
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_5-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    N     219      E     221          2.633
LGA    P     220      K     222          2.129
LGA    E     221      I     223          1.248
LGA    K     222      R     224          1.352
LGA    I     223      L     225          3.122
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          4.615
LGA    L     225      E     264          3.044
LGA    L     226      G     265          2.972
LGA    K     227      F     266          2.807
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          3.557
LGA    H     231      I     279          3.324
LGA    T     232      D     280          2.637
LGA    M     233      H     281          1.992
LGA    K     234      L     282          1.806
LGA    N     235      P     283          2.942
LGA    T     236      P     284          3.888
LGA    G     237      -       -           -
LGA    R     238      E     285          2.893
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     17    2.89     0.00     13.234     0.569

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.154162 * X  +   0.891832 * Y  +   0.425288 * Z  + -41.445679
  Y_new =   0.883316 * X  +   0.068460 * Y  +  -0.463752 * Z  +  61.558189
  Z_new =  -0.442704 * X  +   0.447157 * Y  +  -0.777215 * Z  +  51.382042 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.619509   -0.522084  [ DEG:   150.0868    -29.9132 ]
  Theta =   0.458612    2.682980  [ DEG:    26.2766    153.7234 ]
  Phi   =   1.398010   -1.743582  [ DEG:    80.1001    -99.8999 ]
 
# 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_5-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_5-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   17   2.89    0.00  13.234
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_5-D2
PFRMAT TS
TARGET T0386
MODEL  5  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      -0.293  57.934  80.102  1.00  0.00
ATOM   1471  CA  ASN   219       0.517  58.092  78.791  1.00  0.00
ATOM   1472  C   ASN   219       2.113  58.375  78.650  1.00  0.00
ATOM   1473  O   ASN   219       2.681  58.788  79.672  1.00  0.00
ATOM   1474  CB  ASN   219      -0.194  59.207  78.012  1.00  0.00
ATOM   1475  CG  ASN   219      -1.571  58.828  77.499  1.00  0.00
ATOM   1476  OD1 ASN   219      -2.516  59.579  77.616  1.00  0.00
ATOM   1477  ND2 ASN   219      -1.684  57.636  76.971  1.00  0.00
ATOM   1478  N   PRO   220       2.872  58.439  77.408  1.00  0.00
ATOM   1479  CA  PRO   220       4.348  58.581  77.189  1.00  0.00
ATOM   1480  C   PRO   220       5.350  59.871  77.118  1.00  0.00
ATOM   1481  O   PRO   220       5.874  60.189  78.175  1.00  0.00
ATOM   1482  CB  PRO   220       4.627  57.784  75.944  1.00  0.00
ATOM   1483  CG  PRO   220       3.325  58.163  75.080  1.00  0.00
ATOM   1484  CD  PRO   220       2.292  58.582  76.082  1.00  0.00
ATOM   1485  N   GLU   221       5.692  60.551  75.938  1.00  0.00
ATOM   1486  CA  GLU   221       6.713  61.600  75.662  1.00  0.00
ATOM   1487  C   GLU   221       6.828  62.894  76.547  1.00  0.00
ATOM   1488  O   GLU   221       7.862  63.587  76.369  1.00  0.00
ATOM   1489  CB  GLU   221       6.546  61.969  74.149  1.00  0.00
ATOM   1490  CG  GLU   221       7.220  60.975  73.151  1.00  0.00
ATOM   1491  CD  GLU   221       8.707  60.854  73.266  1.00  0.00
ATOM   1492  OE1 GLU   221       9.544  61.492  72.626  1.00  0.00
ATOM   1493  OE2 GLU   221       9.009  60.054  74.191  1.00  0.00
ATOM   1494  N   LYS   222       5.933  63.269  77.387  1.00  0.00
ATOM   1495  CA  LYS   222       6.130  64.581  78.079  1.00  0.00
