
#######################################################
#                                                     #
#                        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 (  159),  selected   19 , name T0386TS349_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS349_4-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    N     219      Y     254          3.109
LGA    P     220      T     255          3.140
LGA    E     221      G     256          2.050
LGA    K     222      T     257          3.690
LGA    I     223      Y     258          0.896
LGA    R     224      R     259          1.808
LGA    L     225      G     260          3.477
LGA    L     226      A     261          2.098
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    K     227      G     265          2.767
LGA    E     228      F     266          2.683
LGA    F     229      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    M     230      G     277           #
LGA    H     231      N     278          2.640
LGA    T     232      I     279          4.127
LGA    M     233      D     280          4.570
LGA    K     234      H     281          4.515
LGA    N     235      L     282          4.140
LGA    T     236      P     283          2.410
LGA    G     237      P     284          4.208
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     17    3.24     5.88     13.088     0.509

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.245928 * X  +  -0.735402 * Y  +   0.631429 * Z  +  59.717735
  Y_new =   0.794501 * X  +   0.220221 * Y  +   0.565924 * Z  +  55.927170
  Z_new =  -0.555236 * X  +   0.640848 * Y  +   0.530120 * Z  +  48.979401 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.879679   -2.261914  [ DEG:    50.4019   -129.5981 ]
  Theta =   0.588647    2.552946  [ DEG:    33.7270    146.2730 ]
  Phi   =   1.870980   -1.270613  [ DEG:   107.1993    -72.8007 ]
 
# 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: T0386TS349_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS349_4-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   17   3.24    5.88  13.088
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS349_4-D2
PFRMAT TS
TARGET T0386
MODEL  4  REFINED
PARENT 2G03_A
ATOM   1478  N   ASN   219      22.527  52.129  85.052  1.00  0.00
ATOM   1479  CA  ASN   219      23.302  53.303  85.527  1.00  0.00
ATOM   1480  C   ASN   219      23.454  54.523  84.502  1.00  0.00
ATOM   1481  O   ASN   219      24.350  54.426  83.666  1.00  0.00
ATOM   1482  CB  ASN   219      24.724  52.760  85.895  1.00  0.00
ATOM   1483  CG  ASN   219      24.787  51.795  87.097  1.00  0.00
ATOM   1484  OD1 ASN   219      25.480  50.769  87.033  1.00  0.00
ATOM   1485  ND2 ASN   219      24.004  52.048  88.137  1.00  0.00
ATOM   1486  N   PRO   220      22.727  55.679  84.536  1.00  0.00
ATOM   1487  CA  PRO   220      22.984  56.758  83.691  1.00  0.00
ATOM   1488  C   PRO   220      24.163  57.644  84.162  1.00  0.00
ATOM   1489  O   PRO   220      24.300  57.976  85.342  1.00  0.00
ATOM   1490  CB  PRO   220      21.757  57.686  83.580  1.00  0.00
ATOM   1491  CG  PRO   220      21.162  57.393  84.977  1.00  0.00
ATOM   1492  CD  PRO   220      21.419  55.914  85.229  1.00  0.00
