
#######################################################
#                                                     #
#                        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   20 (  170),  selected   20 , name T0386TS298_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_2-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    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    N     219      N     239          3.740
LGA    P     220      V     240          0.703
LGA    E     221      N     241          2.830
LGA    -       -      D     242           -
LGA    K     222      R     243          1.331
LGA    I     223      P     244          2.932
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    R     224      K     271          4.617
LGA    L     225      G     272          5.113
LGA    L     226      A     273          4.443
LGA    K     227      Y     274          4.014
LGA    E     228      I     275          2.489
LGA    F     229      I     276          3.337
LGA    M     230      -       -           -
LGA    H     231      -       -           -
LGA    T     232      G     277          3.484
LGA    M     233      -       -           -
LGA    K     234      -       -           -
LGA    N     235      N     278          3.560
LGA    T     236      I     279          0.975
LGA    G     237      D     280          2.321
LGA    R     238      H     281          1.839
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)   20   81    5.0     16    3.24    12.50     12.333     0.479

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.698546 * X  +  -0.518265 * Y  +  -0.493391 * Z  +  52.629444
  Y_new =  -0.574462 * X  +  -0.817284 * Y  +   0.045160 * Z  + 105.870789
  Z_new =  -0.426645 * X  +   0.251889 * Y  +  -0.868634 * Z  +  54.634010 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.859352   -0.282241  [ DEG:   163.8288    -16.1712 ]
  Theta =   0.440780    2.700812  [ DEG:    25.2549    154.7451 ]
  Phi   =  -0.688232    2.453360  [ DEG:   -39.4328    140.5672 ]
 
# 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: T0386TS298_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   81   5.0   16   3.24   12.50  12.333
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_2-D2
PFRMAT TS
TARGET T0386
MODEL  2  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      20.758  70.821  74.197  1.00  0.00
ATOM   1471  CA  ASN   219      21.514  70.400  72.930  1.00  0.00
ATOM   1472  C   ASN   219      21.006  69.068  72.135  1.00  0.00
ATOM   1473  O   ASN   219      20.442  68.239  72.846  1.00  0.00
ATOM   1474  CB  ASN   219      23.005  70.157  73.310  1.00  0.00
ATOM   1475  CG  ASN   219      24.082  70.187  72.185  1.00  0.00
ATOM   1476  OD1 ASN   219      24.260  71.178  71.484  1.00  0.00
ATOM   1477  ND2 ASN   219      24.774  69.046  72.015  1.00  0.00
ATOM   1478  N   PRO   220      21.165  68.772  70.757  1.00  0.00
ATOM   1479  CA  PRO   220      20.570  67.586  69.990  1.00  0.00
ATOM   1480  C   PRO   220      21.239  66.094  70.008  1.00  0.00
ATOM   1481  O   PRO   220      21.208  65.513  71.094  1.00  0.00
ATOM   1482  CB  PRO   220      20.360  68.025  68.549  1.00  0.00
ATOM   1483  CG  PRO   220      21.641  68.906  68.367  1.00  0.00
ATOM   1484  CD  PRO   220      21.831  69.598  69.711  1.00  0.00
ATOM   1485  N   GLU   221      21.070  65.412  68.803  1.00  0.00
