
#######################################################
#                                                     #
#                        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   23 (  192),  selected   23 , name T0386TS022_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS022_1-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      N     219          1.883
LGA    E     221      P     220          2.403
LGA    K     222      E     221          2.705
LGA    I     223      K     222          1.675
LGA    R     224      I     223          0.733
LGA    L     225      R     224          1.170
LGA    L     226      L     225          2.110
LGA    K     227      L     226          2.093
LGA    E     228      K     227          0.956
LGA    F     229      E     228          1.595
LGA    M     230      F     229          2.764
LGA    H     231      M     230          2.243
LGA    T     232      H     231          1.018
LGA    M     233      T     232          1.008
LGA    K     234      M     233          1.634
LGA    N     235      K     234          1.797
LGA    T     236      N     235          3.480
LGA    G     237      T     236          1.437
LGA    R     238      G     237          2.627
LGA    N     239      R     238          1.940
LGA    V     240      N     239          2.637
LGA    N     241      V     240          3.605
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    -       -      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    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
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)   23   81    5.0     22    2.12     4.55     24.214     0.990

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.350110 * X  +  -0.622184 * Y  +   0.700221 * Z  +  15.645818
  Y_new =  -0.699606 * X  +   0.323394 * Y  +   0.637156 * Z  +  42.032543
  Z_new =  -0.622875 * X  +  -0.712954 * Y  +  -0.322060 * Z  + 120.504623 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.995085    1.146507  [ DEG:  -114.3100     65.6900 ]
  Theta =   0.672413    2.469180  [ DEG:    38.5264    141.4736 ]
  Phi   =  -1.106798    2.034795  [ DEG:   -63.4148    116.5852 ]
 
# 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: T0386TS022_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS022_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   81   5.0   22   2.12    4.55  24.214
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS022_1-D2
PFRMAT TS
TARGET T0386
MODEL  1
PARENT 1c02_A
ATOM   1669  N   ASN   219      -0.702  56.461  73.427  1.00  0.00
ATOM   1670  CA  ASN   219      -0.402  55.458  74.399  1.00  0.00
ATOM   1671  C   ASN   219       0.550  56.036  75.424  1.00  0.00
ATOM   1672  O   ASN   219       0.070  56.699  76.339  1.00  0.00
ATOM   1673  CB  ASN   219       0.250  54.245  73.733  1.00  0.00
ATOM   1674  CG  ASN   219       0.422  53.079  74.688  1.00  0.00
ATOM   1675  OD1 ASN   219       1.180  53.161  75.654  1.00  0.00
ATOM   1676  ND2 ASN   219      -0.284  51.987  74.417  1.00  0.00
ATOM   1677  N   PRO   220       1.858  55.823  75.335  1.00  0.00
