
#######################################################
#                                                     #
#                        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 (  182),  selected   19 , name T0386TS347_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS347_1-D2.T0386_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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
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    N     219      D     242          3.623
LGA    P     220      R     243          4.012
LGA    E     221      P     244          3.976
LGA    K     222      -       -           -
LGA    I     223      V     245          0.845
LGA    R     224      M     246          3.698
LGA    L     225      V     247          4.014
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    L     226      A     273          4.311
LGA    K     227      Y     274          1.916
LGA    E     228      I     275          4.422
LGA    F     229      I     276          1.821
LGA    M     230      -       -           -
LGA    H     231      -       -           -
LGA    T     232      G     277          2.617
LGA    M     233      N     278          3.091
LGA    K     234      -       -           -
LGA    N     235      I     279          1.035
LGA    T     236      -       -           -
LGA    G     237      D     280          3.356
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)   19   81    5.0     14    3.27     0.00     10.416     0.416

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.160983 * X  +   0.391798 * Y  +  -0.905858 * Z  +  -8.892005
  Y_new =  -0.914240 * X  +  -0.404976 * Y  +  -0.012686 * Z  +  67.425613
  Z_new =  -0.371821 * X  +   0.826129 * Y  +   0.423391 * Z  +  26.921852 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.097199   -2.044394  [ DEG:    62.8649   -117.1351 ]
  Theta =   0.380969    2.760623  [ DEG:    21.8279    158.1721 ]
  Phi   =  -1.745094    1.396499  [ DEG:   -99.9865     80.0135 ]
 
# 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: T0386TS347_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS347_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   81   5.0   14   3.27    0.00  10.416
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS347_1-D2
PFRMAT TS
TARGET T0386
MODEL  1
PARENT 1aab 1aac 1aaf 1aaj 1aalA
ATOM   1683  H   ASN   219      20.023  63.766  68.413  1.00  1.00              
ATOM   1684  N   ASN   219      20.158  62.858  68.621  1.00  1.82              
ATOM   1685  CA  ASN   219      21.413  62.467  69.230  1.00  4.13              
ATOM   1686  CB  ASN   219      22.205  63.699  69.690  1.00  1.00              
ATOM   1687  C   ASN   219      21.149  61.542  70.405  1.00  1.00              
ATOM   1688  O   ASN   219      20.369  61.860  71.306  1.00  1.00              
ATOM   1689  CG  ASN   219      23.582  63.357  70.237  1.00  1.00              
ATOM   1690  ND2 ASN   219      24.502  64.310  70.147  1.00  1.00              
ATOM   1691 HD21 ASN   219      24.261  65.134  69.761  1.00  1.00              
ATOM   1692 HD22 ASN   219      25.342  64.175  70.550  1.00  1.00              
ATOM   1693  OD1 ASN   219      23.755  62.342  70.920  1.00  4.96              
ATOM   1694  N   PRO   220      21.587  60.294  70.252  1.00  1.18              
ATOM   1695  CA  PRO   220      21.175  59.216  71.143  1.00  3.08              
ATOM   1696  CB  PRO   220      21.871  57.975  70.576  1.00  1.00              
ATOM   1697  C   PRO   220      21.681  59.478  72.534  1.00  2.89              
ATOM   1698  O   PRO   220      21.068  58.949  73.412  1.00  7.19              
ATOM   1699  CG  PRO   220      23.077  58.525  69.877  1.00  1.00              
ATOM   1700  CD  PRO   220      22.620  59.846  69.301  1.00  1.00              
ATOM   1701  H   GLU   221      23.181  60.648  72.006  1.00  1.00              
ATOM   1702  N   GLU   221      22.760  60.233  72.746  1.00  1.96              
ATOM   1703  CA  GLU   221      23.198  60.574  74.105  1.00  3.16              
ATOM   1704  CB  GLU   221      24.659  61.035  74.075  1.00  1.00              
ATOM   1705  C   GLU   221      22.276  61.636  74.695  1.00  2.32              
ATOM   1706  O   GLU   221      22.102  61.691  75.910  1.00  4.84              
