
#######################################################
#                                                     #
#                        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   19 (  145),  selected   19 , name T0316TS021_2_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS021_2_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      G     220          1.123
LGA    M     222      R     221          1.820
LGA    M     223      M     222          3.712
LGA    T     224      M     223          2.885
LGA    V     225      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    D     226      H     233          2.117
LGA    G     227      A     234           -
LGA    R     228      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    D     229      Y     239          4.440
LGA    M     230      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    G     231      G     245          4.623
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    E     232      F     261          4.289
LGA    H     233      V     262          1.981
LGA    -       -      V     263           -
LGA    A     234      G     264          3.013
LGA    G     235      K     265          1.663
LGA    L     236      D     266          2.494
LGA    M     237      L     267          1.845
LGA    Y     238      S     268          2.438
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
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)   19   60    5.0     14    2.95    14.29     15.041     0.459

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.873858 * X  +   0.292817 * Y  +  -0.388112 * Z  +  58.259800
  Y_new =   0.370293 * X  +   0.918147 * Y  +  -0.141026 * Z  + -10.318082
  Z_new =   0.315049 * X  +  -0.266952 * Y  +  -0.910758 * Z  +  42.787804 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.856469    0.285123  [ DEG:  -163.6637     16.3364 ]
  Theta =  -0.320508   -2.821084  [ DEG:   -18.3638   -161.6362 ]
  Phi   =   2.740785   -0.400807  [ DEG:   157.0354    -22.9646 ]
 
# 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: T0316TS021_2_1-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS021_2_1-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   60   5.0   14   2.95   14.29  15.041
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS021_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0316
PARENT N/A
ATOM   1736  N   GLY   220      49.137  24.226 -20.616  1.00115.68       1SG1737
ATOM   1737  CA  GLY   220      49.441  22.832 -20.588  1.00115.68       1SG1738
ATOM   1738  C   GLY   220      48.126  22.142 -20.531  1.00115.68       1SG1739
ATOM   1739  O   GLY   220      47.935  21.194 -19.772  1.00115.68       1SG1740
ATOM   1740  N   ARG   221      47.179  22.612 -21.363  1.00 66.13       1SG1741
ATOM   1741  CA  ARG   221      45.881  22.018 -21.368  1.00 66.13       1SG1742
ATOM   1742  CB  ARG   221      44.896  22.698 -20.406  1.00 66.13       1SG1743
ATOM   1743  CG  ARG   221      45.382  22.641 -18.958  1.00 66.13       1SG1744
ATOM   1744  CD  ARG   221      44.347  23.074 -17.918  1.00 66.13       1SG1745
ATOM   1745  NE  ARG   221      45.068  23.178 -16.618  1.00 66.13       1SG1746
ATOM   1746  CZ  ARG   221      45.324  22.057 -15.881  1.00 66.13       1SG1747
ATOM   1747  NH1 ARG   221      44.899  20.837 -16.320  1.00 66.13       1SG1748
ATOM   1748  NH2 ARG   221      46.018  22.157 -14.710  1.00 66.13       1SG1749
ATOM   1749  C   ARG   221      45.347  22.145 -22.753  1.00 66.13       1SG1750