ATOM   1678  CA  PRO   220       2.766  56.275  76.364  1.00  0.00
ATOM   1679  C   PRO   220       2.577  57.713  76.693  1.00  0.00
ATOM   1680  O   PRO   220       2.824  58.559  75.834  1.00  0.00
ATOM   1681  CB  PRO   220       4.153  56.029  75.767  1.00  0.00
ATOM   1682  CG  PRO   220       3.922  55.978  74.293  1.00  0.00
ATOM   1683  CD  PRO   220       2.570  55.347  74.105  1.00  0.00
ATOM   1684  N   GLU   221       2.151  58.020  77.925  1.00  0.00
ATOM   1685  CA  GLU   221       2.133  59.393  78.308  1.00  0.00
ATOM   1686  C   GLU   221       3.569  59.766  78.453  1.00  0.00
ATOM   1687  O   GLU   221       4.046  60.734  77.865  1.00  0.00
ATOM   1688  CB  GLU   221       1.376  59.572  79.626  1.00  0.00
ATOM   1689  CG  GLU   221      -0.122  59.345  79.517  1.00  0.00
ATOM   1690  CD  GLU   221      -0.818  59.390  80.863  1.00  0.00
ATOM   1691  OE1 GLU   221      -0.119  59.529  81.888  1.00  0.00
ATOM   1692  OE2 GLU   221      -2.063  59.286  80.892  1.00  0.00
ATOM   1693  N   LYS   222       4.314  58.884  79.146  1.00  0.00
ATOM   1694  CA  LYS   222       5.669  59.103  79.556  1.00  0.00
ATOM   1695  C   LYS   222       6.511  59.438  78.374  1.00  0.00
ATOM   1696  O   LYS   222       7.298  60.382  78.416  1.00  0.00
ATOM   1697  CB  LYS   222       6.237  57.849  80.223  1.00  0.00
ATOM   1698  CG  LYS   222       7.693  57.973  80.641  1.00  0.00
ATOM   1699  CD  LYS   222       7.871  59.036  81.713  1.00  0.00
ATOM   1700  CE  LYS   222       9.214  58.898  82.411  1.00  0.00
ATOM   1701  NZ  LYS   222      10.350  59.175  81.487  1.00  0.00
ATOM   1702  N   ILE   223       6.358  58.687  77.274  1.00  0.00
ATOM   1703  CA  ILE   223       7.200  58.940  76.146  1.00  0.00
ATOM   1704  C   ILE   223       6.928  60.331  75.676  1.00  0.00
ATOM   1705  O   ILE   223       7.850  61.081  75.362  1.00  0.00
ATOM   1706  CB  ILE   223       6.920  57.951  75.000  1.00  0.00
ATOM   1707  CG1 ILE   223       7.268  56.525  75.430  1.00  0.00
ATOM   1708  CG2 ILE   223       7.755  58.303  73.777  1.00  0.00
ATOM   1709  CD1 ILE   223       8.725  56.332  75.788  1.00  0.00
ATOM   1710  N   ARG   224       5.640  60.708  75.620  1.00  0.00
ATOM   1711  CA  ARG   224       5.256  61.995  75.122  1.00  0.00
ATOM   1712  C   ARG   224       5.821  63.086  75.976  1.00  0.00
ATOM   1713  O   ARG   224       6.380  64.053  75.458  1.00  0.00
ATOM   1714  CB  ARG   224       3.732  62.134  75.115  1.00  0.00
ATOM   1715  CG  ARG   224       3.232  63.447  74.537  1.00  0.00
ATOM   1716  CD  ARG   224       1.719  63.557  74.645  1.00  0.00
ATOM   1717  NE  ARG   224       1.274  63.631  76.035  1.00  0.00
ATOM   1718  CZ  ARG   224       1.338  64.729  76.782  1.00  0.00
ATOM   1719  NH1 ARG   224       0.909  64.703  78.036  1.00  0.00
ATOM   1720  NH2 ARG   224       1.832  65.849  76.273  1.00  0.00
ATOM   1721  N   LEU   225       5.713  62.957  77.312  1.00  0.00
ATOM   1722  CA  LEU   225       6.156  64.024  78.161  1.00  0.00
