
#######################################################
#                                                     #
#                        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 (  193),  selected   23 , name T0386TS349_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS349_3-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    N     219      M     233          0.852
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    P     220      R     238          2.585
LGA    E     221      N     239          0.518
LGA    K     222      V     240          2.406
LGA    I     223      N     241          1.933
LGA    R     224      D     242          2.365
LGA    L     225      R     243          1.528
LGA    L     226      P     244          2.719
LGA    K     227      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    E     228      N     269          5.170
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    F     229      A     273          4.399
LGA    M     230      Y     274          2.821
LGA    H     231      I     275          3.188
LGA    T     232      -       -           -
LGA    M     233      I     276          1.702
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      -       -           -
LGA    G     237      G     277          1.897
LGA    R     238      N     278          3.444
LGA    N     239      I     279          2.333
LGA    V     240      -       -           -
LGA    N     241      D     280          1.418
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     17    2.68     5.88     14.226     0.610

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.274745 * X  +   0.082191 * Y  +   0.957998 * Z  + -18.645483
  Y_new =  -0.356642 * X  +   0.916556 * Y  +  -0.180917 * Z  +  -8.929636
  Z_new =  -0.892929 * X  +  -0.391368 * Y  +  -0.222507 * Z  + 107.339157 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.087758    1.053834  [ DEG:  -119.6197     60.3803 ]
  Theta =   1.103809    2.037783  [ DEG:    63.2436    116.7564 ]
  Phi   =  -2.227205    0.914388  [ DEG:  -127.6095     52.3905 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS349_3-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   17   2.68    5.88  14.226
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS349_3-D2
PFRMAT TS
TARGET T0386
MODEL  3  REFINED
PARENT 2F6S_B
ATOM   1457  N   ASN   219      17.856  74.057  76.333  1.00  0.00
ATOM   1458  CA  ASN   219      17.851  73.289  75.111  1.00  0.00
ATOM   1459  C   ASN   219      19.108  73.274  74.211  1.00  0.00
ATOM   1460  O   ASN   219      19.404  74.380  73.675  1.00  0.00
ATOM   1461  CB  ASN   219      16.702  73.940  74.262  1.00  0.00
ATOM   1462  CG  ASN   219      15.300  73.341  74.511  1.00  0.00
ATOM   1463  OD1 ASN   219      15.116  72.122  74.635  1.00  0.00
ATOM   1464  ND2 ASN   219      14.331  74.264  74.534  1.00  0.00
ATOM   1465  N   PRO   220      20.060  72.253  74.180  1.00  0.00
ATOM   1466  CA  PRO   220      21.157  72.361  73.275  1.00  0.00
ATOM   1467  C   PRO   220      20.777  71.957  71.843  1.00  0.00