ATOM   1750  O   ARG   221      45.863  22.916 -23.559  1.00 66.13       1SG1751
ATOM   1751  N   MET   222      44.291  21.379 -23.070  1.00101.42       1SG1752
ATOM   1752  CA  MET   222      43.783  21.423 -24.405  1.00101.42       1SG1753
ATOM   1753  CB  MET   222      43.650  20.038 -25.058  1.00101.42       1SG1754
ATOM   1754  CG  MET   222      45.012  19.418 -25.377  1.00101.42       1SG1755
ATOM   1755  SD  MET   222      44.963  17.688 -25.926  1.00101.42       1SG1756
ATOM   1756  CE  MET   222      44.877  17.002 -24.246  1.00101.42       1SG1757
ATOM   1757  C   MET   222      42.449  22.084 -24.402  1.00101.42       1SG1758
ATOM   1758  O   MET   222      41.869  22.371 -23.356  1.00101.42       1SG1759
ATOM   1759  N   MET   223      41.949  22.362 -25.617  1.00129.30       1SG1760
ATOM   1760  CA  MET   223      40.698  23.022 -25.824  1.00129.30       1SG1761
ATOM   1761  CB  MET   223      40.362  23.147 -27.319  1.00129.30       1SG1762
ATOM   1762  CG  MET   223      40.273  21.792 -28.017  1.00129.30       1SG1763
ATOM   1763  SD  MET   223      39.853  21.859 -29.782  1.00129.30       1SG1764
ATOM   1764  CE  MET   223      39.912  20.055 -29.973  1.00129.30       1SG1765
ATOM   1765  C   MET   223      39.635  22.171 -25.234  1.00129.30       1SG1766
ATOM   1766  O   MET   223      38.694  22.670 -24.621  1.00129.30       1SG1767
ATOM   1767  N   THR   224      39.769  20.845 -25.403  1.00 94.72       1SG1768
ATOM   1768  CA  THR   224      38.758  19.949 -24.943  1.00 94.72       1SG1769
ATOM   1769  CB  THR   224      39.112  18.518 -25.202  1.00 94.72       1SG1770
ATOM   1770  OG1 THR   224      39.331  18.310 -26.589  1.00 94.72       1SG1771
ATOM   1771  CG2 THR   224      37.956  17.634 -24.707  1.00 94.72       1SG1772
ATOM   1772  C   THR   224      38.599  20.097 -23.462  1.00 94.72       1SG1773
ATOM   1773  O   THR   224      37.479  20.209 -22.967  1.00 94.72       1SG1774
ATOM   1774  N   VAL   225      39.716  20.101 -22.710  1.00 96.93       1SG1775
ATOM   1775  CA  VAL   225      39.605  20.177 -21.280  1.00 96.93       1SG1776
ATOM   1776  CB  VAL   225      40.906  19.986 -20.555  1.00 96.93       1SG1777
ATOM   1777  CG1 VAL   225      41.439  18.581 -20.881  1.00 96.93       1SG1778
ATOM   1778  CG2 VAL   225      41.863  21.133 -20.909  1.00 96.93       1SG1779
ATOM   1779  C   VAL   225      39.048  21.505 -20.880  1.00 96.93       1SG1780
ATOM   1780  O   VAL   225      38.194  21.584 -19.999  1.00 96.93       1SG1781
ATOM   1781  N   ASP   226      39.518  22.592 -21.520  1.00 46.39       1SG1782
ATOM   1782  CA  ASP   226      39.064  23.903 -21.150  1.00 46.39       1SG1783
ATOM   1783  CB  ASP   226      39.741  25.021 -21.961  1.00 46.39       1SG1784
ATOM   1784  CG  ASP   226      41.193  25.119 -21.517  1.00 46.39       1SG1785
ATOM   1785  OD1 ASP   226      41.444  25.027 -20.285  1.00 46.39       1SG1786
ATOM   1786  OD2 ASP   226      42.074  25.276 -22.404  1.00 46.39       1SG1787
ATOM   1787  C   ASP   226      37.592  23.993 -21.399  1.00 46.39       1SG1788
ATOM   1788  O   ASP   226      36.842  24.497 -20.564  1.00 46.39       1SG1789
ATOM   1789  N   GLY   227      37.139  23.491 -22.561  1.00 30.22       1SG1790
ATOM   1790  CA  GLY   227      35.752  23.560 -22.918  1.00 30.22       1SG1791
ATOM   1791  C   GLY   227      34.950  22.742 -21.961  1.00 30.22       1SG1792
ATOM   1792  O   GLY   227      33.853  23.127 -21.563  1.00 30.22       1SG1793
ATOM   1793  N   ARG   228      35.482  21.569 -21.577  1.00139.77       1SG1794