ATOM   1496  C   LYS   222       7.407  64.632  78.993  1.00  0.00
ATOM   1497  O   LYS   222       7.691  63.700  79.759  1.00  0.00
ATOM   1498  CB  LYS   222       4.877  64.915  78.893  1.00  0.00
ATOM   1499  CG  LYS   222       4.946  66.302  79.559  1.00  0.00
ATOM   1500  CD  LYS   222       4.823  67.450  78.552  1.00  0.00
ATOM   1501  CE  LYS   222       4.828  68.827  79.222  1.00  0.00
ATOM   1502  NZ  LYS   222       4.864  69.936  78.261  1.00  0.00
ATOM   1503  N   ILE   223       8.249  65.656  78.749  1.00  0.00
ATOM   1504  CA  ILE   223       9.449  65.914  79.569  1.00  0.00
ATOM   1505  C   ILE   223       9.049  66.004  81.096  1.00  0.00
ATOM   1506  O   ILE   223       9.823  65.521  81.912  1.00  0.00
ATOM   1507  CB  ILE   223      10.244  67.144  79.015  1.00  0.00
ATOM   1508  CG1 ILE   223       9.485  68.448  79.256  1.00  0.00
ATOM   1509  CG2 ILE   223      10.729  66.867  77.552  1.00  0.00
ATOM   1510  CD1 ILE   223       9.787  69.726  78.440  1.00  0.00
ATOM   1511  N   ARG   224       7.997  66.751  81.510  1.00  0.00
ATOM   1512  CA  ARG   224       7.465  66.845  82.890  1.00  0.00
ATOM   1513  C   ARG   224       7.172  65.399  83.435  1.00  0.00
ATOM   1514  O   ARG   224       7.665  65.120  84.522  1.00  0.00
ATOM   1515  CB  ARG   224       6.244  67.800  82.813  1.00  0.00
ATOM   1516  CG  ARG   224       6.624  69.250  82.427  1.00  0.00
ATOM   1517  CD  ARG   224       7.748  69.831  83.174  1.00  0.00
ATOM   1518  NE  ARG   224       7.405  69.783  84.614  1.00  0.00
ATOM   1519  CZ  ARG   224       8.254  69.916  85.608  1.00  0.00
ATOM   1520  NH1 ARG   224       9.552  70.134  85.502  1.00  0.00
ATOM   1521  NH2 ARG   224       7.761  69.884  86.874  1.00  0.00
ATOM   1522  N   LEU   225       6.395  64.547  82.751  1.00  0.00
ATOM   1523  CA  LEU   225       6.109  63.159  83.125  1.00  0.00
ATOM   1524  C   LEU   225       7.427  62.341  83.422  1.00  0.00
ATOM   1525  O   LEU   225       7.473  61.734  84.485  1.00  0.00
ATOM   1526  CB  LEU   225       5.363  62.571  81.919  1.00  0.00
ATOM   1527  CG  LEU   225       3.914  62.939  81.642  1.00  0.00
ATOM   1528  CD1 LEU   225       3.338  62.032  80.548  1.00  0.00
ATOM   1529  CD2 LEU   225       3.042  62.809  82.894  1.00  0.00
ATOM   1530  N   LEU   226       8.346  62.216  82.449  1.00  0.00
ATOM   1531  CA  LEU   226       9.602  61.543  82.545  1.00  0.00
ATOM   1532  C   LEU   226      10.478  62.080  83.723  1.00  0.00
ATOM   1533  O   LEU   226      10.948  61.237  84.480  1.00  0.00
ATOM   1534  CB  LEU   226      10.296  61.754  81.208  1.00  0.00
ATOM   1535  CG  LEU   226       9.839  61.054  79.981  1.00  0.00
ATOM   1536  CD1 LEU   226      10.696  61.462  78.789  1.00  0.00
ATOM   1537  CD2 LEU   226      10.023  59.573  80.130  1.00  0.00
ATOM   1538  N   LYS   227      10.866  63.374  83.765  1.00  0.00
ATOM   1539  CA  LYS   227      11.701  63.946  84.862  1.00  0.00
ATOM   1540  C   LYS   227      11.020  63.808  86.251  1.00  0.00
ATOM   1541  O   LYS   227      11.774  63.511  87.188  1.00  0.00
ATOM   1542  CB  LYS   227      12.003  65.407  84.524  1.00  0.00
ATOM   1543  CG  LYS   227      12.829  65.704  83.323  1.00  0.00
ATOM   1544  CD  LYS   227      13.116  67.196  83.171  1.00  0.00
ATOM   1545  CE  LYS   227      14.016  67.758  84.240  1.00  0.00
ATOM   1546  NZ  LYS   227      15.379  67.134  84.170  1.00  0.00
ATOM   1547  N   GLU   228       9.824  64.417  86.473  1.00  0.00
ATOM   1548  CA  GLU   228       9.153  64.258  87.790  1.00  0.00
ATOM   1549  C   GLU   228       9.144  62.740  88.149  1.00  0.00
ATOM   1550  O   GLU   228       9.257  62.474  89.352  1.00  0.00
ATOM   1551  CB  GLU   228       7.734  64.765  87.817  1.00  0.00
