
#######################################################
#                                                     #
#                        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   20 (  157),  selected   20 , name T0316TS211_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS211_4-D2.T0316_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    G     220      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    R     221      A     234          1.447
LGA    M     222      G     235          0.271
LGA    -       -      L     236           -
LGA    M     223      M     237          3.186
LGA    T     224      Y     238          1.760
LGA    V     225      Y     239          5.111
LGA    D     226      T     240          2.882
LGA    G     227      I     241          3.521
LGA    R     228      G     242           #
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    D     229      G     245           #
LGA    M     230      G     246          4.185
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    G     231      I     249          2.599
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    E     232      Y     273          4.796
LGA    H     233      V     274          1.995
LGA    A     234      G     275          0.478
LGA    G     235      Q     276          2.858
LGA    L     236      -       -           -
LGA    M     237      G     277          0.913
LGA    Y     238      F     278          2.789
LGA    Y     239      Y     279          3.870
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20   60    5.0     16    3.02    12.50     17.093     0.514

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.148513 * X  +  -0.980577 * Y  +   0.128109 * Z  +  37.972370
  Y_new =  -0.142866 * X  +  -0.149462 * Y  +  -0.978392 * Z  +  23.508722
  Z_new =   0.978536 * X  +   0.127001 * Y  +  -0.162288 * Z  +   7.264698 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.477575   -0.664018  [ DEG:   141.9546    -38.0454 ]
  Theta =  -1.363234   -1.778358  [ DEG:   -78.1076   -101.8924 ]
  Phi   =  -0.766023    2.375570  [ DEG:   -43.8899    136.1101 ]
 
# 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: T0316TS211_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS211_4-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   60   5.0   16   3.02   12.50  17.093
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS211_4-D2
PFRMAT     TS
TARGET     T0316
MODEL      4 
PARENT     1j1z_A
ATOM   1691  N   GLY   220      43.108  31.925 -13.714  1.00  0.00           N  
ATOM   1692  CA  GLY   220      43.914  31.032 -14.577  1.00  0.00           C  
ATOM   1693  C   GLY   220      43.142  29.823 -15.154  1.00  0.00           C  
ATOM   1694  O   GLY   220      42.235  29.275 -14.518  1.00  0.00           O  
ATOM   1695  N   ARG   221      43.536  29.398 -16.364  1.00  0.00           N  
ATOM   1696  CA  ARG   221      42.991  28.164 -16.999  1.00  0.00           C  
ATOM   1697  C   ARG   221      43.497  26.889 -16.259  1.00  0.00           C  
ATOM   1698  O   ARG   221      44.622  26.861 -15.747  1.00  0.00           O  
ATOM   1699  CB  ARG   221      43.374  28.094 -18.501  1.00  0.00           C  
ATOM   1700  CG  ARG   221      42.793  29.212 -19.398  1.00  0.00           C  
ATOM   1701  CD  ARG   221      43.209  29.036 -20.869  1.00  0.00           C  
ATOM   1702  NE  ARG   221      42.720  30.168 -21.692  1.00  0.00           N  
ATOM   1703  CZ  ARG   221      43.034  30.360 -22.984  1.00  0.00           C  
ATOM   1704  NH1 ARG   221      42.548  31.424 -23.587  1.00  0.00           N  
ATOM   1705  NH2 ARG   221      43.805  29.542 -23.689  1.00  0.00           N  
ATOM   1706  N   MET   222      42.639  25.853 -16.183  1.00  0.00           N  
