
#######################################################
#                                                     #
#                        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 (  164),  selected   21 , name T0316TS212_1_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS212_1_1-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      -       -           -
LGA    R     221      -       -           -
LGA    M     222      -       -           -
LGA    M     223      G     220          3.186
LGA    T     224      R     221          3.043
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    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
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    V     225      N     270          2.941
LGA    D     226      I     271          1.057
LGA    G     227      L     272          2.145
LGA    R     228      Y     273          1.903
LGA    D     229      V     274          3.669
LGA    M     230      G     275          0.835
LGA    G     231      Q     276          0.624
LGA    E     232      G     277          1.389
LGA    H     233      F     278          2.255
LGA    A     234      Y     279          1.724
LGA    G     235      H     280           #
LGA    L     236      D     281           -
LGA    M     237      S     282           -
LGA    Y     238      L     283           -
LGA    Y     239      -       -           -
LGA    T     240      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21   60    5.0     12    2.27     0.00     16.362     0.506

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.741767 * X  +   0.323262 * Y  +  -0.587608 * Z  +  66.731277
  Y_new =   0.081447 * X  +   0.826261 * Y  +   0.557368 * Z  + -77.028725
  Z_new =   0.665693 * X  +  -0.461296 * Y  +   0.586565 * Z  + -62.141136 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.666416    2.475177  [ DEG:   -38.1828    141.8172 ]
  Theta =  -0.728423   -2.413170  [ DEG:   -41.7355   -138.2645 ]
  Phi   =   0.109363   -3.032230  [ DEG:     6.2660   -173.7340 ]
 
# 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: T0316TS212_1_1-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS212_1_1-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   60   5.0   12   2.27    0.00  16.362
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS212_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0316
PARENT 2c5s_A
ATOM   1736  N   GLY   220      51.791  29.781 -26.284  1.00 59.77       1SG1737
ATOM   1737  CA  GLY   220      51.345  28.686 -25.485  1.00 59.77       1SG1738
ATOM   1738  C   GLY   220      49.963  29.057 -25.106  1.00 59.77       1SG1739
ATOM   1739  O   GLY   220      49.712  29.549 -24.007  1.00 59.77       1SG1740
ATOM   1740  N   ARG   221      49.015  28.795 -26.017  1.00 57.78       1SG1741
ATOM   1741  CA  ARG   221      47.679  29.223 -25.764  1.00 57.78       1SG1742
ATOM   1742  CB  ARG   221      46.699  28.845 -26.886  1.00 57.78       1SG1743
ATOM   1743  CG  ARG   221      46.847  29.701 -28.144  1.00 57.78       1SG1744
ATOM   1744  CD  ARG   221      46.018  30.986 -28.106  1.00 57.78       1SG1745