ATOM   1493  N   GLU   221      24.739  58.287  83.161  1.00  0.00
ATOM   1494  CA  GLU   221      25.793  59.283  83.219  1.00  0.00
ATOM   1495  C   GLU   221      25.163  60.716  83.273  1.00  0.00
ATOM   1496  O   GLU   221      25.884  61.610  83.699  1.00  0.00
ATOM   1497  CB  GLU   221      26.709  59.114  81.969  1.00  0.00
ATOM   1498  CG  GLU   221      26.568  60.211  80.903  1.00  0.00
ATOM   1499  CD  GLU   221      27.633  60.089  79.859  1.00  0.00
ATOM   1500  OE1 GLU   221      27.960  58.859  79.617  1.00  0.00
ATOM   1501  OE2 GLU   221      28.166  61.029  79.320  1.00  0.00
ATOM   1502  N   LYS   222      23.866  60.919  82.932  1.00  0.00
ATOM   1503  CA  LYS   222      23.160  62.167  83.037  1.00  0.00
ATOM   1504  C   LYS   222      22.664  62.302  84.522  1.00  0.00
ATOM   1505  O   LYS   222      21.474  62.176  84.839  1.00  0.00
ATOM   1506  CB  LYS   222      21.946  62.162  82.116  1.00  0.00
ATOM   1507  CG  LYS   222      22.294  62.141  80.680  1.00  0.00
ATOM   1508  CD  LYS   222      21.195  62.746  79.821  1.00  0.00
ATOM   1509  CE  LYS   222      21.600  62.583  78.359  1.00  0.00
ATOM   1510  NZ  LYS   222      20.645  63.216  77.461  1.00  0.00
ATOM   1511  N   ILE   223      23.654  62.594  85.391  1.00  0.00
ATOM   1512  CA  ILE   223      23.519  62.780  86.832  1.00  0.00
ATOM   1513  C   ILE   223      22.496  63.916  87.149  1.00  0.00
ATOM   1514  O   ILE   223      21.793  63.802  88.140  1.00  0.00
ATOM   1515  CB  ILE   223      24.866  63.047  87.546  1.00  0.00
ATOM   1516  CG1 ILE   223      25.733  64.102  86.873  1.00  0.00
ATOM   1517  CG2 ILE   223      25.683  61.714  87.512  1.00  0.00
ATOM   1518  CD1 ILE   223      26.500  64.928  87.870  1.00  0.00
ATOM   1519  N   ARG   224      22.483  65.030  86.408  1.00  0.00
ATOM   1520  CA  ARG   224      21.606  66.190  86.633  1.00  0.00
ATOM   1521  C   ARG   224      20.410  66.282  85.693  1.00  0.00
ATOM   1522  O   ARG   224      19.701  67.297  85.826  1.00  0.00
ATOM   1523  CB  ARG   224      22.470  67.432  86.493  1.00  0.00
ATOM   1524  CG  ARG   224      23.044  68.243  87.620  1.00  0.00
ATOM   1525  CD  ARG   224      23.325  69.642  87.083  1.00  0.00
ATOM   1526  NE  ARG   224      22.051  70.318  86.846  1.00  0.00
ATOM   1527  CZ  ARG   224      21.764  71.180  85.831  1.00  0.00
ATOM   1528  NH1 ARG   224      20.510  71.612  85.874  1.00  0.00
ATOM   1529  NH2 ARG   224      22.581  71.524  84.797  1.00  0.00
ATOM   1530  N   LEU   225      19.945  65.202  85.079  1.00  0.00
ATOM   1531  CA  LEU   225      18.850  65.376  84.143  1.00  0.00
ATOM   1532  C   LEU   225      17.516  65.465  84.937  1.00  0.00
ATOM   1533  O   LEU   225      17.161  64.529  85.669  1.00  0.00
ATOM   1534  CB  LEU   225      18.904  64.282  83.010  1.00  0.00
ATOM   1535  CG  LEU   225      17.789  64.437  81.985  1.00  0.00
ATOM   1536  CD1 LEU   225      18.312  63.767  80.727  1.00  0.00
ATOM   1537  CD2 LEU   225      16.562  63.624  82.381  1.00  0.00
ATOM   1538  N   LEU   226      16.719  66.478  84.570  1.00  0.00
ATOM   1539  CA  LEU   226      15.470  66.718  85.266  1.00  0.00
ATOM   1540  C   LEU   226      14.464  65.500  85.216  1.00  0.00