ATOM   1723  C   LEU   225       7.625  64.217  78.006  1.00  0.00
ATOM   1724  O   LEU   225       8.108  65.348  77.992  1.00  0.00
ATOM   1725  CB  LEU   225       5.854  63.704  79.626  1.00  0.00
ATOM   1726  CG  LEU   225       4.379  63.706  80.031  1.00  0.00
ATOM   1727  CD1 LEU   225       4.211  63.198  81.455  1.00  0.00
ATOM   1728  CD2 LEU   225       3.803  65.113  79.957  1.00  0.00
ATOM   1729  N   LEU   226       8.382  63.112  77.898  1.00  0.00
ATOM   1730  CA  LEU   226       9.804  63.236  77.798  1.00  0.00
ATOM   1731  C   LEU   226      10.141  63.961  76.535  1.00  0.00
ATOM   1732  O   LEU   226      11.004  64.837  76.523  1.00  0.00
ATOM   1733  CB  LEU   226      10.462  61.854  77.775  1.00  0.00
ATOM   1734  CG  LEU   226      11.989  61.832  77.686  1.00  0.00
ATOM   1735  CD1 LEU   226      12.608  62.522  78.893  1.00  0.00
ATOM   1736  CD2 LEU   226      12.504  60.402  77.641  1.00  0.00
ATOM   1737  N   LYS   227       9.436  63.633  75.437  1.00  0.00
ATOM   1738  CA  LYS   227       9.729  64.215  74.159  1.00  0.00
ATOM   1739  C   LYS   227       9.554  65.700  74.240  1.00  0.00
ATOM   1740  O   LYS   227      10.409  66.467  73.801  1.00  0.00
ATOM   1741  CB  LYS   227       8.789  63.659  73.088  1.00  0.00
ATOM   1742  CG  LYS   227       9.056  64.192  71.690  1.00  0.00
ATOM   1743  CD  LYS   227       8.135  63.547  70.668  1.00  0.00
ATOM   1744  CE  LYS   227       8.368  64.116  69.278  1.00  0.00
ATOM   1745  NZ  LYS   227       7.455  63.510  68.269  1.00  0.00
ATOM   1746  N   GLU   228       8.433  66.147  74.830  1.00  0.00
ATOM   1747  CA  GLU   228       8.113  67.542  74.876  1.00  0.00
ATOM   1748  C   GLU   228       9.115  68.247  75.734  1.00  0.00
ATOM   1749  O   GLU   228       9.514  69.378  75.456  1.00  0.00
ATOM   1750  CB  GLU   228       6.716  67.752  75.464  1.00  0.00
ATOM   1751  CG  GLU   228       5.587  67.288  74.557  1.00  0.00
ATOM   1752  CD  GLU   228       4.227  67.397  75.219  1.00  0.00
ATOM   1753  OE1 GLU   228       4.174  67.768  76.411  1.00  0.00
ATOM   1754  OE2 GLU   228       3.214  67.112  74.546  1.00  0.00
ATOM   1755  N   PHE   229       9.554  67.577  76.808  1.00  0.00
ATOM   1756  CA  PHE   229      10.530  68.112  77.708  1.00  0.00
ATOM   1757  C   PHE   229      11.810  68.306  76.954  1.00  0.00
ATOM   1758  O   PHE   229      12.475  69.331  77.094  1.00  0.00
ATOM   1759  CB  PHE   229      10.765  67.153  78.875  1.00  0.00
ATOM   1760  CG  PHE   229      11.786  67.640  79.865  1.00  0.00
ATOM   1761  CD1 PHE   229      11.452  68.592  80.813  1.00  0.00
ATOM   1762  CD2 PHE   229      13.079  67.146  79.847  1.00  0.00
ATOM   1763  CE1 PHE   229      12.391  69.040  81.723  1.00  0.00
ATOM   1764  CE2 PHE   229      14.017  67.594  80.757  1.00  0.00
ATOM   1765  CZ  PHE   229      13.678  68.538  81.692  1.00  0.00
ATOM   1766  N   MET   230      12.183  67.319  76.117  1.00  0.00
ATOM   1767  CA  MET   230      13.441  67.361  75.429  1.00  0.00
ATOM   1768  C   MET   230      13.497  68.555  74.534  1.00  0.00