ATOM   1486  CA  GLU   221      21.291  63.984  68.428  1.00  0.00
ATOM   1487  C   GLU   221      22.284  63.056  69.194  1.00  0.00
ATOM   1488  O   GLU   221      22.211  61.842  68.916  1.00  0.00
ATOM   1489  CB  GLU   221      21.776  64.034  66.968  1.00  0.00
ATOM   1490  CG  GLU   221      21.144  65.148  66.124  1.00  0.00
ATOM   1491  CD  GLU   221      21.204  65.319  64.645  1.00  0.00
ATOM   1492  OE1 GLU   221      20.736  66.317  64.091  1.00  0.00
ATOM   1493  OE2 GLU   221      21.759  64.376  64.027  1.00  0.00
ATOM   1494  N   LYS   222      23.088  63.471  70.173  1.00  0.00
ATOM   1495  CA  LYS   222      23.992  62.453  70.795  1.00  0.00
ATOM   1496  C   LYS   222      23.237  61.231  71.427  1.00  0.00
ATOM   1497  O   LYS   222      22.252  61.410  72.144  1.00  0.00
ATOM   1498  CB  LYS   222      24.820  63.156  71.887  1.00  0.00
ATOM   1499  CG  LYS   222      25.869  62.217  72.528  1.00  0.00
ATOM   1500  CD  LYS   222      27.030  61.875  71.589  1.00  0.00
ATOM   1501  CE  LYS   222      28.090  60.996  72.256  1.00  0.00
ATOM   1502  NZ  LYS   222      29.129  60.537  71.323  1.00  0.00
ATOM   1503  N   ILE   223      23.746  60.008  71.179  1.00  0.00
ATOM   1504  CA  ILE   223      23.258  58.739  71.753  1.00  0.00
ATOM   1505  C   ILE   223      23.228  58.787  73.334  1.00  0.00
ATOM   1506  O   ILE   223      22.238  58.294  73.871  1.00  0.00
ATOM   1507  CB  ILE   223      24.105  57.582  71.147  1.00  0.00
ATOM   1508  CG1 ILE   223      23.492  56.223  71.535  1.00  0.00
ATOM   1509  CG2 ILE   223      25.613  57.701  71.571  1.00  0.00
ATOM   1510  CD1 ILE   223      24.036  55.374  72.728  1.00  0.00
ATOM   1511  N   ARG   224      24.295  59.200  74.044  1.00  0.00
ATOM   1512  CA  ARG   224      24.328  59.363  75.511  1.00  0.00
ATOM   1513  C   ARG   224      23.232  60.372  75.981  1.00  0.00
ATOM   1514  O   ARG   224      22.587  60.070  76.983  1.00  0.00
ATOM   1515  CB  ARG   224      25.760  59.772  75.868  1.00  0.00
ATOM   1516  CG  ARG   224      26.150  59.258  77.237  1.00  0.00
ATOM   1517  CD  ARG   224      27.598  59.464  77.471  1.00  0.00
ATOM   1518  NE  ARG   224      28.459  58.407  76.926  1.00  0.00
ATOM   1519  CZ  ARG   224      29.786  58.508  77.207  1.00  0.00
ATOM   1520  NH1 ARG   224      30.308  59.487  77.951  1.00  0.00
ATOM   1521  NH2 ARG   224      30.623  57.594  76.715  1.00  0.00
ATOM   1522  N   LEU   225      23.201  61.617  75.455  1.00  0.00
ATOM   1523  CA  LEU   225      22.166  62.602  75.764  1.00  0.00
ATOM   1524  C   LEU   225      20.725  61.968  75.669  1.00  0.00
ATOM   1525  O   LEU   225      20.105  61.821  76.711  1.00  0.00
ATOM   1526  CB  LEU   225      22.349  63.715  74.718  1.00  0.00
ATOM   1527  CG  LEU   225      23.487  64.711  74.838  1.00  0.00
ATOM   1528  CD1 LEU   225      23.289  65.858  73.840  1.00  0.00
ATOM   1529  CD2 LEU   225      23.590  65.300  76.247  1.00  0.00
ATOM   1530  N   LEU   226      20.301  61.465  74.495  1.00  0.00
ATOM   1531  CA  LEU   226      19.058  60.777  74.255  1.00  0.00
ATOM   1532  C   LEU   226      18.794  59.590  75.256  1.00  0.00
ATOM   1533  O   LEU   226      17.682  59.582  75.792  1.00  0.00
ATOM   1534  CB  LEU   226      19.055  60.268  72.842  1.00  0.00
ATOM   1535  CG  LEU   226      18.922  61.212  71.683  1.00  0.00
ATOM   1536  CD1 LEU   226      18.993  60.448  70.366  1.00  0.00
ATOM   1537  CD2 LEU   226      17.564  61.849  71.715  1.00  0.00