ATOM   1707  CG  GLU   221      25.621  59.918  73.692  1.00  1.00              
ATOM   1708  CD  GLU   221      27.055  60.372  73.496  1.00  1.00              
ATOM   1709  OE1 GLU   221      27.313  61.584  73.645  1.00  1.00              
ATOM   1710  OE2 GLU   221      27.856  59.579  72.957  1.00  1.00              
ATOM   1711  H   LYS   222      21.814  62.480  72.943  1.00  1.00              
ATOM   1712  N   LYS   222      21.662  62.498  73.880  1.00  2.98              
ATOM   1713  CA  LYS   222      20.698  63.428  74.459  1.00  5.02              
ATOM   1714  CB  LYS   222      20.365  64.615  73.556  1.00  2.06              
ATOM   1715  C   LYS   222      19.408  62.755  74.882  1.00  8.29              
ATOM   1716  O   LYS   222      19.158  62.556  76.074  1.00  1.00              
ATOM   1717  CG  LYS   222      19.346  65.512  74.238  1.00  2.58              
ATOM   1718  CD  LYS   222      18.802  66.617  73.350  1.00  1.78              
ATOM   1719  CE  LYS   222      17.635  67.299  74.052  1.00  1.60              
ATOM   1720  NZ  LYS   222      16.430  67.378  73.177  1.00 14.73              
ATOM   1721  H   ILE   223      19.102  62.288  73.019  1.00  1.00              
ATOM   1722  N   ILE   223      18.869  62.060  73.900  1.00 17.77              
ATOM   1723  CA  ILE   223      17.882  61.009  74.072  1.00 40.55              
ATOM   1724  CB  ILE   223      16.496  61.643  74.042  1.00  7.76              
ATOM   1725  C   ILE   223      17.860  60.158  72.849  1.00 28.15              
ATOM   1726  O   ILE   223      18.261  59.010  72.931  1.00  3.87              
ATOM   1727  CG1 ILE   223      16.567  63.155  74.264  1.00  5.95              
ATOM   1728  CD1 ILE   223      16.019  63.973  73.104  1.00 11.51              
ATOM   1729  CG2 ILE   223      15.708  60.903  75.079  1.00 15.29              
ATOM   1730  H   ARG   224      16.590  61.487  72.170  1.00  1.00              
ATOM   1731  N   ARG   224      16.739  60.552  72.272  1.00 30.16              
ATOM   1732  CA  ARG   224      15.748  59.647  71.780  1.00 24.81              
ATOM   1733  CB  ARG   224      16.316  59.129  70.463  1.00 10.66              
ATOM   1734  C   ARG   224      15.270  58.626  72.867  1.00 30.92              
ATOM   1735  O   ARG   224      14.098  58.749  73.231  1.00  1.42              
ATOM   1736  CG  ARG   224      15.966  59.815  69.152  1.00  4.62              
ATOM   1737  CD  ARG   224      16.495  58.906  68.042  1.00  1.63              
ATOM   1738  NE  ARG   224      16.091  59.299  66.697  1.00  6.03              
ATOM   1739  CZ  ARG   224      16.151  58.501  65.630  1.00  2.03              
ATOM   1740  NH1 ARG   224      16.572  57.248  65.782  1.00  3.70              
ATOM   1741  NH2 ARG   224      16.184  59.051  64.422  1.00  1.20              
ATOM   1742  H   LEU   225      17.040  57.881  73.335  1.00  1.00              
ATOM   1743  N   LEU   225      16.158  57.967  73.661  1.00 29.81              
ATOM   1744  CA  LEU   225      15.919  57.388  74.997  1.00 19.68              
ATOM   1745  CB  LEU   225      15.249  56.001  74.900  1.00  4.69              
ATOM   1746  C   LEU   225      17.190  57.401  75.915  1.00 20.48              
ATOM   1747  O   LEU   225      17.204  56.681  76.914  1.00  1.45              
ATOM   1748  CG  LEU   225      13.726  56.045  74.717  1.00  4.92              
ATOM   1749  CD1 LEU   225      13.151  54.911  73.901  1.00  3.50              
ATOM   1750  CD2 LEU   225      13.058  55.970  76.061  1.00  4.29              
ATOM   1751  H   LEU   226      18.420  58.494  74.843  1.00  1.00              
ATOM   1752  N   LEU   226      18.182  58.306  75.736  1.00 28.98              
ATOM   1753  CA  LEU   226      19.216  58.554  76.768  1.00 24.04              
ATOM   1754  CB  LEU   226      20.612  58.969  76.365  1.00 10.56              
ATOM   1755  C   LEU   226      18.854  59.602  77.815  1.00 13.94              
ATOM   1756  O   LEU   226      18.109  59.282  78.742  1.00  1.00              
ATOM   1757  CG  LEU   226      21.742  58.079  76.872  1.00  4.00              
ATOM   1758  CD1 LEU   226      22.249  57.203  75.737  1.00  4.78              
