
#######################################################
#                                                     #
#                        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   24 (  200),  selected   24 , name T0386TS030_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS030_2-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           -
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    -       -      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    N     219      Y     258          1.935
LGA    P     220      R     259          1.737
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    E     221      L     268          0.412
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    K     222      Y     274          2.369
LGA    I     223      I     275          1.085
LGA    R     224      I     276          2.970
LGA    L     225      G     277          1.713
LGA    L     226      N     278          1.517
LGA    -       -      I     279           -
LGA    K     227      D     280          4.502
LGA    E     228      H     281          0.433
LGA    F     229      L     282          3.481
LGA    M     230      P     283          1.471
LGA    H     231      P     284          3.567
LGA    T     232      E     285          1.337
LGA    M     233      Q     286          1.944
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    K     234      I     289          0.733
LGA    N     235      L     290          3.644
LGA    T     236      K     291          1.455
LGA    G     237      P     292          1.688
LGA    R     238      G     293          1.493
LGA    N     239      D     294           -
LGA    V     240      K     295           -
LGA    N     241      I     296           -
LGA    D     242      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   81    5.0     20    2.26     5.00     17.803     0.849

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624260 * X  +  -0.426447 * Y  +   0.654555 * Z  +  49.212273
  Y_new =  -0.675846 * X  +   0.715050 * Y  +  -0.178705 * Z  +  47.837555
  Z_new =  -0.391831 * X  +  -0.553937 * Y  +  -0.734590 * Z  + 120.333031 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.495488    0.646105  [ DEG:  -142.9809     37.0191 ]
  Theta =   0.402621    2.738971  [ DEG:    23.0685    156.9315 ]
  Phi   =  -2.316537    0.825056  [ DEG:  -132.7278     47.2722 ]
 
# 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: T0386TS030_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS030_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   81   5.0   20   2.26    5.00  17.803
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS030_2-D2
PFRMAT TS
TARGET T0386
MODEL 2 
PARENT 2g03A
ATOM   1761  N   ASN   219      22.358  63.621  89.192  1.00  1.00          
ATOM   1762  CA  ASN   219      21.957  62.465  88.400  1.00  1.00          
ATOM   1763  CB  ASN   219      23.174  61.603  88.058  1.00  1.00          
ATOM   1764  CG  ASN   219      22.730  60.198  87.664  1.00  1.00          
ATOM   1765  OD1 ASN   219      21.599  60.005  87.218  1.00  1.00          
ATOM   1766  ND2 ASN   219      23.558  59.200  87.803  1.00  1.00          
ATOM   1767  C   ASN   219      21.243  62.893  87.122  1.00  1.00          
ATOM   1768  O   ASN   219      20.188  62.360  86.778  1.00  1.00          
ATOM   1769  N   PRO   220      21.800  63.843  86.422  1.00  1.00          
ATOM   1770  CA  PRO   220      21.213  64.359  85.154  1.00  1.00          
ATOM   1771  CB  PRO   220      21.973  65.668  84.935  1.00  1.00          
ATOM   1772  CG  PRO   220      23.307  65.434  85.563  1.00  1.00          