ATOM   1745  NE  ARG   221      46.256  31.688 -29.397  1.00 57.78       1SG1746
ATOM   1746  CZ  ARG   221      47.293  32.565 -29.522  1.00 57.78       1SG1747
ATOM   1747  NH1 ARG   221      48.073  32.854 -28.440  1.00 57.78       1SG1748
ATOM   1748  NH2 ARG   221      47.555  33.146 -30.730  1.00 57.78       1SG1749
ATOM   1749  C   ARG   221      47.201  28.565 -24.524  1.00 57.78       1SG1750
ATOM   1750  O   ARG   221      46.695  29.231 -23.624  1.00 57.78       1SG1751
ATOM   1751  N   MET   222      47.386  27.238 -24.411  1.00125.46       1SG1752
ATOM   1752  CA  MET   222      46.818  26.662 -23.237  1.00125.46       1SG1753
ATOM   1753  CB  MET   222      45.304  26.399 -23.355  1.00125.46       1SG1754
ATOM   1754  CG  MET   222      44.454  27.671 -23.361  1.00125.46       1SG1755
ATOM   1755  SD  MET   222      42.733  27.444 -23.893  1.00125.46       1SG1756
ATOM   1756  CE  MET   222      43.114  27.629 -25.658  1.00125.46       1SG1757
ATOM   1757  C   MET   222      47.443  25.353 -22.919  1.00125.46       1SG1758
ATOM   1758  O   MET   222      48.264  24.813 -23.660  1.00125.46       1SG1759
ATOM   1759  N   MET   223      47.050  24.837 -21.742  1.00150.43       1SG1760
ATOM   1760  CA  MET   223      47.438  23.547 -21.277  1.00150.43       1SG1761
ATOM   1761  CB  MET   223      47.837  23.535 -19.792  1.00150.43       1SG1762
ATOM   1762  CG  MET   223      48.695  22.337 -19.385  1.00150.43       1SG1763
ATOM   1763  SD  MET   223      47.843  20.738 -19.404  1.00150.43       1SG1764
ATOM   1764  CE  MET   223      46.869  21.060 -17.907  1.00150.43       1SG1765
ATOM   1765  C   MET   223      46.180  22.757 -21.433  1.00150.43       1SG1766
ATOM   1766  O   MET   223      45.085  23.285 -21.239  1.00150.43       1SG1767
ATOM   1767  N   THR   224      46.289  21.470 -21.801  1.00110.56       1SG1768
ATOM   1768  CA  THR   224      45.088  20.744 -22.088  1.00110.56       1SG1769
ATOM   1769  CB  THR   224      45.218  19.801 -23.249  1.00110.56       1SG1770
ATOM   1770  OG1 THR   224      43.950  19.270 -23.603  1.00110.56       1SG1771
ATOM   1771  CG2 THR   224      46.153  18.657 -22.839  1.00110.56       1SG1772
ATOM   1772  C   THR   224      44.696  19.930 -20.904  1.00110.56       1SG1773
ATOM   1773  O   THR   224      45.523  19.298 -20.249  1.00110.56       1SG1774
ATOM   1774  N   VAL   225      43.385  19.935 -20.605  1.00107.58       1SG1775
ATOM   1775  CA  VAL   225      42.852  19.193 -19.504  1.00107.58       1SG1776
ATOM   1776  CB  VAL   225      42.154  20.045 -18.484  1.00107.58       1SG1777
ATOM   1777  CG1 VAL   225      43.176  20.998 -17.842  1.00107.58       1SG1778
ATOM   1778  CG2 VAL   225      40.976  20.758 -19.171  1.00107.58       1SG1779
ATOM   1779  C   VAL   225      41.805  18.290 -20.063  1.00107.58       1SG1780
ATOM   1780  O   VAL   225      41.357  18.465 -21.195  1.00107.58       1SG1781
ATOM   1781  N   ASP   226      41.401  17.273 -19.280  1.00226.02       1SG1782
ATOM   1782  CA  ASP   226      40.376  16.398 -19.755  1.00226.02       1SG1783
ATOM   1783  CB  ASP   226      40.104  15.191 -18.836  1.00226.02       1SG1784