ATOM   1707  CA  MET   222      42.877  24.640 -15.330  1.00  0.00           C  
ATOM   1708  C   MET   222      42.672  24.826 -13.777  1.00  0.00           C  
ATOM   1709  O   MET   222      42.954  23.896 -13.015  1.00  0.00           O  
ATOM   1710  CB  MET   222      44.199  23.873 -15.663  1.00  0.00           C  
ATOM   1711  CG  MET   222      44.446  23.521 -17.146  1.00  0.00           C  
ATOM   1712  SD  MET   222      43.150  22.443 -17.795  1.00  0.00           S  
ATOM   1713  CE  MET   222      43.642  20.848 -17.113  1.00  0.00           C  
ATOM   1714  N   MET   223      42.140  25.976 -13.301  1.00  0.00           N  
ATOM   1715  CA  MET   223      41.834  26.221 -11.864  1.00  0.00           C  
ATOM   1716  C   MET   223      40.559  25.484 -11.337  1.00  0.00           C  
ATOM   1717  O   MET   223      40.610  24.936 -10.232  1.00  0.00           O  
ATOM   1718  CB  MET   223      41.746  27.760 -11.653  1.00  0.00           C  
ATOM   1719  CG  MET   223      41.672  28.225 -10.186  1.00  0.00           C  
ATOM   1720  SD  MET   223      41.248  29.977 -10.098  1.00  0.00           S  
ATOM   1721  CE  MET   223      39.456  29.930 -10.340  1.00  0.00           C  
ATOM   1722  N   THR   224      39.426  25.500 -12.078  1.00  0.00           N  
ATOM   1723  CA  THR   224      38.115  25.004 -11.573  1.00  0.00           C  
ATOM   1724  C   THR   224      38.108  23.447 -11.457  1.00  0.00           C  
ATOM   1725  O   THR   224      38.279  22.721 -12.442  1.00  0.00           O  
ATOM   1726  CB  THR   224      36.943  25.531 -12.460  1.00  0.00           C  
ATOM   1727  OG1 THR   224      37.009  26.949 -12.590  1.00  0.00           O  
ATOM   1728  CG2 THR   224      35.543  25.216 -11.899  1.00  0.00           C  
ATOM   1729  N   VAL   225      37.878  22.974 -10.223  1.00  0.00           N  
ATOM   1730  CA  VAL   225      37.831  21.525  -9.878  1.00  0.00           C  
ATOM   1731  C   VAL   225      36.394  20.958 -10.103  1.00  0.00           C  
ATOM   1732  O   VAL   225      36.218  20.042 -10.911  1.00  0.00           O  
ATOM   1733  CB  VAL   225      38.376  21.305  -8.419  1.00  0.00           C  
ATOM   1734  CG1 VAL   225      38.242  19.848  -7.912  1.00  0.00           C  
ATOM   1735  CG2 VAL   225      39.839  21.765  -8.235  1.00  0.00           C  
ATOM   1736  N   ASP   226      35.398  21.476  -9.355  1.00  0.00           N  
ATOM   1737  CA  ASP   226      34.037  20.879  -9.254  1.00  0.00           C  
ATOM   1738  C   ASP   226      33.223  20.934 -10.579  1.00  0.00           C  
ATOM   1739  O   ASP   226      32.785  19.890 -11.071  1.00  0.00           O  
ATOM   1740  CB  ASP   226      33.259  21.538  -8.076  1.00  0.00           C  
ATOM   1741  CG  ASP   226      33.830  21.391  -6.657  1.00  0.00           C  
ATOM   1742  OD1 ASP   226      33.260  22.001  -5.726  1.00  0.00           O  
ATOM   1743  OD2 ASP   226      34.841  20.681  -6.464  1.00  0.00           O  
ATOM   1744  N   GLY   227      33.060  22.136 -11.162  1.00  0.00           N  
ATOM   1745  CA  GLY   227      32.513  22.289 -12.522  1.00  0.00           C  
ATOM   1746  C   GLY   227      33.543  22.011 -13.637  1.00  0.00           C  
ATOM   1747  O   GLY   227      34.739  22.297 -13.516  1.00  0.00           O  
ATOM   1748  N   ARG   228      33.022  21.514 -14.766  1.00  0.00           N  
ATOM   1749  CA  ARG   228      33.773  21.476 -16.052  1.00  0.00           C  
ATOM   1750  C   ARG   228      33.865  22.905 -16.677  1.00  0.00           C  
ATOM   1751  O   ARG   228      33.076  23.803 -16.352  1.00  0.00           O  
ATOM   1752  CB  ARG   228      33.065  20.490 -17.028  1.00  0.00           C  
ATOM   1753  CG  ARG   228      33.027  19.008 -16.583  1.00  0.00           C  