ATOM   1541  O   LEU   226      13.881  65.244  86.271  1.00  0.00
ATOM   1542  CB  LEU   226      14.948  68.036  84.730  1.00  0.00
ATOM   1543  CG  LEU   226      14.496  68.012  83.255  1.00  0.00
ATOM   1544  CD1 LEU   226      13.123  67.388  83.013  1.00  0.00
ATOM   1545  CD2 LEU   226      14.386  69.461  82.737  1.00  0.00
ATOM   1546  N   LYS   227      14.175  64.880  84.059  1.00  0.00
ATOM   1547  CA  LYS   227      13.277  63.715  83.902  1.00  0.00
ATOM   1548  C   LYS   227      13.791  62.509  84.765  1.00  0.00
ATOM   1549  O   LYS   227      12.936  61.765  85.245  1.00  0.00
ATOM   1550  CB  LYS   227      13.153  63.315  82.405  1.00  0.00
ATOM   1551  CG  LYS   227      11.985  62.314  82.243  1.00  0.00
ATOM   1552  CD  LYS   227      11.910  61.841  80.801  1.00  0.00
ATOM   1553  CE  LYS   227      10.671  60.936  80.589  1.00  0.00
ATOM   1554  NZ  LYS   227      10.671  60.554  79.138  1.00  0.00
ATOM   1555  N   GLU   228      15.089  62.154  84.710  1.00  0.00
ATOM   1556  CA  GLU   228      15.652  61.110  85.527  1.00  0.00
ATOM   1557  C   GLU   228      15.453  61.351  87.012  1.00  0.00
ATOM   1558  O   GLU   228      14.892  60.484  87.604  1.00  0.00
ATOM   1559  CB  GLU   228      17.131  61.044  85.271  1.00  0.00
ATOM   1560  CG  GLU   228      17.559  60.615  83.920  1.00  0.00
ATOM   1561  CD  GLU   228      19.044  60.420  83.648  1.00  0.00
ATOM   1562  OE1 GLU   228      19.390  60.621  82.452  1.00  0.00
ATOM   1563  OE2 GLU   228      19.684  60.001  84.716  1.00  0.00
ATOM   1564  N   PHE   229      15.946  62.450  87.603  1.00  0.00
ATOM   1565  CA  PHE   229      15.733  62.780  89.030  1.00  0.00
ATOM   1566  C   PHE   229      14.191  62.805  89.377  1.00  0.00
ATOM   1567  O   PHE   229      13.856  62.332  90.487  1.00  0.00
ATOM   1568  CB  PHE   229      16.452  64.104  89.423  1.00  0.00
ATOM   1569  CG  PHE   229      17.914  63.903  89.749  1.00  0.00
ATOM   1570  CD1 PHE   229      18.580  65.037  90.309  1.00  0.00
ATOM   1571  CD2 PHE   229      18.642  62.750  89.577  1.00  0.00
ATOM   1572  CE1 PHE   229      19.919  64.950  90.659  1.00  0.00
ATOM   1573  CE2 PHE   229      19.954  62.634  89.951  1.00  0.00
ATOM   1574  CZ  PHE   229      20.605  63.758  90.489  1.00  0.00
ATOM   1575  N   MET   230      13.298  63.465  88.595  1.00  0.00
ATOM   1576  CA  MET   230      11.831  63.476  88.900  1.00  0.00
ATOM   1577  C   MET   230      11.216  62.069  88.811  1.00  0.00
ATOM   1578  O   MET   230      10.554  61.703  89.755  1.00  0.00
ATOM   1579  CB  MET   230      11.129  64.515  88.024  1.00  0.00
ATOM   1580  CG  MET   230      11.569  65.920  88.294  1.00  0.00
ATOM   1581  SD  MET   230      11.319  66.406  90.000  1.00  0.00
ATOM   1582  CE  MET   230      11.698  68.143  90.032  1.00  0.00
ATOM   1583  N   HIS   231      11.281  61.426  87.671  1.00  0.00
ATOM   1584  CA  HIS   231      10.730  60.078  87.497  1.00  0.00
ATOM   1585  C   HIS   231      11.427  59.131  88.527  1.00  0.00
ATOM   1586  O   HIS   231      10.791  58.146  88.849  1.00  0.00
ATOM   1587  CB  HIS   231      10.856  59.582  86.056  1.00  0.00
ATOM   1588  CG  HIS   231       9.981  60.335  85.126  1.00  0.00