ATOM   1759  CD2 LEU   226      22.861  58.938  77.438  1.00  9.88              
ATOM   1760  H   LYS   227      20.198  60.927  77.161  1.00  1.00              
ATOM   1761  N   LYS   227      19.678  60.660  77.909  1.00  9.26              
ATOM   1762  CA  LYS   227      19.699  61.452  79.145  1.00  5.57              
ATOM   1763  CB  LYS   227      20.601  62.690  79.077  1.00  1.00              
ATOM   1764  C   LYS   227      18.214  61.802  79.326  1.00  6.13              
ATOM   1765  O   LYS   227      17.669  61.765  80.458  1.00  1.00              
ATOM   1766  CG  LYS   227      22.088  62.388  79.001  1.00  1.00              
ATOM   1767  CD  LYS   227      22.895  63.673  78.860  1.00  1.00              
ATOM   1768  CE  LYS   227      24.390  63.397  78.774  1.00  1.00              
ATOM   1769  NZ  LYS   227      25.173  64.656  78.605  1.00  1.00              
ATOM   1770  H   GLU   228      17.965  62.524  77.488  1.00  1.00              
ATOM   1771  N   GLU   228      17.515  62.078  78.191  1.00 12.89              
ATOM   1772  CA  GLU   228      16.142  62.451  78.463  1.00 15.88              
ATOM   1773  CB  GLU   228      15.167  63.159  77.535  1.00 17.24              
ATOM   1774  C   GLU   228      15.425  61.193  79.029  1.00  5.78              
ATOM   1775  O   GLU   228      14.652  61.311  80.026  1.00  1.00              
ATOM   1776  CG  GLU   228      13.815  62.452  77.568  1.00  6.80              
ATOM   1777  CD  GLU   228      12.966  62.695  76.323  1.00  1.30              
ATOM   1778  OE1 GLU   228      13.350  63.519  75.458  1.00 21.08              
ATOM   1779  OE2 GLU   228      12.042  61.889  76.093  1.00 17.71              
ATOM   1780  H   PHE   229      15.817  59.892  77.578  1.00  1.00              
ATOM   1781  N   PHE   229      15.580  59.980  78.490  1.00  5.79              
ATOM   1782  CA  PHE   229      14.715  58.966  79.097  1.00  9.34              
ATOM   1783  CB  PHE   229      14.800  57.529  78.653  1.00  6.44              
ATOM   1784  C   PHE   229      15.023  58.878  80.598  1.00  1.78              
ATOM   1785  O   PHE   229      14.133  58.637  81.453  1.00  1.00              
ATOM   1786  CG  PHE   229      13.717  56.729  79.343  1.00  1.00              
ATOM   1787  CD1 PHE   229      12.398  57.161  79.314  1.00  1.00              
ATOM   1788  CE1 PHE   229      11.389  56.408  79.910  1.00  1.00              
ATOM   1789  CZ  PHE   229      11.708  55.224  80.562  1.00  1.00              
ATOM   1790  CD2 PHE   229      14.042  55.649  80.156  1.00  1.00              
ATOM   1791  CE2 PHE   229      13.040  54.881  80.751  1.00  1.00              
ATOM   1792  H   MET   230      16.968  59.070  80.228  1.00  1.00              
ATOM   1793  N   MET   230      16.328  58.859  80.894  1.00  1.75              
ATOM   1794  CA  MET   230      16.789  58.528  82.233  1.00  3.63              
ATOM   1795  CB  MET   230      18.302  58.728  82.357  1.00  2.75              
ATOM   1796  C   MET   230      16.096  59.507  83.175  1.00  1.84              
ATOM   1797  O   MET   230      15.479  59.092  84.176  1.00  1.00              
ATOM   1798  CG  MET   230      19.146  57.745  81.561  1.00  2.88              
ATOM   1799  SD  MET   230      20.367  56.909  82.599  1.00 16.13              
ATOM   1800  CE  MET   230      19.354  56.520  84.017  1.00 17.70              
ATOM   1801  H   HIS   231      16.578  61.099  82.035  1.00  1.00              
ATOM   1802  N   HIS   231      16.016  60.783  82.766  1.00  2.76              
ATOM   1803  CA  HIS   231      15.220  61.709  83.583  1.00  2.86              
ATOM   1804  CB  HIS   231      15.485  63.189  83.285  1.00  1.12              
ATOM   1805  C   HIS   231      13.729  61.369  83.572  1.00  1.91              
ATOM   1806  O   HIS   231      13.091  61.436  84.630  1.00  1.00              
ATOM   1807  CG  HIS   231      14.977  64.086  84.381  1.00  1.00              
ATOM   1808  ND1 HIS   231      15.508  64.063  85.654  1.00  1.00              
ATOM   1809  HD1 HIS   231      16.289  63.591  85.923  1.00  1.00              
ATOM   1810  CE1 HIS   231      14.664  64.654  86.482  1.00  1.00              
ATOM   1811  NE2 HIS   231      13.683  65.186  85.771  1.00  1.00              