ATOM   1769  O   MET   230      14.475  69.304  74.542  1.00  0.00
ATOM   1770  CB  MET   230      13.628  66.104  74.578  1.00  0.00
ATOM   1771  CG  MET   230      14.929  66.073  73.793  1.00  0.00
ATOM   1772  SD  MET   230      15.078  64.609  72.750  1.00  0.00
ATOM   1773  CE  MET   230      13.890  64.985  71.465  1.00  0.00
ATOM   1774  N   HIS   231      12.435  68.778  73.742  1.00  0.00
ATOM   1775  CA  HIS   231      12.509  69.842  72.786  1.00  0.00
ATOM   1776  C   HIS   231      12.543  71.160  73.487  1.00  0.00
ATOM   1777  O   HIS   231      13.290  72.060  73.099  1.00  0.00
ATOM   1778  CB  HIS   231      11.295  69.814  71.857  1.00  0.00
ATOM   1779  CG  HIS   231      11.314  70.878  70.804  1.00  0.00
ATOM   1780  ND1 HIS   231      12.206  70.870  69.753  1.00  0.00
ATOM   1781  CD2 HIS   231      10.552  72.089  70.537  1.00  0.00
ATOM   1782  CE1 HIS   231      11.980  71.946  68.979  1.00  0.00
ATOM   1783  NE2 HIS   231      10.989  72.683  69.444  1.00  0.00
ATOM   1784  N   THR   232      11.742  71.312  74.556  1.00  0.00
ATOM   1785  CA  THR   232      11.718  72.578  75.227  1.00  0.00
ATOM   1786  C   THR   232      13.081  72.868  75.775  1.00  0.00
ATOM   1787  O   THR   232      13.568  73.991  75.661  1.00  0.00
ATOM   1788  CB  THR   232      10.709  72.582  76.390  1.00  0.00
ATOM   1789  OG1 THR   232       9.389  72.349  75.883  1.00  0.00
ATOM   1790  CG2 THR   232      10.731  73.921  77.110  1.00  0.00
ATOM   1791  N   MET   233      13.745  71.855  76.365  1.00  0.00
ATOM   1792  CA  MET   233      15.042  72.063  76.944  1.00  0.00
ATOM   1793  C   MET   233      15.941  72.463  75.829  1.00  0.00
ATOM   1794  O   MET   233      16.760  73.372  75.966  1.00  0.00
ATOM   1795  CB  MET   233      15.547  70.779  77.605  1.00  0.00
ATOM   1796  CG  MET   233      16.875  70.934  78.327  1.00  0.00
ATOM   1797  SD  MET   233      16.776  72.061  79.732  1.00  0.00
ATOM   1798  CE  MET   233      15.887  71.050  80.915  1.00  0.00
ATOM   1799  N   LYS   234      15.793  71.789  74.675  1.00  0.00
ATOM   1800  CA  LYS   234      16.560  72.177  73.537  1.00  0.00
ATOM   1801  C   LYS   234      16.069  73.544  73.223  1.00  0.00
ATOM   1802  O   LYS   234      14.958  73.924  73.554  1.00  0.00
ATOM   1803  CB  LYS   234      16.323  71.210  72.376  1.00  0.00
ATOM   1804  CG  LYS   234      17.145  71.517  71.134  1.00  0.00
ATOM   1805  CD  LYS   234      16.869  70.512  70.027  1.00  0.00
ATOM   1806  CE  LYS   234      17.714  70.801  68.797  1.00  0.00
ATOM   1807  NZ  LYS   234      17.419  69.854  67.686  1.00  0.00
ATOM   1808  N   ASN   235      16.908  74.387  72.637  1.00  0.00
ATOM   1809  CA  ASN   235      16.481  75.718  72.317  1.00  0.00
ATOM   1810  C   ASN   235      16.330  76.527  73.574  1.00  0.00
ATOM   1811  O   ASN   235      16.274  77.754  73.511  1.00  0.00
ATOM   1812  CB  ASN   235      15.136  75.689  71.589  1.00  0.00
ATOM   1813  CG  ASN   235      15.220  75.012  70.235  1.00  0.00
ATOM   1814  OD1 ASN   235      16.276  74.999  69.601  1.00  0.00
