
#######################################################
#                                                     #
#                        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   21 (  177),  selected   21 , name T0386TS028_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS028_3-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    N     219      P     220          2.358
LGA    P     220      E     221          2.911
LGA    -       -      K     222           -
LGA    E     221      I     223          0.777
LGA    K     222      R     224          1.137
LGA    I     223      L     225          2.179
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    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    R     224      L     263          4.835
LGA    L     225      E     264          2.990
LGA    L     226      G     265          3.546
LGA    K     227      F     266          3.768
LGA    E     228      A     267           -
LGA    F     229      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    M     230      N     278          2.849
LGA    H     231      I     279          2.409
LGA    T     232      D     280          1.970
LGA    M     233      H     281          1.497
LGA    K     234      L     282          1.373
LGA    N     235      P     283          2.639
LGA    T     236      -       -           -
LGA    G     237      -       -           -
LGA    R     238      P     284          4.703
LGA    N     239      E     285          1.902
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)   21   81    5.0     17    2.81     0.00     13.917     0.584

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.891626 * X  +   0.402029 * Y  +   0.208270 * Z  +   2.651619
  Y_new =  -0.030147 * X  +   0.511680 * Y  +  -0.858647 * Z  +  30.510164
  Z_new =  -0.451768 * X  +   0.759313 * Y  +   0.468347 * Z  +  37.580627 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.018113   -2.123480  [ DEG:    58.3335   -121.6665 ]
  Theta =   0.468746    2.672846  [ DEG:    26.8572    153.1428 ]
  Phi   =  -0.033799    3.107794  [ DEG:    -1.9365    178.0635 ]
 
# 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: T0386TS028_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS028_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   81   5.0   17   2.81    0.00  13.917
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS028_3-D2
PFRMAT TS
TARGET T0386
MODEL 3
PARENT 2f6s-A
ATOM   1470  N   ASN   219      -0.295  59.945  77.536  1.00  9.00
ATOM   1471  CA  ASN   219       0.642  61.001  77.133  1.00  9.00
ATOM   1472  C   ASN   219       2.080  60.510  77.359  1.00  9.00
ATOM   1473  O   ASN   219       2.722  60.891  78.345  1.00  9.00
ATOM   1474  CB  ASN   219       0.301  62.201  78.019  1.00  9.00
ATOM   1475  CG  ASN   219       0.959  63.529  77.633  1.00  9.00
ATOM   1476  OD1 ASN   219       0.855  64.495  78.393  1.00  9.00
ATOM   1477  ND2 ASN   219       1.557  63.603  76.456  1.00  9.00
ATOM   1478  N   PRO   220       2.615  59.758  76.404  1.00  9.00
ATOM   1479  CA  PRO   220       3.844  58.990  76.639  1.00  9.00
ATOM   1480  C   PRO   220       5.142  59.763  76.365  1.00  9.00
ATOM   1481  O   PRO   220       6.231  59.224  76.578  1.00  9.00
ATOM   1482  CB  PRO   220       3.732  57.833  75.694  1.00  9.00
ATOM   1483  CG  PRO   220       2.675  58.150  74.645  1.00  9.00
ATOM   1484  CD  PRO   220       2.036  59.455  75.088  1.00  9.00
ATOM   1485  N   GLU   221       5.033  60.999  75.908  1.00  9.00
ATOM   1486  CA  GLU   221       6.213  61.731  75.439  1.00  9.00