ATOM   1784  CG  ASP   226      41.277  14.222 -18.931  1.00226.02       1SG1785
ATOM   1785  OD1 ASP   226      42.172  14.452 -19.787  1.00226.02       1SG1786
ATOM   1786  OD2 ASP   226      41.288  13.232 -18.153  1.00226.02       1SG1787
ATOM   1787  C   ASP   226      39.131  17.215 -19.793  1.00226.02       1SG1788
ATOM   1788  O   ASP   226      39.012  18.213 -19.084  1.00226.02       1SG1789
ATOM   1789  N   GLY   227      38.167  16.816 -20.642  1.00154.11       1SG1790
ATOM   1790  CA  GLY   227      36.963  17.582 -20.747  1.00154.11       1SG1791
ATOM   1791  C   GLY   227      35.810  16.671 -20.496  1.00154.11       1SG1792
ATOM   1792  O   GLY   227      35.969  15.456 -20.388  1.00154.11       1SG1793
ATOM   1793  N   ARG   228      34.602  17.259 -20.397  1.00262.55       1SG1794
ATOM   1794  CA  ARG   228      33.421  16.493 -20.142  1.00262.55       1SG1795
ATOM   1795  CB  ARG   228      32.684  16.864 -18.845  1.00262.55       1SG1796
ATOM   1796  CG  ARG   228      33.378  16.357 -17.584  1.00262.55       1SG1797
ATOM   1797  CD  ARG   228      34.603  17.169 -17.169  1.00262.55       1SG1798
ATOM   1798  NE  ARG   228      35.175  16.483 -15.977  1.00262.55       1SG1799
ATOM   1799  CZ  ARG   228      34.568  16.612 -14.762  1.00262.55       1SG1800
ATOM   1800  NH1 ARG   228      33.447  17.381 -14.636  1.00262.55       1SG1801
ATOM   1801  NH2 ARG   228      35.073  15.957 -13.677  1.00262.55       1SG1802
ATOM   1802  C   ARG   228      32.460  16.744 -21.252  1.00262.55       1SG1803
ATOM   1803  O   ARG   228      32.795  17.364 -22.259  1.00262.55       1SG1804
ATOM   1804  N   ASP   229      31.223  16.243 -21.081  1.00237.94       1SG1805
ATOM   1805  CA  ASP   229      30.227  16.397 -22.095  1.00237.94       1SG1806
ATOM   1806  CB  ASP   229      28.887  15.736 -21.743  1.00237.94       1SG1807
ATOM   1807  CG  ASP   229      28.332  16.425 -20.502  1.00237.94       1SG1808
ATOM   1808  OD1 ASP   229      29.022  16.386 -19.447  1.00237.94       1SG1809
ATOM   1809  OD2 ASP   229      27.208  16.989 -20.591  1.00237.94       1SG1810
ATOM   1810  C   ASP   229      29.964  17.854 -22.254  1.00237.94       1SG1811
ATOM   1811  O   ASP   229      30.312  18.661 -21.394  1.00237.94       1SG1812
ATOM   1812  N   MET   230      29.362  18.225 -23.400  1.00295.73       1SG1813
ATOM   1813  CA  MET   230      29.089  19.602 -23.661  1.00295.73       1SG1814
ATOM   1814  CB  MET   230      30.066  20.206 -24.680  1.00295.73       1SG1815
ATOM   1815  CG  MET   230      30.157  21.731 -24.642  1.00295.73       1SG1816
ATOM   1816  SD  MET   230      31.532  22.397 -25.627  1.00295.73       1SG1817
ATOM   1817  CE  MET   230      32.815  21.536 -24.670  1.00295.73       1SG1818
ATOM   1818  C   MET   230      27.711  19.659 -24.233  1.00295.73       1SG1819
ATOM   1819  O   MET   230      27.092  18.626 -24.490  1.00295.73       1SG1820
ATOM   1820  N   GLY   231      27.182  20.879 -24.432  1.00111.31       1SG1821
ATOM   1821  CA  GLY   231      25.853  21.005 -24.949  1.00111.31       1SG1822
ATOM   1822  C   GLY   231      24.956  21.074 -23.764  1.00111.31       1SG1823