ATOM   1538  N   LYS   227      19.641  58.526  75.327  1.00  0.00
ATOM   1539  CA  LYS   227      19.435  57.399  76.201  1.00  0.00
ATOM   1540  C   LYS   227      19.437  57.744  77.723  1.00  0.00
ATOM   1541  O   LYS   227      18.604  57.142  78.414  1.00  0.00
ATOM   1542  CB  LYS   227      20.405  56.256  75.912  1.00  0.00
ATOM   1543  CG  LYS   227      20.416  55.676  74.533  1.00  0.00
ATOM   1544  CD  LYS   227      21.439  54.553  74.391  1.00  0.00
ATOM   1545  CE  LYS   227      21.126  53.330  75.214  1.00  0.00
ATOM   1546  NZ  LYS   227      19.848  52.693  74.752  1.00  0.00
ATOM   1547  N   GLU   228      20.562  58.256  78.303  1.00  0.00
ATOM   1548  CA  GLU   228      20.568  58.671  79.721  1.00  0.00
ATOM   1549  C   GLU   228      19.292  59.465  80.037  1.00  0.00
ATOM   1550  O   GLU   228      18.828  59.340  81.162  1.00  0.00
ATOM   1551  CB  GLU   228      21.762  59.526  80.075  1.00  0.00
ATOM   1552  CG  GLU   228      23.152  59.033  79.910  1.00  0.00
ATOM   1553  CD  GLU   228      23.269  57.742  80.566  1.00  0.00
ATOM   1554  OE1 GLU   228      23.337  56.645  79.992  1.00  0.00
ATOM   1555  OE2 GLU   228      23.206  57.933  81.916  1.00  0.00
ATOM   1556  N   PHE   229      18.944  60.514  79.242  1.00  0.00
ATOM   1557  CA  PHE   229      17.728  61.316  79.337  1.00  0.00
ATOM   1558  C   PHE   229      16.427  60.454  79.454  1.00  0.00
ATOM   1559  O   PHE   229      15.591  60.820  80.229  1.00  0.00
ATOM   1560  CB  PHE   229      17.533  62.270  78.131  1.00  0.00
ATOM   1561  CG  PHE   229      16.083  62.575  77.652  1.00  0.00
ATOM   1562  CD1 PHE   229      15.199  63.333  78.428  1.00  0.00
ATOM   1563  CD2 PHE   229      15.598  61.979  76.495  1.00  0.00
ATOM   1564  CE1 PHE   229      13.869  63.485  78.079  1.00  0.00
ATOM   1565  CE2 PHE   229      14.268  62.136  76.152  1.00  0.00
ATOM   1566  CZ  PHE   229      13.408  62.878  76.938  1.00  0.00
ATOM   1567  N   MET   230      16.109  59.552  78.476  1.00  0.00
ATOM   1568  CA  MET   230      14.968  58.669  78.592  1.00  0.00
ATOM   1569  C   MET   230      14.951  58.034  80.023  1.00  0.00
ATOM   1570  O   MET   230      13.837  57.784  80.485  1.00  0.00
ATOM   1571  CB  MET   230      14.954  57.646  77.432  1.00  0.00
ATOM   1572  CG  MET   230      14.556  58.353  76.115  1.00  0.00
ATOM   1573  SD  MET   230      14.373  57.137  74.833  1.00  0.00
ATOM   1574  CE  MET   230      16.017  56.396  74.774  1.00  0.00
ATOM   1575  N   HIS   231      16.038  57.371  80.460  1.00  0.00
ATOM   1576  CA  HIS   231      16.216  56.813  81.797  1.00  0.00
ATOM   1577  C   HIS   231      15.810  57.864  82.880  1.00  0.00
ATOM   1578  O   HIS   231      15.073  57.468  83.790  1.00  0.00
ATOM   1579  CB  HIS   231      17.665  56.306  81.898  1.00  0.00
ATOM   1580  CG  HIS   231      18.016  55.796  83.265  1.00  0.00
ATOM   1581  ND1 HIS   231      19.239  55.193  83.445  1.00  0.00
ATOM   1582  CD2 HIS   231      17.274  55.667  84.444  1.00  0.00
ATOM   1583  CE1 HIS   231      19.264  54.826  84.754  1.00  0.00
ATOM   1584  NE2 HIS   231      18.103  55.082  85.346  1.00  0.00
ATOM   1585  N   THR   232      16.425  59.071  82.955  1.00  0.00
ATOM   1586  CA  THR   232      16.043  60.124  83.910  1.00  0.00
ATOM   1587  C   THR   232      14.512  60.491  83.790  1.00  0.00
ATOM   1588  O   THR   232      13.939  60.778  84.831  1.00  0.00