ATOM   1589  ND1 HIS   231       8.745  59.853  84.741  1.00  0.00
ATOM   1590  CD2 HIS   231      10.181  61.527  84.490  1.00  0.00
ATOM   1591  CE1 HIS   231       8.231  60.739  83.877  1.00  0.00
ATOM   1592  NE2 HIS   231       9.071  61.758  83.720  1.00  0.00
ATOM   1593  N   THR   232      12.762  59.227  88.796  1.00  0.00
ATOM   1594  CA  THR   232      13.427  58.426  89.815  1.00  0.00
ATOM   1595  C   THR   232      12.668  58.585  91.169  1.00  0.00
ATOM   1596  O   THR   232      12.562  57.585  91.839  1.00  0.00
ATOM   1597  CB  THR   232      14.978  58.684  89.938  1.00  0.00
ATOM   1598  OG1 THR   232      15.234  60.027  90.531  1.00  0.00
ATOM   1599  CG2 THR   232      15.720  58.242  88.743  1.00  0.00
ATOM   1600  N   MET   233      12.550  59.797  91.738  1.00  0.00
ATOM   1601  CA  MET   233      11.840  60.093  92.957  1.00  0.00
ATOM   1602  C   MET   233      10.414  59.457  92.951  1.00  0.00
ATOM   1603  O   MET   233       9.947  59.197  94.059  1.00  0.00
ATOM   1604  CB  MET   233      11.764  61.617  93.021  1.00  0.00
ATOM   1605  CG  MET   233      13.086  62.252  93.318  1.00  0.00
ATOM   1606  SD  MET   233      12.732  64.077  93.246  1.00  0.00
ATOM   1607  CE  MET   233      14.206  64.662  92.360  1.00  0.00
ATOM   1608  N   LYS   234       9.607  59.701  91.890  1.00  0.00
ATOM   1609  CA  LYS   234       8.302  59.076  91.765  1.00  0.00
ATOM   1610  C   LYS   234       8.448  57.534  91.931  1.00  0.00
ATOM   1611  O   LYS   234       7.576  56.954  92.606  1.00  0.00
ATOM   1612  CB  LYS   234       7.709  59.411  90.403  1.00  0.00
ATOM   1613  CG  LYS   234       7.057  60.743  90.280  1.00  0.00
ATOM   1614  CD  LYS   234       6.186  60.769  89.031  1.00  0.00
ATOM   1615  CE  LYS   234       4.853  60.074  89.294  1.00  0.00
ATOM   1616  NZ  LYS   234       4.086  60.957  90.242  1.00  0.00
ATOM   1617  N   ASN   235       9.328  56.858  91.166  1.00  0.00
ATOM   1618  CA  ASN   235       9.625  55.465  91.275  1.00  0.00
ATOM   1619  C   ASN   235      10.064  55.091  92.721  1.00  0.00
ATOM   1620  O   ASN   235       9.489  54.114  93.235  1.00  0.00
ATOM   1621  CB  ASN   235      10.612  55.049  90.204  1.00  0.00
ATOM   1622  CG  ASN   235      10.885  53.582  90.110  1.00  0.00
ATOM   1623  OD1 ASN   235      11.605  52.962  90.912  1.00  0.00
ATOM   1624  ND2 ASN   235      10.446  53.027  89.034  1.00  0.00
ATOM   1625  N   THR   236      11.100  55.717  93.316  1.00  0.00
ATOM   1626  CA  THR   236      11.519  55.463  94.673  1.00  0.00
ATOM   1627  C   THR   236      10.359  55.653  95.709  1.00  0.00
ATOM   1628  O   THR   236      10.254  54.776  96.581  1.00  0.00
ATOM   1629  CB  THR   236      12.830  56.299  94.896  1.00  0.00
ATOM   1630  OG1 THR   236      12.698  57.712  94.707  1.00  0.00
ATOM   1631  CG2 THR   236      13.958  55.782  93.890  1.00  0.00
ATOM   1632  N   GLY   237       9.558  56.733  95.664  1.00  0.00
ATOM   1633  CA  GLY   237       8.422  56.914  96.565  1.00  0.00
ATOM   1634  C   GLY   237       7.351  55.847  96.248  1.00  0.00
ATOM   1635  O   GLY   237       6.574  55.455  97.111  1.00  0.00
ATOM   1636  OXT GLY   237       7.275  55.468  95.058  1.00  0.00
TER
END