ATOM   1823  O   GLY   231      25.419  21.006 -22.627  1.00111.31       1SG1824
ATOM   1824  N   GLU   232      23.637  21.213 -23.989  1.00256.32       1SG1825
ATOM   1825  CA  GLU   232      22.776  21.326 -22.853  1.00256.32       1SG1826
ATOM   1826  CB  GLU   232      21.329  21.729 -23.181  1.00256.32       1SG1827
ATOM   1827  CG  GLU   232      20.508  21.998 -21.918  1.00256.32       1SG1828
ATOM   1828  CD  GLU   232      19.171  22.601 -22.318  1.00256.32       1SG1829
ATOM   1829  OE1 GLU   232      18.910  22.720 -23.545  1.00256.32       1SG1830
ATOM   1830  OE2 GLU   232      18.389  22.952 -21.394  1.00256.32       1SG1831
ATOM   1831  C   GLU   232      22.743  20.009 -22.156  1.00256.32       1SG1832
ATOM   1832  O   GLU   232      22.699  18.951 -22.783  1.00256.32       1SG1833
ATOM   1833  N   HIS   233      22.777  20.063 -20.813  1.00273.29       1SG1834
ATOM   1834  CA  HIS   233      22.751  18.883 -20.007  1.00273.29       1SG1835
ATOM   1835  ND1 HIS   233      24.862  17.278 -17.224  1.00273.29       1SG1836
ATOM   1836  CG  HIS   233      24.034  17.500 -18.300  1.00273.29       1SG1837
ATOM   1837  CB  HIS   233      23.906  18.824 -18.993  1.00273.29       1SG1838
ATOM   1838  NE2 HIS   233      23.875  15.337 -17.677  1.00273.29       1SG1839
ATOM   1839  CD2 HIS   233      23.438  16.305 -18.566  1.00273.29       1SG1840
ATOM   1840  CE1 HIS   233      24.727  15.969 -16.891  1.00273.29       1SG1841
ATOM   1841  C   HIS   233      21.488  18.965 -19.222  1.00273.29       1SG1842
ATOM   1842  O   HIS   233      20.933  20.049 -19.049  1.00273.29       1SG1843
ATOM   1843  N   ALA   234      20.977  17.819 -18.739  1.00220.18       1SG1844
ATOM   1844  CA  ALA   234      19.755  17.897 -18.000  1.00220.18       1SG1845
ATOM   1845  CB  ALA   234      18.638  17.001 -18.565  1.00220.18       1SG1846
ATOM   1846  C   ALA   234      20.014  17.448 -16.604  1.00220.18       1SG1847
ATOM   1847  O   ALA   234      20.738  16.482 -16.366  1.00220.18       1SG1848
ATOM   1848  N   GLY   235      19.430  18.177 -15.635  1.00101.30       1SG1849
ATOM   1849  CA  GLY   235      19.539  17.800 -14.261  1.00101.30       1SG1850
ATOM   1850  C   GLY   235      18.265  17.098 -13.935  1.00101.30       1SG1851
ATOM   1851  O   GLY   235      17.551  16.647 -14.828  1.00101.30       1SG1852
ATOM   1852  N   LEU   236      17.947  16.983 -12.634  1.00225.17       1SG1853
ATOM   1853  CA  LEU   236      16.711  16.356 -12.282  1.00225.17       1SG1854
ATOM   1854  CB  LEU   236      16.743  15.682 -10.900  1.00225.17       1SG1855
ATOM   1855  CG  LEU   236      17.756  14.528 -10.788  1.00225.17       1SG1856
ATOM   1856  CD1 LEU   236      19.196  15.011 -11.028  1.00225.17       1SG1857
ATOM   1857  CD2 LEU   236      17.601  13.788  -9.450  1.00225.17       1SG1858
ATOM   1858  C   LEU   236      15.697  17.448 -12.192  1.00225.17       1SG1859
ATOM   1859  O   LEU   236      15.701  18.226 -11.239  1.00225.17       1SG1860
ATOM   1860  N   MET   237      14.802  17.541 -13.194  1.00343.61       1SG1861