ATOM   1773  CD  PRO   220      23.057  64.527  86.769  1.00  1.00          
ATOM   1774  C   PRO   220      21.461  63.410  83.987  1.00  1.00          
ATOM   1775  O   PRO   220      22.378  63.613  83.191  1.00  1.00          
ATOM   1776  N   GLU   221      20.638  62.370  83.890  1.00  1.00          
ATOM   1777  CA  GLU   221      20.767  61.387  82.822  1.00  1.00          
ATOM   1778  CB  GLU   221      20.000  60.111  83.172  1.00  1.00          
ATOM   1779  CG  GLU   221      18.775  60.467  84.017  1.00  1.00          
ATOM   1780  CD  GLU   221      18.314  59.249  84.810  1.00  1.00          
ATOM   1781  OE1 GLU   221      17.785  58.334  84.200  1.00  1.00          
ATOM   1782  OE2 GLU   221      18.496  59.248  86.017  1.00  1.00          
ATOM   1783  C   GLU   221      20.271  61.948  81.493  1.00  1.00          
ATOM   1784  O   GLU   221      20.450  63.132  81.203  1.00  1.00          
ATOM   1785  N   LYS   222      19.647  61.093  80.690  1.00  1.00          
ATOM   1786  CA  LYS   222      19.124  61.501  79.392  1.00  1.00          
ATOM   1787  CB  LYS   222      18.071  62.598  79.560  1.00  1.00          
ATOM   1788  CG  LYS   222      17.534  63.006  78.186  1.00  1.00          
ATOM   1789  CD  LYS   222      16.337  63.941  78.363  1.00  1.00          
ATOM   1790  CE  LYS   222      16.647  64.965  79.458  1.00  1.00          
ATOM   1791  NZ  LYS   222      18.099  65.298  79.430  1.00  1.00          
ATOM   1792  C   LYS   222      18.532  60.316  78.638  1.00  1.00          
ATOM   1793  O   LYS   222      18.733  60.172  77.432  1.00  1.00          
ATOM   1794  N   ILE   223      17.802  59.469  79.356  1.00  1.00          
ATOM   1795  CA  ILE   223      17.180  58.296  78.757  1.00  1.00          
ATOM   1796  CB  ILE   223      18.130  57.097  78.814  1.00  1.00          
ATOM   1797  CG1 ILE   223      19.561  57.591  79.030  1.00  1.00          
ATOM   1798  CG2 ILE   223      18.051  56.320  77.498  1.00  1.00          
ATOM   1799  CD1 ILE   223      20.298  56.629  79.965  1.00  1.00          
ATOM   1800  C   ILE   223      15.864  57.954  79.449  1.00  1.00          
ATOM   1801  O   ILE   223      14.791  58.090  78.864  1.00  1.00          
ATOM   1802  N   ARG   224      15.957  57.511  80.699  1.00  1.00          
ATOM   1803  CA  ARG   224      14.775  57.149  81.473  1.00  1.00          
ATOM   1804  CB  ARG   224      15.057  55.921  82.339  1.00  1.00          
ATOM   1805  CG  ARG   224      13.892  54.935  82.220  1.00  1.00          
ATOM   1806  CD  ARG   224      13.878  54.327  80.817  1.00  1.00          
ATOM   1807  NE  ARG   224      13.001  55.094  79.938  1.00  1.00          
ATOM   1808  CZ  ARG   224      11.684  54.921  79.943  1.00  1.00          
ATOM   1809  NH1 ARG   224      11.115  54.211  79.007  1.00  1.00          
ATOM   1810  NH2 ARG   224      10.958  55.462  80.884  1.00  1.00          
ATOM   1811  C   ARG   224      14.311  58.311  82.345  1.00  1.00          
ATOM   1812  O   ARG   224      15.016  58.729  83.264  1.00  1.00          
ATOM   1813  N   LEU   225      13.121  58.825  82.054  1.00  1.00          
ATOM   1814  CA  LEU   225      12.561  59.938  82.812  1.00  1.00          
ATOM   1815  CB  LEU   225      12.801  61.259  82.078  1.00  1.00          
ATOM   1816  CG  LEU   225      11.488  61.742  81.455  1.00  1.00          
ATOM   1817  CD1 LEU   225      11.169  63.150  81.961  1.00  1.00          
ATOM   1818  CD2 LEU   225      11.626  61.766  79.930  1.00  1.00          
ATOM   1819  C   LEU   225      11.070  59.740  83.061  1.00  1.00          