ATOM   1468  O   PRO   220      19.620  72.026  71.454  1.00  0.00
ATOM   1469  CB  PRO   220      22.171  71.328  73.746  1.00  0.00
ATOM   1470  CG  PRO   220      21.306  70.246  74.200  1.00  0.00
ATOM   1471  CD  PRO   220      20.001  70.852  74.674  1.00  0.00
ATOM   1472  N   GLU   221      21.829  71.940  70.978  1.00  0.00
ATOM   1473  CA  GLU   221      21.861  71.537  69.581  1.00  0.00
ATOM   1474  C   GLU   221      22.468  70.086  69.350  1.00  0.00
ATOM   1475  O   GLU   221      22.629  69.723  68.176  1.00  0.00
ATOM   1476  CB  GLU   221      22.716  72.585  68.810  1.00  0.00
ATOM   1477  CG  GLU   221      21.952  73.921  68.534  1.00  0.00
ATOM   1478  CD  GLU   221      22.783  75.000  67.766  1.00  0.00
ATOM   1479  OE1 GLU   221      23.986  75.167  68.132  1.00  0.00
ATOM   1480  OE2 GLU   221      22.226  75.682  66.825  1.00  0.00
ATOM   1481  N   LYS   222      22.909  69.327  70.402  1.00  0.00
ATOM   1482  CA  LYS   222      23.431  67.987  70.271  1.00  0.00
ATOM   1483  C   LYS   222      22.206  67.041  70.261  1.00  0.00
ATOM   1484  O   LYS   222      21.999  66.244  71.188  1.00  0.00
ATOM   1485  CB  LYS   222      24.478  67.708  71.346  1.00  0.00
ATOM   1486  CG  LYS   222      25.395  66.534  71.082  1.00  0.00
ATOM   1487  CD  LYS   222      26.362  66.305  72.264  1.00  0.00
ATOM   1488  CE  LYS   222      27.443  65.254  71.957  1.00  0.00
ATOM   1489  NZ  LYS   222      28.346  65.104  73.103  1.00  0.00
ATOM   1490  N   ILE   223      21.486  67.046  69.129  1.00  0.00
ATOM   1491  CA  ILE   223      20.234  66.286  68.993  1.00  0.00
ATOM   1492  C   ILE   223      20.492  64.749  68.798  1.00  0.00
ATOM   1493  O   ILE   223      19.658  63.993  69.168  1.00  0.00
ATOM   1494  CB  ILE   223      19.466  66.978  67.802  1.00  0.00
ATOM   1495  CG1 ILE   223      18.244  67.755  68.405  1.00  0.00
ATOM   1496  CG2 ILE   223      19.142  66.144  66.545  1.00  0.00
ATOM   1497  CD1 ILE   223      18.804  68.898  69.350  1.00  0.00
ATOM   1498  N   ARG   224      21.558  64.342  68.057  1.00  0.00
ATOM   1499  CA  ARG   224      21.738  62.931  67.787  1.00  0.00
ATOM   1500  C   ARG   224      22.581  62.150  68.862  1.00  0.00
ATOM   1501  O   ARG   224      22.562  60.914  68.761  1.00  0.00
ATOM   1502  CB  ARG   224      22.441  62.844  66.409  1.00  0.00
ATOM   1503  CG  ARG   224      21.575  63.365  65.263  1.00  0.00
ATOM   1504  CD  ARG   224      22.324  63.416  63.949  1.00  0.00
ATOM   1505  NE  ARG   224      23.338  64.474  64.024  1.00  0.00
ATOM   1506  CZ  ARG   224      24.227  64.800  63.088  1.00  0.00
ATOM   1507  NH1 ARG   224      24.221  64.096  61.962  1.00  0.00
ATOM   1508  NH2 ARG   224      25.077  65.819  63.281  1.00  0.00
ATOM   1509  N   LEU   225      23.184  62.798  69.909  1.00  0.00
ATOM   1510  CA  LEU   225      24.016  62.028  70.825  1.00  0.00
ATOM   1511  C   LEU   225      23.120  61.005  71.542  1.00  0.00
ATOM   1512  O   LEU   225      22.116  61.374  72.182  1.00  0.00