ATOM   1794  CA  ARG   228      34.770  20.685 -20.707  1.00139.77       1SG1795
ATOM   1795  CB  ARG   228      35.565  19.400 -20.430  1.00139.77       1SG1796
ATOM   1796  CG  ARG   228      35.710  18.511 -21.665  1.00139.77       1SG1797
ATOM   1797  CD  ARG   228      34.860  17.244 -21.598  1.00139.77       1SG1798
ATOM   1798  NE  ARG   228      35.418  16.413 -20.497  1.00139.77       1SG1799
ATOM   1799  CZ  ARG   228      35.334  15.054 -20.560  1.00139.77       1SG1800
ATOM   1800  NH1 ARG   228      34.717  14.459 -21.622  1.00139.77       1SG1801
ATOM   1801  NH2 ARG   228      35.878  14.289 -19.569  1.00139.77       1SG1802
ATOM   1802  C   ARG   228      34.546  21.381 -19.405  1.00139.77       1SG1803
ATOM   1803  O   ARG   228      33.454  21.326 -18.842  1.00139.77       1SG1804
ATOM   1804  N   ASP   229      35.586  22.061 -18.892  1.00 39.86       1SG1805
ATOM   1805  CA  ASP   229      35.469  22.731 -17.631  1.00 39.86       1SG1806
ATOM   1806  CB  ASP   229      36.803  23.342 -17.167  1.00 39.86       1SG1807
ATOM   1807  CG  ASP   229      36.683  23.714 -15.696  1.00 39.86       1SG1808
ATOM   1808  OD1 ASP   229      35.605  24.223 -15.289  1.00 39.86       1SG1809
ATOM   1809  OD2 ASP   229      37.679  23.494 -14.955  1.00 39.86       1SG1810
ATOM   1810  C   ASP   229      34.469  23.842 -17.755  1.00 39.86       1SG1811
ATOM   1811  O   ASP   229      33.618  24.021 -16.886  1.00 39.86       1SG1812
ATOM   1812  N   MET   230      34.537  24.606 -18.862  1.00150.53       1SG1813
ATOM   1813  CA  MET   230      33.693  25.751 -19.072  1.00150.53       1SG1814
ATOM   1814  CB  MET   230      34.062  26.519 -20.354  1.00150.53       1SG1815
ATOM   1815  CG  MET   230      33.544  27.959 -20.380  1.00150.53       1SG1816
ATOM   1816  SD  MET   230      31.743  28.129 -20.535  1.00150.53       1SG1817
ATOM   1817  CE  MET   230      31.737  27.952 -22.342  1.00150.53       1SG1818
ATOM   1818  C   MET   230      32.272  25.290 -19.180  1.00150.53       1SG1819
ATOM   1819  O   MET   230      31.351  25.953 -18.706  1.00150.53       1SG1820
ATOM   1820  N   GLY   231      32.077  24.122 -19.813  1.00 64.10       1SG1821
ATOM   1821  CA  GLY   231      30.797  23.505 -20.014  1.00 64.10       1SG1822
ATOM   1822  C   GLY   231      30.234  23.203 -18.667  1.00 64.10       1SG1823
ATOM   1823  O   GLY   231      29.019  23.109 -18.499  1.00 64.10       1SG1824
ATOM   1824  N   GLU   232      31.125  23.039 -17.672  1.00240.53       1SG1825
ATOM   1825  CA  GLU   232      30.735  22.678 -16.343  1.00240.53       1SG1826
ATOM   1826  CB  GLU   232      29.537  23.498 -15.833  1.00240.53       1SG1827
ATOM   1827  CG  GLU   232      29.199  23.268 -14.361  1.00240.53       1SG1828
ATOM   1828  CD  GLU   232      28.003  24.147 -14.029  1.00240.53       1SG1829
ATOM   1829  OE1 GLU   232      27.432  24.746 -14.979  1.00240.53       1SG1830
ATOM   1830  OE2 GLU   232      27.645  24.234 -12.825  1.00240.53       1SG1831
ATOM   1831  C   GLU   232      30.367  21.234 -16.334  1.00240.53       1SG1832
ATOM   1832  O   GLU   232      29.564  20.786 -15.518  1.00240.53       1SG1833
ATOM   1833  N   HIS   233      30.960  20.464 -17.266  1.00383.42       1SG1834
ATOM   1834  CA  HIS   233      30.789  19.043 -17.244  1.00383.42       1SG1835
ATOM   1835  ND1 HIS   233      30.414  19.793 -20.524  1.00383.42       1SG1836
ATOM   1836  CG  HIS   233      30.235  18.702 -19.703  1.00383.42       1SG1837