ATOM   1820  O   LEU   225      10.381  59.083  82.279  1.00  1.00          
ATOM   1821  N   LEU   226      10.577  60.312  84.155  1.00  1.00          
ATOM   1822  CA  LEU   226       9.167  60.199  84.510  1.00  1.00          
ATOM   1823  CB  LEU   226       8.284  60.588  83.323  1.00  1.00          
ATOM   1824  CG  LEU   226       8.236  62.113  83.200  1.00  1.00          
ATOM   1825  CD1 LEU   226       6.826  62.608  83.532  1.00  1.00          
ATOM   1826  CD2 LEU   226       9.239  62.735  84.174  1.00  1.00          
ATOM   1827  C   LEU   226       8.826  58.787  84.975  1.00  1.00          
ATOM   1828  O   LEU   226       7.941  58.136  84.419  1.00  1.00          
ATOM   1829  N   LYS   227       9.534  58.320  85.999  1.00  1.00          
ATOM   1830  CA  LYS   227       9.308  56.985  86.541  1.00  1.00          
ATOM   1831  CB  LYS   227       9.251  55.952  85.413  1.00  1.00          
ATOM   1832  CG  LYS   227       9.139  54.549  86.014  1.00  1.00          
ATOM   1833  CD  LYS   227       7.687  54.072  85.928  1.00  1.00          
ATOM   1834  CE  LYS   227       7.339  53.756  84.473  1.00  1.00          
ATOM   1835  NZ  LYS   227       8.523  54.017  83.609  1.00  1.00          
ATOM   1836  C   LYS   227      10.393  56.607  87.545  1.00  1.00          
ATOM   1837  O   LYS   227      11.580  56.617  87.223  1.00  1.00          
ATOM   1838  N   GLU   228       9.973  56.273  88.761  1.00  1.00          
ATOM   1839  CA  GLU   228      10.907  55.892  89.814  1.00  1.00          
ATOM   1840  CB  GLU   228      10.431  54.618  90.516  1.00  1.00          
ATOM   1841  CG  GLU   228      10.425  53.457  89.520  1.00  1.00          
ATOM   1842  CD  GLU   228      11.564  52.493  89.832  1.00  1.00          
ATOM   1843  OE1 GLU   228      12.709  52.884  89.666  1.00  1.00          
ATOM   1844  OE2 GLU   228      11.276  51.377  90.233  1.00  1.00          
ATOM   1845  C   GLU   228      11.083  57.016  90.830  1.00  1.00          
ATOM   1846  O   GLU   228      12.133  57.655  90.887  1.00  1.00          
ATOM   1847  N   PHE   229      10.048  57.252  91.629  1.00  1.00          
ATOM   1848  CA  PHE   229      10.085  58.299  92.642  1.00  1.00          
ATOM   1849  CB  PHE   229       8.963  58.098  93.664  1.00  1.00          
ATOM   1850  CG  PHE   229       7.785  58.968  93.296  1.00  1.00          
ATOM   1851  CD1 PHE   229       7.173  58.826  92.045  1.00  1.00          
ATOM   1852  CD2 PHE   229       7.307  59.918  94.206  1.00  1.00          
ATOM   1853  CE1 PHE   229       6.081  59.633  91.704  1.00  1.00          
ATOM   1854  CE2 PHE   229       6.215  60.725  93.865  1.00  1.00          
ATOM   1855  CZ  PHE   229       5.601  60.583  92.614  1.00  1.00          
ATOM   1856  C   PHE   229      11.437  58.334  93.349  1.00  1.00          
ATOM   1857  O   PHE   229      11.941  59.403  93.693  1.00  1.00          
ATOM   1858  N   MET   230      12.017  57.157  93.564  1.00  1.00          
ATOM   1859  CA  MET   230      13.309  57.051  94.230  1.00  1.00          
ATOM   1860  CB  MET   230      13.983  55.722  93.881  1.00  1.00          
ATOM   1861  CG  MET   230      15.454  55.971  93.540  1.00  1.00          
ATOM   1862  SD  MET   230      15.633  57.614  92.801  1.00  1.00          
ATOM   1863  CE  MET   230      15.829  57.071  91.085  1.00  1.00          
ATOM   1864  C   MET   230      13.163  57.183  95.743  1.00  1.00          
ATOM   1865  O   MET   230      12.567  58.140  96.237  1.00  1.00          
ATOM   1866  N   HIS   231      13.710  56.217  96.472  1.00  1.00          