ATOM   1513  CB  LEU   225      24.718  62.894  71.874  1.00  0.00
ATOM   1514  CG  LEU   225      25.470  62.138  72.971  1.00  0.00
ATOM   1515  CD1 LEU   225      26.655  61.370  72.372  1.00  0.00
ATOM   1516  CD2 LEU   225      25.946  63.120  74.036  1.00  0.00
ATOM   1517  N   LEU   226      23.502  59.743  71.433  1.00  0.00
ATOM   1518  CA  LEU   226      22.866  58.619  72.096  1.00  0.00
ATOM   1519  C   LEU   226      22.809  58.830  73.666  1.00  0.00
ATOM   1520  O   LEU   226      21.748  58.593  74.221  1.00  0.00
ATOM   1521  CB  LEU   226      23.797  57.414  71.872  1.00  0.00
ATOM   1522  CG  LEU   226      23.315  56.009  72.398  1.00  0.00
ATOM   1523  CD1 LEU   226      22.079  55.497  71.662  1.00  0.00
ATOM   1524  CD2 LEU   226      24.407  54.962  72.256  1.00  0.00
ATOM   1525  N   LYS   227      23.964  58.992  74.364  1.00  0.00
ATOM   1526  CA  LYS   227      24.054  59.252  75.821  1.00  0.00
ATOM   1527  C   LYS   227      23.237  60.450  76.224  1.00  0.00
ATOM   1528  O   LYS   227      22.726  60.392  77.345  1.00  0.00
ATOM   1529  CB  LYS   227      25.535  59.435  76.257  1.00  0.00
ATOM   1530  CG  LYS   227      25.806  61.024  76.462  1.00  0.00
ATOM   1531  CD  LYS   227      27.078  61.331  77.382  1.00  0.00
ATOM   1532  CE  LYS   227      26.688  62.278  78.514  1.00  0.00
ATOM   1533  NZ  LYS   227      26.306  61.563  79.794  1.00  0.00
ATOM   1534  N   GLU   228      23.365  61.638  75.559  1.00  0.00
ATOM   1535  CA  GLU   228      22.585  62.773  75.923  1.00  0.00
ATOM   1536  C   GLU   228      21.118  62.369  75.909  1.00  0.00
ATOM   1537  O   GLU   228      20.489  62.461  76.958  1.00  0.00
ATOM   1538  CB  GLU   228      22.926  63.932  75.035  1.00  0.00
ATOM   1539  CG  GLU   228      22.693  65.294  75.588  1.00  0.00
ATOM   1540  CD  GLU   228      23.490  65.700  76.833  1.00  0.00
ATOM   1541  OE1 GLU   228      24.728  65.705  76.850  1.00  0.00
ATOM   1542  OE2 GLU   228      22.848  66.087  77.802  1.00  0.00
ATOM   1543  N   PHE   229      20.561  61.845  74.793  1.00  0.00
ATOM   1544  CA  PHE   229      19.199  61.347  74.710  1.00  0.00
ATOM   1545  C   PHE   229      18.891  60.351  75.873  1.00  0.00
ATOM   1546  O   PHE   229      17.793  60.391  76.429  1.00  0.00
ATOM   1547  CB  PHE   229      18.849  60.668  73.361  1.00  0.00
ATOM   1548  CG  PHE   229      18.433  61.730  72.347  1.00  0.00
ATOM   1549  CD1 PHE   229      18.259  63.079  72.687  1.00  0.00
ATOM   1550  CD2 PHE   229      18.119  61.288  71.064  1.00  0.00
ATOM   1551  CE1 PHE   229      17.767  63.983  71.754  1.00  0.00
ATOM   1552  CE2 PHE   229      17.623  62.202  70.131  1.00  0.00
ATOM   1553  CZ  PHE   229      17.447  63.545  70.474  1.00  0.00
ATOM   1554  N   MET   230      19.767  59.370  76.171  1.00  0.00
ATOM   1555  CA  MET   230      19.647  58.410  77.229  1.00  0.00
ATOM   1556  C   MET   230      19.414  59.096  78.614  1.00  0.00
ATOM   1557  O   MET   230      18.672  58.504  79.394  1.00  0.00
ATOM   1558  CB  MET   230      20.986  57.654  77.248  1.00  0.00