ATOM   1837  CB  HIS   233      31.150  18.345 -18.568  1.00383.42       1SG1838
ATOM   1838  NE2 HIS   233      28.579  18.757 -21.234  1.00383.42       1SG1839
ATOM   1839  CD2 HIS   233      29.110  18.081 -20.150  1.00383.42       1SG1840
ATOM   1840  CE1 HIS   233      29.396  19.777 -21.422  1.00383.42       1SG1841
ATOM   1841  C   HIS   233      31.747  18.558 -16.208  1.00383.42       1SG1842
ATOM   1842  O   HIS   233      32.749  19.215 -15.932  1.00383.42       1SG1843
ATOM   1843  N   ALA   234      31.461  17.411 -15.569  1.00879.62       1SG1844
ATOM   1844  CA  ALA   234      32.399  16.974 -14.581  1.00879.62       1SG1845
ATOM   1845  CB  ALA   234      31.944  15.728 -13.801  1.00879.62       1SG1846
ATOM   1846  C   ALA   234      33.652  16.625 -15.306  1.00879.62       1SG1847
ATOM   1847  O   ALA   234      33.640  15.813 -16.230  1.00879.62       1SG1848
ATOM   1848  N   GLY   235      34.777  17.235 -14.893  1.00403.43       1SG1849
ATOM   1849  CA  GLY   235      36.015  16.960 -15.551  1.00403.43       1SG1850
ATOM   1850  C   GLY   235      36.555  15.704 -14.967  1.00403.43       1SG1851
ATOM   1851  O   GLY   235      36.204  15.322 -13.852  1.00403.43       1SG1852
ATOM   1852  N   LEU   236      37.440  15.028 -15.718  1.00771.71       1SG1853
ATOM   1853  CA  LEU   236      38.037  13.835 -15.211  1.00771.71       1SG1854
ATOM   1854  CB  LEU   236      37.974  12.640 -16.178  1.00771.71       1SG1855
ATOM   1855  CG  LEU   236      38.624  11.361 -15.619  1.00771.71       1SG1856
ATOM   1856  CD1 LEU   236      37.892  10.862 -14.361  1.00771.71       1SG1857
ATOM   1857  CD2 LEU   236      38.749  10.280 -16.703  1.00771.71       1SG1858
ATOM   1858  C   LEU   236      39.471  14.157 -14.998  1.00771.71       1SG1859
ATOM   1859  O   LEU   236      40.044  14.966 -15.725  1.00771.71       1SG1860
ATOM   1860  N   MET   237      40.096  13.554 -13.969  1.00393.20       1SG1861
ATOM   1861  CA  MET   237      41.479  13.862 -13.802  1.00393.20       1SG1862
ATOM   1862  CB  MET   237      42.080  13.378 -12.470  1.00393.20       1SG1863
ATOM   1863  CG  MET   237      43.491  13.916 -12.221  1.00393.20       1SG1864
ATOM   1864  SD  MET   237      44.201  13.485 -10.603  1.00393.20       1SG1865
ATOM   1865  CE  MET   237      44.439  11.727 -10.989  1.00393.20       1SG1866
ATOM   1866  C   MET   237      42.176  13.162 -14.916  1.00393.20       1SG1867
ATOM   1867  O   MET   237      42.063  11.948 -15.072  1.00393.20       1SG1868
ATOM   1868  N   TYR   238      42.904  13.932 -15.745  1.00287.12       1SG1869
ATOM   1869  CA  TYR   238      43.568  13.351 -16.869  1.00287.12       1SG1870
ATOM   1870  CB  TYR   238      42.788  13.572 -18.179  1.00287.12       1SG1871
ATOM   1871  CG  TYR   238      43.587  13.064 -19.329  1.00287.12       1SG1872
ATOM   1872  CD1 TYR   238      43.641  11.720 -19.620  1.00287.12       1SG1873
ATOM   1873  CD2 TYR   238      44.276  13.947 -20.129  1.00287.12       1SG1874
ATOM   1874  CE1 TYR   238      44.379  11.266 -20.689  1.00287.12       1SG1875
ATOM   1875  CE2 TYR   238      45.015  13.499 -21.198  1.00287.12       1SG1876
ATOM   1876  CZ  TYR   238      45.068  12.156 -21.478  1.00287.12       1SG1877
ATOM   1877  OH  TYR   238      45.825  11.693 -22.576  1.00287.12       1SG1878
ATOM   1878  C   TYR   238      44.918  14.043 -17.000  1.00287.12       1SG1879
ATOM   1879  O   TYR   238      45.098  15.109 -16.352  1.00287.12       1SG1880
ATOM   1880  OXT TYR   238      45.783  13.519 -17.750  1.00287.12       1SG1881
TER
END