ATOM   1754  CD  ARG   228      32.296  18.107 -17.593  1.00  0.00           C  
ATOM   1755  NE  ARG   228      32.229  16.714 -17.081  1.00  0.00           N  
ATOM   1756  CZ  ARG   228      31.547  15.716 -17.665  1.00  0.00           C  
ATOM   1757  NH1 ARG   228      31.568  14.533 -17.089  1.00  0.00           N  
ATOM   1758  NH2 ARG   228      30.854  15.852 -18.789  1.00  0.00           N  
ATOM   1759  N   ASP   229      34.804  23.108 -17.622  1.00  0.00           N  
ATOM   1760  CA  ASP   229      34.838  24.350 -18.447  1.00  0.00           C  
ATOM   1761  C   ASP   229      33.586  24.424 -19.378  1.00  0.00           C  
ATOM   1762  O   ASP   229      33.150  23.410 -19.930  1.00  0.00           O  
ATOM   1763  CB  ASP   229      36.172  24.402 -19.239  1.00  0.00           C  
ATOM   1764  CG  ASP   229      36.525  25.789 -19.791  1.00  0.00           C  
ATOM   1765  OD1 ASP   229      37.317  26.511 -19.148  1.00  0.00           O  
ATOM   1766  OD2 ASP   229      36.007  26.163 -20.867  1.00  0.00           O  
ATOM   1767  N   MET   230      33.006  25.627 -19.535  1.00  0.00           N  
ATOM   1768  CA  MET   230      31.829  25.843 -20.433  1.00  0.00           C  
ATOM   1769  C   MET   230      32.096  25.616 -21.960  1.00  0.00           C  
ATOM   1770  O   MET   230      31.223  25.075 -22.644  1.00  0.00           O  
ATOM   1771  CB  MET   230      31.181  27.227 -20.165  1.00  0.00           C  
ATOM   1772  CG  MET   230      30.580  27.424 -18.756  1.00  0.00           C  
ATOM   1773  SD  MET   230      29.429  26.099 -18.305  1.00  0.00           S  
ATOM   1774  CE  MET   230      28.019  26.421 -19.385  1.00  0.00           C  
ATOM   1775  N   GLY   231      33.298  25.957 -22.473  1.00  0.00           N  
ATOM   1776  CA  GLY   231      33.802  25.418 -23.763  1.00  0.00           C  
ATOM   1777  C   GLY   231      34.002  23.882 -23.863  1.00  0.00           C  
ATOM   1778  O   GLY   231      33.632  23.299 -24.886  1.00  0.00           O  
ATOM   1779  N   GLU   232      34.550  23.233 -22.814  1.00  0.00           N  
ATOM   1780  CA  GLU   232      34.643  21.740 -22.736  1.00  0.00           C  
ATOM   1781  C   GLU   232      33.384  21.001 -22.138  1.00  0.00           C  
ATOM   1782  O   GLU   232      33.494  19.851 -21.700  1.00  0.00           O  
ATOM   1783  CB  GLU   232      35.939  21.344 -21.962  1.00  0.00           C  
ATOM   1784  CG  GLU   232      37.296  21.916 -22.443  1.00  0.00           C  
ATOM   1785  CD  GLU   232      37.671  21.572 -23.887  1.00  0.00           C  
ATOM   1786  OE1 GLU   232      38.003  20.399 -24.163  1.00  0.00           O  
ATOM   1787  OE2 GLU   232      37.636  22.477 -24.749  1.00  0.00           O  
ATOM   1788  N   HIS   233      32.180  21.614 -22.167  1.00  0.00           N  
ATOM   1789  CA  HIS   233      30.910  20.964 -21.747  1.00  0.00           C  
ATOM   1790  C   HIS   233      30.299  20.128 -22.922  1.00  0.00           C  
ATOM   1791  O   HIS   233      30.766  20.164 -24.068  1.00  0.00           O  
ATOM   1792  CB  HIS   233      29.985  22.098 -21.196  1.00  0.00           C  
ATOM   1793  CG  HIS   233      28.779  21.629 -20.373  1.00  0.00           C  
ATOM   1794  ND1 HIS   233      28.883  21.006 -19.131  1.00  0.00           N  
ATOM   1795  CD2 HIS   233      27.436  21.669 -20.798  1.00  0.00           C  
ATOM   1796  CE1 HIS   233      27.556  20.714 -18.927  1.00  0.00           C  
ATOM   1797  NE2 HIS   233      26.620  21.068 -19.860  1.00  0.00           N  
ATOM   1798  N   ALA   234      29.225  19.371 -22.631  1.00  0.00           N  
ATOM   1799  CA  ALA   234      28.431  18.663 -23.665  1.00  0.00           C  
ATOM   1800  C   ALA   234      27.761  19.629 -24.687  1.00  0.00           C  