ATOM   1867  CA  HIS   231      13.642  56.223  97.928  1.00  1.00          
ATOM   1868  CB  HIS   231      12.215  55.938  98.399  1.00  1.00          
ATOM   1869  CG  HIS   231      12.184  55.874  99.901  1.00  1.00          
ATOM   1870  ND1 HIS   231      13.110  55.140 100.628  1.00  1.00          
ATOM   1871  CD2 HIS   231      11.348  56.445 100.827  1.00  1.00          
ATOM   1872  CE1 HIS   231      12.811  55.289 101.930  1.00  1.00          
ATOM   1873  NE2 HIS   231      11.746  56.075 102.110  1.00  1.00          
ATOM   1874  C   HIS   231      14.125  57.554  98.497  1.00  1.00          
ATOM   1875  O   HIS   231      13.461  58.156  99.342  1.00  1.00          
ATOM   1876  N   THR   232      15.284  58.006  98.030  1.00  1.00          
ATOM   1877  CA  THR   232      15.857  59.264  98.491  1.00  1.00          
ATOM   1878  CB  THR   232      16.576  59.067  99.828  1.00  1.00          
ATOM   1879  OG1 THR   232      16.099  57.885 100.453  1.00  1.00          
ATOM   1880  CG2 THR   232      16.306  60.270 100.735  1.00  1.00          
ATOM   1881  C   THR   232      16.818  59.844  97.460  1.00  1.00          
ATOM   1882  O   THR   232      17.163  59.186  96.479  1.00  1.00          
ATOM   1883  N   MET   233      17.247  61.082  97.686  1.00  1.00          
ATOM   1884  CA  MET   233      18.168  61.753  96.778  1.00  1.00          
ATOM   1885  CB  MET   233      17.395  62.504  95.690  1.00  1.00          
ATOM   1886  CG  MET   233      15.907  62.526  96.045  1.00  1.00          
ATOM   1887  SD  MET   233      15.068  63.781  95.047  1.00  1.00          
ATOM   1888  CE  MET   233      14.567  62.695  93.689  1.00  1.00          
ATOM   1889  C   MET   233      19.082  62.714  97.530  1.00  1.00          
ATOM   1890  O   MET   233      19.453  62.463  98.677  1.00  1.00          
ATOM   1891  N   LYS   234      19.440  63.817  96.878  1.00  1.00          
ATOM   1892  CA  LYS   234      20.309  64.817  97.485  1.00  1.00          
ATOM   1893  CB  LYS   234      19.870  65.042  98.932  1.00  1.00          
ATOM   1894  CG  LYS   234      18.355  65.250  98.979  1.00  1.00          
ATOM   1895  CD  LYS   234      17.803  64.691 100.294  1.00  1.00          
ATOM   1896  CE  LYS   234      16.277  64.796 100.293  1.00  1.00          
ATOM   1897  NZ  LYS   234      15.757  64.490 101.656  1.00  1.00          
ATOM   1898  C   LYS   234      20.228  66.133  96.710  1.00  1.00          
ATOM   1899  O   LYS   234      19.197  66.800  96.773  1.00  1.00          
ATOM   1900  N   ASN   235      21.308  66.534  95.992  1.00  1.00          
ATOM   1901  CA  ASN   235      21.223  67.811  95.254  1.00  1.00          
ATOM   1902  CB  ASN   235      19.833  68.000  94.627  1.00  1.00          
ATOM   1903  CG  ASN   235      19.863  67.686  93.133  1.00  1.00          
ATOM   1904  OD1 ASN   235      19.481  66.592  92.722  1.00  1.00          
ATOM   1905  ND2 ASN   235      20.287  68.587  92.292  1.00  1.00          
ATOM   1906  C   ASN   235      22.305  68.108  94.202  1.00  1.00          
ATOM   1907  O   ASN   235      22.248  69.147  93.545  1.00  1.00          
ATOM   1908  N   THR   236      23.300  67.247  94.055  1.00  1.00          
ATOM   1909  CA  THR   236      24.372  67.509  93.092  1.00  1.00          
ATOM   1910  CB  THR   236      25.742  67.586  93.767  1.00  1.00          
ATOM   1911  OG1 THR   236      25.993  66.393  94.488  1.00  1.00          
ATOM   1912  CG2 THR   236      25.776  68.782  94.720  1.00  1.00          
ATOM   1913  C   THR   236      24.392  66.524  91.934  1.00  1.00          