ATOM   1487  C   GLU   221       6.471  63.028  76.198  1.00  9.00
ATOM   1488  O   GLU   221       7.431  63.737  75.879  1.00  9.00
ATOM   1489  CB  GLU   221       6.012  62.044  73.962  1.00  9.00
ATOM   1490  CG  GLU   221       5.981  60.771  73.123  1.00  9.00
ATOM   1491  CD  GLU   221       5.596  61.101  71.686  1.00  9.00
ATOM   1492  OE1 GLU   221       5.393  62.276  71.419  1.00  9.00
ATOM   1493  OE2 GLU   221       5.304  60.164  70.956  1.00  9.00
ATOM   1494  N   LYS   222       5.611  63.364  77.144  1.00  9.00
ATOM   1495  CA  LYS   222       5.816  64.613  77.880  1.00  9.00
ATOM   1496  C   LYS   222       6.913  64.419  78.920  1.00  9.00
ATOM   1497  O   LYS   222       6.728  63.683  79.898  1.00  9.00
ATOM   1498  CB  LYS   222       4.508  65.018  78.548  1.00  9.00
ATOM   1499  CG  LYS   222       4.626  66.363  79.258  1.00  9.00
ATOM   1500  CD  LYS   222       3.320  66.735  79.944  1.00  9.00
ATOM   1501  CE  LYS   222       3.462  68.002  80.776  1.00  9.00
ATOM   1502  NZ  LYS   222       2.240  68.258  81.552  1.00  9.00
ATOM   1503  N   ILE   223       7.983  65.189  78.786  1.00  9.00
ATOM   1504  CA  ILE   223       9.143  65.010  79.665  1.00  9.00
ATOM   1505  C   ILE   223       8.932  65.549  81.081  1.00  9.00
ATOM   1506  O   ILE   223       9.586  65.045  81.997  1.00  9.00
ATOM   1507  CB  ILE   223      10.377  65.648  79.031  1.00  9.00
ATOM   1508  CG1 ILE   223      10.214  67.151  78.833  1.00  9.00
ATOM   1509  CG2 ILE   223      10.694  64.973  77.701  1.00  9.00
ATOM   1510  CD1 ILE   223      11.491  67.775  78.278  1.00  9.00
ATOM   1511  N   ARG   224       7.886  66.330  81.309  1.00  9.00
ATOM   1512  CA  ARG   224       7.570  66.731  82.681  1.00  9.00
ATOM   1513  C   ARG   224       6.909  65.576  83.423  1.00  9.00
ATOM   1514  O   ARG   224       7.307  65.273  84.555  1.00  9.00
ATOM   1515  CB  ARG   224       6.612  67.912  82.667  1.00  9.00
ATOM   1516  CG  ARG   224       7.222  69.152  82.029  1.00  9.00
ATOM   1517  CD  ARG   224       6.227  70.302  82.081  1.00  9.00
ATOM   1518  NE  ARG   224       6.797  71.542  81.535  1.00  9.00
ATOM   1519  CZ  ARG   224       6.076  72.654  81.387  1.00  9.00
ATOM   1520  NH1 ARG   224       6.652  73.769  80.933  1.00  9.00
ATOM   1521  NH2 ARG   224       4.786  72.660  81.730  1.00  9.00
ATOM   1522  N   LEU   225       6.150  64.778  82.691  1.00  9.00
ATOM   1523  CA  LEU   225       5.517  63.604  83.286  1.00  9.00
ATOM   1524  C   LEU   225       6.557  62.522  83.513  1.00  9.00
ATOM   1525  O   LEU   225       6.724  62.085  84.656  1.00  9.00
ATOM   1526  CB  LEU   225       4.447  63.067  82.346  1.00  9.00
ATOM   1527  CG  LEU   225       3.233  63.980  82.271  1.00  9.00
ATOM   1528  CD1 LEU   225       2.229  63.444  81.259  1.00  9.00
ATOM   1529  CD2 LEU   225       2.583  64.137  83.642  1.00  9.00
ATOM   1530  N   LEU   226       7.446  62.372  82.544  1.00  9.00
ATOM   1531  CA  LEU   226       8.516  61.372  82.632  1.00  9.00
ATOM   1532  C   LEU   226       9.516  61.671  83.748  1.00  9.00
ATOM   1533  O   LEU   226       9.822  60.772  84.543  1.00  9.00
ATOM   1534  CB  LEU   226       9.240  61.362  81.290  1.00  9.00
ATOM   1535  CG  LEU   226       8.390  60.711  80.206  1.00  9.00
ATOM   1536  CD1 LEU   226       8.844  61.109  78.806  1.00  9.00
ATOM   1537  CD2 LEU   226       8.386  59.196  80.369  1.00  9.00
ATOM   1538  N   LYS   227       9.775  62.946  83.982  1.00  9.00
ATOM   1539  CA  LYS   227      10.693  63.352  85.047  1.00  9.00