ATOM   1559  CG  MET   230      20.949  56.508  76.270  1.00  0.00
ATOM   1560  SD  MET   230      21.241  54.909  77.037  1.00  0.00
ATOM   1561  CE  MET   230      22.987  54.824  76.614  1.00  0.00
ATOM   1562  N   HIS   231      20.375  59.939  79.060  1.00  0.00
ATOM   1563  CA  HIS   231      20.243  60.709  80.265  1.00  0.00
ATOM   1564  C   HIS   231      18.888  61.459  80.275  1.00  0.00
ATOM   1565  O   HIS   231      18.329  61.545  81.372  1.00  0.00
ATOM   1566  CB  HIS   231      21.492  61.573  80.528  1.00  0.00
ATOM   1567  CG  HIS   231      22.583  60.892  81.216  1.00  0.00
ATOM   1568  ND1 HIS   231      23.550  60.192  80.568  1.00  0.00
ATOM   1569  CD2 HIS   231      22.836  60.766  82.539  1.00  0.00
ATOM   1570  CE1 HIS   231      24.367  59.651  81.464  1.00  0.00
ATOM   1571  NE2 HIS   231      24.026  60.078  82.669  1.00  0.00
ATOM   1572  N   THR   232      18.459  62.165  79.186  1.00  0.00
ATOM   1573  CA  THR   232      17.190  62.833  79.114  1.00  0.00
ATOM   1574  C   THR   232      16.069  61.798  79.438  1.00  0.00
ATOM   1575  O   THR   232      15.243  62.137  80.281  1.00  0.00
ATOM   1576  CB  THR   232      17.048  63.568  77.759  1.00  0.00
ATOM   1577  OG1 THR   232      17.810  62.981  76.594  1.00  0.00
ATOM   1578  CG2 THR   232      17.447  65.035  77.611  1.00  0.00
ATOM   1579  N   MET   233      15.908  60.669  78.685  1.00  0.00
ATOM   1580  CA  MET   233      14.954  59.585  78.938  1.00  0.00
ATOM   1581  C   MET   233      15.034  59.112  80.436  1.00  0.00
ATOM   1582  O   MET   233      13.971  58.719  80.926  1.00  0.00
ATOM   1583  CB  MET   233      15.072  58.396  77.971  1.00  0.00
ATOM   1584  CG  MET   233      14.491  58.792  76.609  1.00  0.00
ATOM   1585  SD  MET   233      14.912  57.354  75.530  1.00  0.00
ATOM   1586  CE  MET   233      16.680  57.049  75.779  1.00  0.00
ATOM   1587  N   LYS   234      16.186  58.702  80.972  1.00  0.00
ATOM   1588  CA  LYS   234      16.354  58.343  82.374  1.00  0.00
ATOM   1589  C   LYS   234      15.638  59.414  83.276  1.00  0.00
ATOM   1590  O   LYS   234      14.873  58.997  84.130  1.00  0.00
ATOM   1591  CB  LYS   234      17.857  58.191  82.660  1.00  0.00
ATOM   1592  CG  LYS   234      18.135  57.082  83.632  1.00  0.00
ATOM   1593  CD  LYS   234      19.405  57.491  84.554  1.00  0.00
ATOM   1594  CE  LYS   234      19.431  56.751  85.810  1.00  0.00
ATOM   1595  NZ  LYS   234      18.906  57.531  86.950  1.00  0.00
ATOM   1596  N   ASN   235      16.025  60.701  83.209  1.00  0.00
ATOM   1597  CA  ASN   235      15.363  61.750  83.954  1.00  0.00
ATOM   1598  C   ASN   235      13.814  61.797  83.654  1.00  0.00
ATOM   1599  O   ASN   235      13.089  62.164  84.585  1.00  0.00
ATOM   1600  CB  ASN   235      15.991  63.113  83.698  1.00  0.00
ATOM   1601  CG  ASN   235      15.257  64.200  84.473  1.00  0.00
ATOM   1602  OD1 ASN   235      15.537  64.432  85.721  1.00  0.00
ATOM   1603  ND2 ASN   235      14.383  64.883  83.805  1.00  0.00