ATOM   1812  CD2 HIS   231      13.882  64.880  84.446  1.00  1.00              
ATOM   1813  H   THR   232      13.596  61.019  81.585  1.00  1.00              
ATOM   1814  N   THR   232      13.173  60.899  82.454  1.00  2.54              
ATOM   1815  CA  THR   232      11.745  60.512  82.540  1.00  2.31              
ATOM   1816  CB  THR   232      11.230  59.979  81.183  1.00  1.00              
ATOM   1817  C   THR   232      11.511  59.452  83.607  1.00  1.87              
ATOM   1818  O   THR   232      10.474  59.515  84.312  1.00  1.00              
ATOM   1819  CG2 THR   232       9.795  59.482  81.281  1.00  1.00              
ATOM   1820  OG1 THR   232      11.316  61.012  80.194  1.00  9.55              
ATOM   1821  H   MET   233      13.065  58.381  82.934  1.00  1.00              
ATOM   1822  N   MET   233      12.425  58.465  83.660  1.00  5.09              
ATOM   1823  CA  MET   233      12.298  57.386  84.656  1.00  5.64              
ATOM   1824  CB  MET   233      13.014  56.095  84.273  1.00  3.12              
ATOM   1825  C   MET   233      12.671  57.851  86.064  1.00  2.40              
ATOM   1826  O   MET   233      11.989  57.489  87.031  1.00  1.00              
ATOM   1827  CG  MET   233      12.238  54.888  84.776  1.00  2.76              
ATOM   1828  SD  MET   233      13.097  53.321  84.552  1.00  1.08              
ATOM   1829  CE  MET   233      14.208  53.332  85.953  1.00  3.59              
ATOM   1830  H   LYS   234      14.197  58.974  85.478  1.00  1.00              
ATOM   1831  N   LYS   234      13.529  58.864  86.161  1.00  1.43              
ATOM   1832  CA  LYS   234      13.702  59.565  87.442  1.00  1.00              
ATOM   1833  CB  LYS   234      14.789  60.637  87.307  1.00  1.00              
ATOM   1834  C   LYS   234      12.409  60.210  87.938  1.00  1.00              
ATOM   1835  O   LYS   234      12.154  60.204  89.146  1.00  1.00              
ATOM   1836  CG  LYS   234      16.197  60.085  87.145  1.00  1.00              
ATOM   1837  CD  LYS   234      17.219  61.205  87.014  1.00  1.00              
ATOM   1838  CE  LYS   234      18.634  60.661  86.862  1.00  1.00              
ATOM   1839  NZ  LYS   234      19.637  61.759  86.740  1.00  1.00              
ATOM   1840  H   ASN   235      11.959  61.050  86.210  1.00  1.00              
ATOM   1841  N   ASN   235      11.603  60.787  87.047  1.00  1.42              
ATOM   1842  CA  ASN   235      10.360  61.414  87.514  1.00  2.00              
ATOM   1843  CB  ASN   235       9.511  61.967  86.374  1.00  1.72              
ATOM   1844  C   ASN   235       9.503  60.383  88.241  1.00  1.36              
ATOM   1845  O   ASN   235       8.849  60.707  89.230  1.00  1.00              
ATOM   1846  CG  ASN   235       9.992  63.261  85.758  1.00  1.18              
ATOM   1847  ND2 ASN   235       9.002  63.962  85.242  1.00 23.50              
ATOM   1848 HD21 ASN   235       8.129  63.625  85.342  1.00  1.00              
ATOM   1849 HD22 ASN   235       9.159  64.845  84.953  1.00  1.00              
ATOM   1850  OD1 ASN   235      10.997  63.816  86.207  1.00 25.27              
ATOM   1851  H   THR   236       9.697  58.956  86.892  1.00  1.00              
ATOM   1852  N   THR   236       9.527  59.126  87.808  1.00  1.00              
ATOM   1853  CA  THR   236       8.809  58.124  88.603  1.00  1.00              
ATOM   1854  CB  THR   236       8.859  56.722  87.967  1.00  1.00              
ATOM   1855  C   THR   236       9.373  58.061  90.020  1.00  1.00              
ATOM   1856  O   THR   236       8.621  57.794  90.962  1.00  1.00              
ATOM   1857  CG2 THR   236       8.125  55.724  88.852  1.00  1.00              
ATOM   1858  OG1 THR   236       8.220  56.754  86.682  1.00  1.00              
ATOM   1859  H   GLY   237      11.238  58.039  89.393  1.00  1.00              
ATOM   1860  N   GLY   237      10.698  58.052  90.159  1.00  1.00              
ATOM   1861  CA  GLY   237      11.279  57.660  91.436  1.00  1.00              
ATOM   1862  C   GLY   237      12.197  58.690  92.077  1.00  2.73              
ATOM   1863  O   GLY   237      13.428  58.511  91.969  1.00  1.00              
ATOM   1864  OXT GLY   237      11.730  59.381  93.005  1.00  1.10              
TER
END