ATOM   1914  O   THR   236      24.316  65.311  92.130  1.00  1.00          
ATOM   1915  N   GLY   237      24.487  67.063  90.720  1.00  1.00          
ATOM   1916  CA  GLY   237      24.511  66.250  89.503  1.00  1.00          
ATOM   1917  C   GLY   237      25.659  66.639  88.568  1.00  1.00          
ATOM   1918  O   GLY   237      26.340  67.642  88.784  1.00  1.00          
ATOM   1919  N   ARG   238      25.871  65.827  87.528  1.00  1.00          
ATOM   1920  CA  ARG   238      26.943  66.067  86.565  1.00  1.00          
ATOM   1921  CB  ARG   238      27.757  64.790  86.339  1.00  1.00          
ATOM   1922  CG  ARG   238      26.901  63.767  85.589  1.00  1.00          
ATOM   1923  CD  ARG   238      27.803  62.680  85.001  1.00  1.00          
ATOM   1924  NE  ARG   238      28.719  62.173  86.015  1.00  1.00          
ATOM   1925  CZ  ARG   238      29.858  61.570  85.688  1.00  1.00          
ATOM   1926  NH1 ARG   238      30.198  60.456  86.278  1.00  1.00          
ATOM   1927  NH2 ARG   238      30.635  62.090  84.778  1.00  1.00          
ATOM   1928  C   ARG   238      26.440  66.611  85.225  1.00  1.00          
ATOM   1929  O   ARG   238      26.948  66.239  84.168  1.00  1.00          
ATOM   1930  N   ASN   239      25.458  67.505  85.275  1.00  1.00          
ATOM   1931  CA  ASN   239      24.908  68.116  84.072  1.00  1.00          
ATOM   1932  CB  ASN   239      23.382  68.183  84.156  1.00  1.00          
ATOM   1933  CG  ASN   239      22.808  68.704  82.842  1.00  1.00          
ATOM   1934  OD1 ASN   239      22.749  69.914  82.626  1.00  1.00          
ATOM   1935  ND2 ASN   239      22.375  67.856  81.950  1.00  1.00          
ATOM   1936  C   ASN   239      25.485  69.515  83.902  1.00  1.00          
ATOM   1937  O   ASN   239      24.756  70.506  83.917  1.00  1.00          
ATOM   1938  N   VAL   240      26.808  69.577  83.775  1.00  1.00          
ATOM   1939  CA  VAL   240      27.523  70.836  83.629  1.00  1.00          
ATOM   1940  CB  VAL   240      27.359  71.687  84.886  1.00  1.00          
ATOM   1941  CG1 VAL   240      26.219  72.681  84.675  1.00  1.00          
ATOM   1942  CG2 VAL   240      27.028  70.782  86.076  1.00  1.00          
ATOM   1943  C   VAL   240      27.052  71.634  82.416  1.00  1.00          
ATOM   1944  O   VAL   240      27.730  72.560  81.978  1.00  1.00          
ATOM   1945  N   ASN   241      25.887  71.279  81.881  1.00  1.00          
ATOM   1946  CA  ASN   241      25.335  71.979  80.721  1.00  1.00          
ATOM   1947  CB  ASN   241      25.659  71.216  79.435  1.00  1.00          
ATOM   1948  CG  ASN   241      27.067  71.559  78.957  1.00  1.00          
ATOM   1949  OD1 ASN   241      28.050  71.196  79.602  1.00  1.00          
ATOM   1950  ND2 ASN   241      27.223  72.236  77.852  1.00  1.00          
ATOM   1951  C   ASN   241      23.824  72.175  80.844  1.00  1.00          
ATOM   1952  O   ASN   241      23.124  72.288  79.837  1.00  1.00          
ATOM   1953  N   ASP   242      23.327  72.208  82.080  1.00  1.00          
ATOM   1954  CA  ASP   242      21.896  72.380  82.345  1.00  1.00          
ATOM   1955  CB  ASP   242      21.050  71.686  81.275  1.00  1.00          
ATOM   1956  CG  ASP   242      19.630  71.469  81.789  1.00  1.00          
ATOM   1957  OD1 ASP   242      18.749  72.196  81.362  1.00  1.00          
ATOM   1958  OD2 ASP   242      19.445  70.577  82.600  1.00  1.00          
ATOM   1959  C   ASP   242      21.496  73.848  82.472  1.00  1.00          
ATOM   1960  O   ASP   242      22.302  74.692  82.864  1.00  1.00          
TER
END