ATOM   1589  CB  THR   232      17.138  61.244  83.819  1.00  0.00
ATOM   1590  OG1 THR   232      17.247  61.841  82.511  1.00  0.00
ATOM   1591  CG2 THR   232      18.541  60.666  84.221  1.00  0.00
ATOM   1592  N   MET   233      13.944  60.642  82.599  1.00  0.00
ATOM   1593  CA  MET   233      12.514  60.883  82.325  1.00  0.00
ATOM   1594  C   MET   233      11.641  59.767  82.996  1.00  0.00
ATOM   1595  O   MET   233      10.628  60.156  83.586  1.00  0.00
ATOM   1596  CB  MET   233      12.394  60.874  80.761  1.00  0.00
ATOM   1597  CG  MET   233      10.928  61.338  80.417  1.00  0.00
ATOM   1598  SD  MET   233      10.080  59.761  80.016  1.00  0.00
ATOM   1599  CE  MET   233       9.992  59.865  78.212  1.00  0.00
ATOM   1600  N   LYS   234      11.825  58.477  82.663  1.00  0.00
ATOM   1601  CA  LYS   234      11.099  57.403  83.349  1.00  0.00
ATOM   1602  C   LYS   234      11.197  57.540  84.895  1.00  0.00
ATOM   1603  O   LYS   234      10.215  57.208  85.569  1.00  0.00
ATOM   1604  CB  LYS   234      11.649  56.053  82.957  1.00  0.00
ATOM   1605  CG  LYS   234      11.035  55.335  81.813  1.00  0.00
ATOM   1606  CD  LYS   234      10.334  56.147  80.766  1.00  0.00
ATOM   1607  CE  LYS   234       9.584  55.229  79.774  1.00  0.00
ATOM   1608  NZ  LYS   234       8.513  56.031  79.120  1.00  0.00
ATOM   1609  N   ASN   235      12.418  57.669  85.424  1.00  0.00
ATOM   1610  CA  ASN   235      12.725  57.798  86.808  1.00  0.00
ATOM   1611  C   ASN   235      12.058  59.016  87.523  1.00  0.00
ATOM   1612  O   ASN   235      11.809  58.863  88.730  1.00  0.00
ATOM   1613  CB  ASN   235      14.249  57.933  86.956  1.00  0.00
ATOM   1614  CG  ASN   235      14.818  58.231  88.346  1.00  0.00
ATOM   1615  OD1 ASN   235      14.387  59.210  89.009  1.00  0.00
ATOM   1616  ND2 ASN   235      15.827  57.485  88.785  1.00  0.00
ATOM   1617  N   THR   236      11.548  60.057  86.825  1.00  0.00
ATOM   1618  CA  THR   236      10.909  61.157  87.580  1.00  0.00
ATOM   1619  C   THR   236       9.691  60.619  88.424  1.00  0.00
ATOM   1620  O   THR   236       9.673  60.911  89.629  1.00  0.00
ATOM   1621  CB  THR   236      10.590  62.417  86.708  1.00  0.00
ATOM   1622  OG1 THR   236       9.179  62.599  86.370  1.00  0.00
ATOM   1623  CG2 THR   236      11.278  62.445  85.312  1.00  0.00
ATOM   1624  N   GLY   237       8.651  60.001  87.822  1.00  0.00
ATOM   1625  CA  GLY   237       7.456  59.441  88.494  1.00  0.00
ATOM   1626  C   GLY   237       7.739  58.227  89.432  1.00  0.00
ATOM   1627  O   GLY   237       7.020  58.151  90.437  1.00  0.00
ATOM   1628  N   ARG   238       8.325  57.164  88.880  1.00  0.00
ATOM   1629  CA  ARG   238       8.702  55.959  89.594  1.00  0.00
ATOM   1630  C   ARG   238       9.866  55.239  88.851  1.00  0.00
ATOM   1631  O   ARG   238      10.998  55.195  89.354  1.00  0.00
ATOM   1632  CB  ARG   238       7.409  55.140  89.714  1.00  0.00
ATOM   1633  CG  ARG   238       6.858  54.640  88.399  1.00  0.00
ATOM   1634  CD  ARG   238       5.601  53.832  88.793  1.00  0.00
ATOM   1635  NE  ARG   238       5.250  53.253  87.495  1.00  0.00
ATOM   1636  CZ  ARG   238       4.330  52.245  87.380  1.00  0.00
ATOM   1637  NH1 ARG   238       3.786  51.637  88.451  1.00  0.00
ATOM   1638  NH2 ARG   238       3.961  51.992  86.073  1.00  0.00
ATOM   1639  OXT ARG   238       9.655  54.892  87.698  1.00  0.00
TER
END