ATOM   1540  C   LYS   227      10.060  63.245  86.435  1.00  9.00
ATOM   1541  O   LYS   227      10.733  62.777  87.362  1.00  9.00
ATOM   1542  CB  LYS   227      11.102  64.788  84.750  1.00  9.00
ATOM   1543  CG  LYS   227      11.965  65.408  85.838  1.00  9.00
ATOM   1544  CD  LYS   227      12.398  66.809  85.423  1.00  9.00
ATOM   1545  CE  LYS   227      13.109  67.536  86.555  1.00  9.00
ATOM   1546  NZ  LYS   227      13.637  68.830  86.101  1.00  9.00
ATOM   1547  N   GLU   228       8.744  63.375  86.512  1.00  9.00
ATOM   1548  CA  GLU   228       8.051  63.193  87.793  1.00  9.00
ATOM   1549  C   GLU   228       7.892  61.714  88.124  1.00  9.00
ATOM   1550  O   GLU   228       7.994  61.325  89.296  1.00  9.00
ATOM   1551  CB  GLU   228       6.658  63.800  87.691  1.00  9.00
ATOM   1552  CG  GLU   228       6.692  65.311  87.512  1.00  9.00
ATOM   1553  CD  GLU   228       5.296  65.807  87.153  1.00  9.00
ATOM   1554  OE1 GLU   228       4.485  64.985  86.744  1.00  9.00
ATOM   1555  OE2 GLU   228       5.062  67.001  87.283  1.00  9.00
ATOM   1556  N   PHE   229       7.868  60.887  87.095  1.00  9.00
ATOM   1557  CA  PHE   229       7.704  59.452  87.314  1.00  9.00
ATOM   1558  C   PHE   229       9.037  58.833  87.700  1.00  9.00
ATOM   1559  O   PHE   229       9.082  58.035  88.643  1.00  9.00
ATOM   1560  CB  PHE   229       7.181  58.775  86.047  1.00  9.00
ATOM   1561  CG  PHE   229       5.863  59.304  85.486  1.00  9.00
ATOM   1562  CD1 PHE   229       4.949  59.973  86.293  1.00  9.00
ATOM   1563  CD2 PHE   229       5.577  59.105  84.141  1.00  9.00
ATOM   1564  CE1 PHE   229       3.769  60.464  85.754  1.00  9.00
ATOM   1565  CE2 PHE   229       4.394  59.592  83.604  1.00  9.00
ATOM   1566  CZ  PHE   229       3.494  60.275  84.407  1.00  9.00
ATOM   1567  N   MET   230      10.118  59.386  87.174  1.00  9.00
ATOM   1568  CA  MET   230      11.447  58.912  87.568  1.00  9.00
ATOM   1569  C   MET   230      11.871  59.484  88.910  1.00  9.00
ATOM   1570  O   MET   230      12.550  58.791  89.679  1.00  9.00
ATOM   1571  CB  MET   230      12.473  59.324  86.530  1.00  9.00
ATOM   1572  CG  MET   230      12.229  58.638  85.197  1.00  9.00
ATOM   1573  SD  MET   230      13.481  59.023  83.961  1.00  9.00
ATOM   1574  CE  MET   230      13.400  60.824  84.083  1.00  9.00
ATOM   1575  N   HIS   231      11.295  60.613  89.281  1.00  9.00
ATOM   1576  CA  HIS   231      11.557  61.161  90.604  1.00  9.00
ATOM   1577  C   HIS   231      10.883  60.310  91.667  1.00  9.00
ATOM   1578  O   HIS   231      11.579  59.845  92.574  1.00  9.00
ATOM   1579  CB  HIS   231      11.032  62.587  90.672  1.00  9.00
ATOM   1580  CG  HIS   231      11.326  63.266  91.992  1.00  9.00
ATOM   1581  ND1 HIS   231      12.537  63.428  92.556  1.00  9.00
ATOM   1582  CD2 HIS   231      10.409  63.834  92.844  1.00  9.00
ATOM   1583  CE1 HIS   231      12.403  64.075  93.730  1.00  9.00
ATOM   1584  NE2 HIS   231      11.085  64.324  93.908  1.00  9.00
ATOM   1585  N   THR   232       9.690  59.820  91.373  1.00  9.00
ATOM   1586  CA  THR   232       8.992  58.970  92.345  1.00  9.00
ATOM   1587  C   THR   232       9.528  57.540  92.339  1.00  9.00
ATOM   1588  O   THR   232       9.552  56.886  93.389  1.00  9.00
ATOM   1589  CB  THR   232       7.508  58.963  92.022  1.00  9.00
ATOM   1590  OG1 THR   232       7.073  60.311  91.917  1.00  9.00
ATOM   1591  CG2 THR   232       6.716  58.284  93.133  1.00  9.00
ATOM   1592  N   MET   233      10.186  57.180  91.252  1.00  9.00
ATOM   1593  CA  MET   233      10.884  55.901  91.150  1.00  9.00