ATOM   1861  CA  MET   237      13.802  18.564 -13.141  1.00343.61       1SG1862
ATOM   1862  CB  MET   237      14.288  19.933 -13.648  1.00343.61       1SG1863
ATOM   1863  CG  MET   237      13.299  21.071 -13.374  1.00343.61       1SG1864
ATOM   1864  SD  MET   237      13.856  22.711 -13.929  1.00343.61       1SG1865
ATOM   1865  CE  MET   237      12.476  23.627 -13.181  1.00343.61       1SG1866
ATOM   1866  C   MET   237      12.667  18.143 -14.014  1.00343.61       1SG1867
ATOM   1867  O   MET   237      12.816  17.286 -14.884  1.00343.61       1SG1868
ATOM   1868  N   TYR   238      11.480  18.730 -13.776  1.00300.65       1SG1869
ATOM   1869  CA  TYR   238      10.342  18.422 -14.585  1.00300.65       1SG1870
ATOM   1870  CB  TYR   238       9.207  17.753 -13.787  1.00300.65       1SG1871
ATOM   1871  CG  TYR   238       8.057  17.457 -14.691  1.00300.65       1SG1872
ATOM   1872  CD1 TYR   238       8.064  16.338 -15.493  1.00300.65       1SG1873
ATOM   1873  CD2 TYR   238       6.963  18.288 -14.726  1.00300.65       1SG1874
ATOM   1874  CE1 TYR   238       6.998  16.063 -16.321  1.00300.65       1SG1875
ATOM   1875  CE2 TYR   238       5.895  18.020 -15.549  1.00300.65       1SG1876
ATOM   1876  CZ  TYR   238       5.911  16.904 -16.350  1.00300.65       1SG1877
ATOM   1877  OH  TYR   238       4.815  16.627 -17.195  1.00300.65       1SG1878
ATOM   1878  C   TYR   238       9.842  19.734 -15.096  1.00300.65       1SG1879
ATOM   1879  O   TYR   238       9.784  20.717 -14.357  1.00300.65       1SG1880
ATOM   1880  N   TYR   239       9.488  19.793 -16.392  1.00261.19       1SG1881
ATOM   1881  CA  TYR   239       9.000  21.026 -16.934  1.00261.19       1SG1882
ATOM   1882  CB  TYR   239       9.582  21.386 -18.314  1.00261.19       1SG1883
ATOM   1883  CG  TYR   239       8.776  22.517 -18.859  1.00261.19       1SG1884
ATOM   1884  CD1 TYR   239       8.992  23.809 -18.441  1.00261.19       1SG1885
ATOM   1885  CD2 TYR   239       7.793  22.280 -19.793  1.00261.19       1SG1886
ATOM   1886  CE1 TYR   239       8.244  24.845 -18.953  1.00261.19       1SG1887
ATOM   1887  CE2 TYR   239       7.042  23.310 -20.308  1.00261.19       1SG1888
ATOM   1888  CZ  TYR   239       7.264  24.597 -19.885  1.00261.19       1SG1889
ATOM   1889  OH  TYR   239       6.494  25.656 -20.412  1.00261.19       1SG1890
ATOM   1890  C   TYR   239       7.532  20.880 -17.106  1.00261.19       1SG1891
ATOM   1891  O   TYR   239       7.054  19.918 -17.706  1.00261.19       1SG1892
ATOM   1892  N   THR   240       6.774  21.843 -16.550  1.00 32.73       1SG1893
ATOM   1893  CA  THR   240       5.353  21.783 -16.669  1.00 32.73       1SG1894
ATOM   1894  CB  THR   240       4.633  22.348 -15.481  1.00 32.73       1SG1895
ATOM   1895  OG1 THR   240       5.039  21.676 -14.298  1.00 32.73       1SG1896
ATOM   1896  CG2 THR   240       3.121  22.158 -15.694  1.00 32.73       1SG1897
ATOM   1897  C   THR   240       4.999  22.645 -17.870  1.00 32.73       1SG1898
ATOM   1898  O   THR   240       4.459  22.090 -18.864  1.00 32.73       1SG1899
ATOM   1899  OXT THR   240       5.268  23.875 -17.808  1.00 32.73       1SG1900
TER
END