ATOM   1815  ND2 ASN   235      14.106  74.445  69.788  1.00  0.00
ATOM   1816  N   THR   236      16.282  75.886  74.759  1.00  0.00
ATOM   1817  CA  THR   236      16.373  76.663  75.953  1.00  0.00
ATOM   1818  C   THR   236      17.717  76.272  76.459  1.00  0.00
ATOM   1819  O   THR   236      17.928  75.286  77.160  1.00  0.00
ATOM   1820  CB  THR   236      15.246  76.313  76.942  1.00  0.00
ATOM   1821  OG1 THR   236      13.975  76.503  76.308  1.00  0.00
ATOM   1822  CG2 THR   236      15.321  77.204  78.172  1.00  0.00
ATOM   1823  N   GLY   237      18.703  77.081  76.084  1.00  0.00
ATOM   1824  CA  GLY   237      20.055  76.721  76.354  1.00  0.00
ATOM   1825  C   GLY   237      20.676  76.484  75.018  1.00  0.00
ATOM   1826  O   GLY   237      21.896  76.390  74.889  1.00  0.00
ATOM   1827  N   ARG   238      19.825  76.385  73.977  1.00  0.00
ATOM   1828  CA  ARG   238      20.311  76.245  72.637  1.00  0.00
ATOM   1829  C   ARG   238      21.239  75.082  72.559  1.00  0.00
ATOM   1830  O   ARG   238      22.294  75.160  71.932  1.00  0.00
ATOM   1831  CB  ARG   238      21.063  77.506  72.205  1.00  0.00
ATOM   1832  CG  ARG   238      20.192  78.751  72.125  1.00  0.00
ATOM   1833  CD  ARG   238      20.970  79.933  71.573  1.00  0.00
ATOM   1834  NE  ARG   238      20.212  81.178  71.665  1.00  0.00
ATOM   1835  CZ  ARG   238      20.680  82.367  71.301  1.00  0.00
ATOM   1836  NH1 ARG   238      19.918  83.446  71.422  1.00  0.00
ATOM   1837  NH2 ARG   238      21.910  82.475  70.818  1.00  0.00
ATOM   1838  N   ASN   239      20.864  73.962  73.202  1.00  0.00
ATOM   1839  CA  ASN   239      21.686  72.793  73.115  1.00  0.00
ATOM   1840  C   ASN   239      20.814  71.703  72.593  1.00  0.00
ATOM   1841  O   ASN   239      19.637  71.617  72.936  1.00  0.00
ATOM   1842  CB  ASN   239      22.239  72.424  74.494  1.00  0.00
ATOM   1843  CG  ASN   239      23.146  73.497  75.064  1.00  0.00
ATOM   1844  OD1 ASN   239      24.229  73.751  74.538  1.00  0.00
ATOM   1845  ND2 ASN   239      22.704  74.129  76.144  1.00  0.00
ATOM   1846  N   VAL   240      21.365  70.842  71.722  1.00  0.00
ATOM   1847  CA  VAL   240      20.546  69.796  71.198  1.00  0.00
ATOM   1848  C   VAL   240      20.544  68.699  72.206  1.00  0.00
ATOM   1849  O   VAL   240      21.594  68.270  72.684  1.00  0.00
ATOM   1850  CB  VAL   240      21.092  69.270  69.857  1.00  0.00
ATOM   1851  CG1 VAL   240      20.257  68.099  69.365  1.00  0.00
ATOM   1852  CG2 VAL   240      21.055  70.365  68.801  1.00  0.00
ATOM   1853  N   ASN   241      19.335  68.237  72.572  1.00  0.00
ATOM   1854  CA  ASN   241      19.213  67.187  73.533  1.00  0.00
ATOM   1855  C   ASN   241      19.624  65.899  72.834  1.00  0.00
ATOM   1856  O   ASN   241      19.470  64.816  73.459  1.00  0.00
ATOM   1857  CB  ASN   241      17.771  67.083  74.032  1.00  0.00
ATOM   1858  CG  ASN   241      17.651  66.255  75.297  1.00  0.00
ATOM   1859  OD1 ASN   241      17.873  65.045  75.282  1.00  0.00
ATOM   1860  ND2 ASN   241      17.296  66.908  76.398  1.00  0.00
TER
END