ATOM   1594  C   MET   233      12.129  55.897  92.040  1.00  9.00
ATOM   1595  O   MET   233      12.292  54.978  92.854  1.00  9.00
ATOM   1596  CB  MET   233      11.276  55.779  89.686  1.00  9.00
ATOM   1597  CG  MET   233      11.956  54.473  89.328  1.00  9.00
ATOM   1598  SD  MET   233      12.464  54.388  87.599  1.00  9.00
ATOM   1599  CE  MET   233      13.726  55.682  87.623  1.00  9.00
ATOM   1600  N   LYS   234      12.799  57.038  92.110  1.00  9.00
ATOM   1601  CA  LYS   234      13.945  57.190  93.014  1.00  9.00
ATOM   1602  C   LYS   234      13.493  57.392  94.461  1.00  9.00
ATOM   1603  O   LYS   234      14.141  56.873  95.381  1.00  9.00
ATOM   1604  CB  LYS   234      14.755  58.409  92.584  1.00  9.00
ATOM   1605  CG  LYS   234      15.322  58.271  91.176  1.00  9.00
ATOM   1606  CD  LYS   234      16.388  57.185  91.081  1.00  9.00
ATOM   1607  CE  LYS   234      16.897  57.041  89.651  1.00  9.00
ATOM   1608  NZ  LYS   234      17.887  55.959  89.544  1.00  9.00
ATOM   1609  N   ASN   235      12.281  57.893  94.642  1.00  9.00
ATOM   1610  CA  ASN   235      11.728  58.067  95.989  1.00  9.00
ATOM   1611  C   ASN   235      11.279  56.741  96.595  1.00  9.00
ATOM   1612  O   ASN   235      11.426  56.555  97.810  1.00  9.00
ATOM   1613  CB  ASN   235      10.519  58.996  95.940  1.00  9.00
ATOM   1614  CG  ASN   235      10.864  60.404  95.458  1.00  9.00
ATOM   1615  OD1 ASN   235      12.031  60.806  95.357  1.00  9.00
ATOM   1616  ND2 ASN   235       9.810  61.148  95.170  1.00  9.00
ATOM   1617  N   THR   236      11.050  55.753  95.743  1.00  9.00
ATOM   1618  CA  THR   236      10.695  54.408  96.208  1.00  9.00
ATOM   1619  C   THR   236      11.931  53.647  96.698  1.00  9.00
ATOM   1620  O   THR   236      11.814  52.748  97.540  1.00  9.00
ATOM   1621  CB  THR   236      10.045  53.665  95.045  1.00  9.00
ATOM   1622  OG1 THR   236       8.901  54.402  94.632  1.00  9.00
ATOM   1623  CG2 THR   236       9.585  52.269  95.442  1.00  9.00
ATOM   1624  N   GLY   237      13.103  54.159  96.353  1.00  9.00
ATOM   1625  CA  GLY   237      14.365  53.617  96.863  1.00  9.00
ATOM   1626  C   GLY   237      15.001  54.545  97.905  1.00  9.00
ATOM   1627  O   GLY   237      16.227  54.545  98.061  1.00  9.00
ATOM   1628  N   ARG   238      14.162  55.340  98.563  1.00  9.00
ATOM   1629  CA  ARG   238      14.529  56.228  99.686  1.00  9.00
ATOM   1630  C   ARG   238      15.278  57.497  99.275  1.00  9.00
ATOM   1631  O   ARG   238      16.026  58.048 100.090  1.00  9.00
ATOM   1632  CB  ARG   238      15.382  55.495 100.719  1.00  9.00
ATOM   1633  CG  ARG   238      14.679  54.310 101.366  1.00  9.00
ATOM   1634  CD  ARG   238      15.629  53.628 102.343  1.00  9.00
ATOM   1635  NE  ARG   238      15.043  52.414 102.929  1.00  9.00
ATOM   1636  CZ  ARG   238      15.769  51.532 103.622  1.00  9.00
ATOM   1637  NH1 ARG   238      15.189  50.443 104.132  1.00  9.00
ATOM   1638  NH2 ARG   238      17.075  51.741 103.804  1.00  9.00
ATOM   1639  N   ASN   239      15.050  57.989  98.070  1.00  9.00
ATOM   1640  CA  ASN   239      15.629  59.283  97.692  1.00  9.00
ATOM   1641  C   ASN   239      14.545  60.354  97.852  1.00  9.00
ATOM   1642  O   ASN   239      13.388  59.962  97.875  1.00  9.00
ATOM   1643  CB  ASN   239      16.137  59.195  96.252  1.00  9.00
ATOM   1644  CG  ASN   239      17.025  60.380  95.859  1.00  9.00
ATOM   1645  OD1 ASN   239      17.161  61.369  96.589  1.00  9.00
ATOM   1646  ND2 ASN   239      17.652  60.241  94.703  1.00  9.00
TER
END
