ATOM   1810  C   ASN   235      15.627  72.474  77.901  1.00  0.00
ATOM   1811  O   ASN   235      16.335  73.448  78.155  1.00  0.00
ATOM   1812  CB  ASN   235      14.978  70.868  79.642  1.00  0.00
ATOM   1813  CG  ASN   235      14.077  70.596  80.830  1.00  0.00
ATOM   1814  OD1 ASN   235      13.348  71.478  81.284  1.00  0.00
ATOM   1815  ND2 ASN   235      14.125  69.369  81.339  1.00  0.00
ATOM   1816  N   THR   236      15.801  71.741  76.785  1.00  0.00
ATOM   1817  CA  THR   236      16.849  72.151  75.907  1.00  0.00
ATOM   1818  C   THR   236      16.482  73.512  75.420  1.00  0.00
ATOM   1819  O   THR   236      17.300  74.429  75.493  1.00  0.00
ATOM   1820  CB  THR   236      16.998  71.186  74.716  1.00  0.00
ATOM   1821  OG1 THR   236      17.340  69.879  75.196  1.00  0.00
ATOM   1822  CG2 THR   236      18.092  71.666  73.775  1.00  0.00
ATOM   1823  N   GLY   237      15.214  73.670  74.974  1.00  0.00
ATOM   1824  CA  GLY   237      14.684  74.910  74.489  1.00  0.00
ATOM   1825  C   GLY   237      15.687  75.409  73.530  1.00  0.00
ATOM   1826  O   GLY   237      15.869  74.877  72.436  1.00  0.00
ATOM   1827  N   ARG   238      16.370  76.480  73.947  1.00  0.00
ATOM   1828  CA  ARG   238      17.475  76.924  73.177  1.00  0.00
ATOM   1829  C   ARG   238      18.641  76.401  73.939  1.00  0.00
ATOM   1830  O   ARG   238      18.691  76.526  75.161  1.00  0.00
ATOM   1831  CB  ARG   238      17.484  78.451  73.082  1.00  0.00
ATOM   1832  CG  ARG   238      18.582  79.012  72.193  1.00  0.00
ATOM   1833  CD  ARG   238      18.508  80.528  72.115  1.00  0.00
ATOM   1834  NE  ARG   238      19.529  81.080  71.228  1.00  0.00
ATOM   1835  CZ  ARG   238      19.801  82.377  71.118  1.00  0.00
ATOM   1836  NH1 ARG   238      20.748  82.787  70.285  1.00  0.00
ATOM   1837  NH2 ARG   238      19.126  83.259  71.841  1.00  0.00
ATOM   1838  N   ASN   239      19.587  75.753  73.237  1.00  0.00
ATOM   1839  CA  ASN   239      20.720  75.191  73.907  1.00  0.00
ATOM   1840  C   ASN   239      21.383  76.302  74.707  1.00  0.00
ATOM   1841  O   ASN   239      21.391  76.196  75.962  1.00  0.00
ATOM   1842  CB  ASN   239      21.712  74.617  72.894  1.00  0.00
ATOM   1843  CG  ASN   239      22.803  73.794  73.548  1.00  0.00
ATOM   1844  OD1 ASN   239      22.624  73.271  74.648  1.00  0.00
ATOM   1845  ND2 ASN   239      23.940  73.675  72.872  1.00  0.00
TER
END