ATOM   1801  O   ALA   234      27.112  20.610 -24.302  1.00  0.00           O  
ATOM   1802  CB  ALA   234      27.353  17.827 -22.947  1.00  0.00           C  
ATOM   1803  N   GLY   235      27.904  19.316 -25.988  1.00  0.00           N  
ATOM   1804  CA  GLY   235      27.158  20.022 -27.067  1.00  0.00           C  
ATOM   1805  C   GLY   235      25.604  19.965 -27.045  1.00  0.00           C  
ATOM   1806  O   GLY   235      24.958  20.901 -27.522  1.00  0.00           O  
ATOM   1807  N   LEU   236      25.024  18.887 -26.487  1.00  0.00           N  
ATOM   1808  CA  LEU   236      23.566  18.769 -26.232  1.00  0.00           C  
ATOM   1809  C   LEU   236      23.210  19.273 -24.799  1.00  0.00           C  
ATOM   1810  O   LEU   236      23.976  19.103 -23.842  1.00  0.00           O  
ATOM   1811  CB  LEU   236      23.128  17.284 -26.402  1.00  0.00           C  
ATOM   1812  CG  LEU   236      23.378  16.601 -27.778  1.00  0.00           C  
ATOM   1813  CD1 LEU   236      22.990  15.113 -27.716  1.00  0.00           C  
ATOM   1814  CD2 LEU   236      22.647  17.295 -28.944  1.00  0.00           C  
ATOM   1815  N   MET   237      22.007  19.858 -24.659  1.00  0.00           N  
ATOM   1816  CA  MET   237      21.487  20.345 -23.351  1.00  0.00           C  
ATOM   1817  C   MET   237      20.845  19.189 -22.527  1.00  0.00           C  
ATOM   1818  O   MET   237      20.040  18.409 -23.048  1.00  0.00           O  
ATOM   1819  CB  MET   237      20.443  21.474 -23.569  1.00  0.00           C  
ATOM   1820  CG  MET   237      20.989  22.796 -24.146  1.00  0.00           C  
ATOM   1821  SD  MET   237      22.353  23.457 -23.154  1.00  0.00           S  
ATOM   1822  CE  MET   237      21.503  24.046 -21.674  1.00  0.00           C  
ATOM   1823  N   TYR   238      21.189  19.118 -21.228  1.00  0.00           N  
ATOM   1824  CA  TYR   238      20.584  18.144 -20.281  1.00  0.00           C  
ATOM   1825  C   TYR   238      19.362  18.771 -19.538  1.00  0.00           C  
ATOM   1826  O   TYR   238      19.368  19.950 -19.164  1.00  0.00           O  
ATOM   1827  CB  TYR   238      21.688  17.636 -19.303  1.00  0.00           C  
ATOM   1828  CG  TYR   238      21.256  16.451 -18.414  1.00  0.00           C  
ATOM   1829  CD1 TYR   238      21.106  15.174 -18.967  1.00  0.00           C  
ATOM   1830  CD2 TYR   238      20.917  16.660 -17.071  1.00  0.00           C  
ATOM   1831  CE1 TYR   238      20.604  14.128 -18.197  1.00  0.00           C  
ATOM   1832  CE2 TYR   238      20.417  15.612 -16.302  1.00  0.00           C  
ATOM   1833  CZ  TYR   238      20.256  14.349 -16.867  1.00  0.00           C  
ATOM   1834  OH  TYR   238      19.731  13.327 -16.120  1.00  0.00           O  
ATOM   1835  N   TYR   239      18.338  17.933 -19.301  1.00  0.00           N  
ATOM   1836  CA  TYR   239      17.133  18.310 -18.517  1.00  0.00           C  
ATOM   1837  C   TYR   239      17.205  17.594 -17.148  1.00  0.00           C  
ATOM   1838  O   TYR   239      17.085  16.347 -17.086  1.00  0.00           O  
ATOM   1839  CB  TYR   239      15.831  17.957 -19.288  1.00  0.00           C  
ATOM   1840  CG  TYR   239      15.590  18.757 -20.583  1.00  0.00           C  
ATOM   1841  CD1 TYR   239      16.009  18.243 -21.816  1.00  0.00           C  
ATOM   1842  CD2 TYR   239      14.953  20.003 -20.541  1.00  0.00           C  
ATOM   1843  CE1 TYR   239      15.789  18.960 -22.989  1.00  0.00           C  
ATOM   1844  CE2 TYR   239      14.728  20.716 -21.716  1.00  0.00           C  
ATOM   1845  CZ  TYR   239      15.141  20.192 -22.940  1.00  0.00           C  
ATOM   1846  OH  TYR   239      14.887  20.875 -24.100  1.00  0.00           O  
ATOM   1847  OXT TYR   239      17.390  18.287 -16.123  1.00  0.00           O  
TER
END