ATOM   1604  N   THR   236      13.348  61.723  82.375  1.00  0.00
ATOM   1605  CA  THR   236      11.930  61.675  82.048  1.00  0.00
ATOM   1606  C   THR   236      11.186  60.595  82.905  1.00  0.00
ATOM   1607  O   THR   236      10.033  60.866  83.236  1.00  0.00
ATOM   1608  CB  THR   236      11.624  61.462  80.562  1.00  0.00
ATOM   1609  OG1 THR   236      12.015  60.115  80.067  1.00  0.00
ATOM   1610  CG2 THR   236      12.026  62.665  79.717  1.00  0.00
ATOM   1611  N   GLY   237      11.698  59.368  83.005  1.00  0.00
ATOM   1612  CA  GLY   237      11.161  58.294  83.831  1.00  0.00
ATOM   1613  C   GLY   237      11.219  58.685  85.336  1.00  0.00
ATOM   1614  O   GLY   237      10.369  58.196  86.076  1.00  0.00
ATOM   1615  N   ARG   238      12.371  59.179  85.821  1.00  0.00
ATOM   1616  CA  ARG   238      12.545  59.681  87.193  1.00  0.00
ATOM   1617  C   ARG   238      11.347  60.638  87.542  1.00  0.00
ATOM   1618  O   ARG   238      11.006  60.727  88.723  1.00  0.00
ATOM   1619  CB  ARG   238      13.912  60.372  87.282  1.00  0.00
ATOM   1620  CG  ARG   238      14.119  61.149  88.573  1.00  0.00
ATOM   1621  CD  ARG   238      15.448  61.846  88.314  1.00  0.00
ATOM   1622  NE  ARG   238      15.786  62.679  89.447  1.00  0.00
ATOM   1623  CZ  ARG   238      17.004  63.188  89.600  1.00  0.00
ATOM   1624  NH1 ARG   238      18.005  62.972  88.719  1.00  0.00
ATOM   1625  NH2 ARG   238      17.195  63.917  90.697  1.00  0.00
ATOM   1626  N   ASN   239      10.905  61.456  86.559  1.00  0.00
ATOM   1627  CA  ASN   239       9.705  62.339  86.718  1.00  0.00
ATOM   1628  C   ASN   239       8.502  61.577  87.365  1.00  0.00
ATOM   1629  O   ASN   239       7.842  62.215  88.192  1.00  0.00
ATOM   1630  CB  ASN   239       9.251  62.973  85.457  1.00  0.00
ATOM   1631  CG  ASN   239      10.178  63.976  84.862  1.00  0.00
ATOM   1632  OD1 ASN   239      10.688  64.878  85.550  1.00  0.00
ATOM   1633  ND2 ASN   239      10.462  63.817  83.588  1.00  0.00
ATOM   1634  N   VAL   240       8.020  60.448  86.813  1.00  0.00
ATOM   1635  CA  VAL   240       7.036  59.694  87.542  1.00  0.00
ATOM   1636  C   VAL   240       7.835  59.055  88.625  1.00  0.00
ATOM   1637  O   VAL   240       8.575  59.821  89.288  1.00  0.00
ATOM   1638  CB  VAL   240       6.170  58.714  86.729  1.00  0.00
ATOM   1639  CG1 VAL   240       5.269  59.532  85.761  1.00  0.00
ATOM   1640  CG2 VAL   240       7.076  57.813  85.874  1.00  0.00
ATOM   1641  N   ASN   241       7.441  57.918  89.195  1.00  0.00
ATOM   1642  CA  ASN   241       8.315  57.325  90.207  1.00  0.00
ATOM   1643  C   ASN   241       9.473  56.566  89.546  1.00  0.00
ATOM   1644  O   ASN   241      10.453  56.182  90.201  1.00  0.00
ATOM   1645  CB  ASN   241       7.483  56.342  91.026  1.00  0.00
ATOM   1646  CG  ASN   241       6.628  57.023  92.045  1.00  0.00
ATOM   1647  OD1 ASN   241       5.528  56.539  92.326  1.00  0.00
ATOM   1648  ND2 ASN   241       7.025  58.154  92.624  1.00  0.00
ATOM   1649  OXT ASN   241       9.399  56.377  88.315  1.00  0.00
TER
END