ATOM   1552  CG  GLU   228       7.424  66.188  87.551  1.00  0.00
ATOM   1553  CD  GLU   228       8.280  67.014  88.382  1.00  0.00
ATOM   1554  OE1 GLU   228       9.255  67.669  87.987  1.00  0.00
ATOM   1555  OE2 GLU   228       7.882  66.881  89.681  1.00  0.00
ATOM   1556  N   PHE   229       8.577  61.866  87.272  1.00  0.00
ATOM   1557  CA  PHE   229       8.605  60.406  87.478  1.00  0.00
ATOM   1558  C   PHE   229       9.972  59.868  87.924  1.00  0.00
ATOM   1559  O   PHE   229       9.938  58.919  88.716  1.00  0.00
ATOM   1560  CB  PHE   229       8.300  59.752  86.129  1.00  0.00
ATOM   1561  CG  PHE   229       9.030  58.413  85.818  1.00  0.00
ATOM   1562  CD1 PHE   229       8.710  57.226  86.478  1.00  0.00
ATOM   1563  CD2 PHE   229      10.146  58.424  84.973  1.00  0.00
ATOM   1564  CE1 PHE   229       9.490  56.099  86.294  1.00  0.00
ATOM   1565  CE2 PHE   229      10.919  57.290  84.799  1.00  0.00
ATOM   1566  CZ  PHE   229      10.591  56.138  85.464  1.00  0.00
ATOM   1567  N   MET   230      11.078  60.066  87.145  1.00  0.00
ATOM   1568  CA  MET   230      12.413  59.672  87.555  1.00  0.00
ATOM   1569  C   MET   230      12.662  60.097  89.024  1.00  0.00
ATOM   1570  O   MET   230      13.287  59.297  89.714  1.00  0.00
ATOM   1571  CB  MET   230      13.466  60.137  86.555  1.00  0.00
ATOM   1572  CG  MET   230      13.374  59.323  85.241  1.00  0.00
ATOM   1573  SD  MET   230      14.698  59.793  84.153  1.00  0.00
ATOM   1574  CE  MET   230      14.380  61.551  83.905  1.00  0.00
ATOM   1575  N   HIS   231      12.587  61.406  89.366  1.00  0.00
ATOM   1576  CA  HIS   231      12.721  61.911  90.739  1.00  0.00
ATOM   1577  C   HIS   231      11.820  61.098  91.728  1.00  0.00
ATOM   1578  O   HIS   231      12.261  60.972  92.863  1.00  0.00
ATOM   1579  CB  HIS   231      12.443  63.416  90.780  1.00  0.00
ATOM   1580  CG  HIS   231      12.653  64.056  92.129  1.00  0.00
ATOM   1581  ND1 HIS   231      11.899  64.134  93.247  1.00  0.00
ATOM   1582  CD2 HIS   231      13.785  64.782  92.356  1.00  0.00
ATOM   1583  CE1 HIS   231      12.539  64.875  94.119  1.00  0.00
ATOM   1584  NE2 HIS   231      13.643  65.273  93.559  1.00  0.00
ATOM   1585  N   THR   232      10.505  60.927  91.476  1.00  0.00
ATOM   1586  CA  THR   232       9.614  60.097  92.294  1.00  0.00
ATOM   1587  C   THR   232      10.232  58.663  92.432  1.00  0.00
ATOM   1588  O   THR   232      10.072  58.117  93.527  1.00  0.00
ATOM   1589  CB  THR   232       8.124  60.085  91.831  1.00  0.00
ATOM   1590  OG1 THR   232       7.834  59.285  90.723  1.00  0.00
ATOM   1591  CG2 THR   232       7.504  61.468  91.932  1.00  0.00
ATOM   1592  N   MET   233      10.569  57.974  91.339  1.00  0.00
ATOM   1593  CA  MET   233      11.233  56.695  91.297  1.00  0.00
ATOM   1594  C   MET   233      12.456  56.653  92.261  1.00  0.00
ATOM   1595  O   MET   233      12.549  55.680  93.023  1.00  0.00
ATOM   1596  CB  MET   233      11.576  56.447  89.793  1.00  0.00
ATOM   1597  CG  MET   233      12.099  54.966  89.674  1.00  0.00
ATOM   1598  SD  MET   233      13.923  55.147  89.613  1.00  0.00
ATOM   1599  CE  MET   233      14.241  54.867  87.854  1.00  0.00
ATOM   1600  N   LYS   234      13.451  57.559  92.118  1.00  0.00
ATOM   1601  CA  LYS   234      14.572  57.642  93.039  1.00  0.00
ATOM   1602  C   LYS   234      14.049  57.740  94.501  1.00  0.00
ATOM   1603  O   LYS   234      14.655  57.098  95.362  1.00  0.00
ATOM   1604  CB  LYS   234      15.376  58.883  92.700  1.00  0.00
ATOM   1605  CG  LYS   234      16.537  58.750  91.796  1.00  0.00
ATOM   1606  CD  LYS   234      16.517  57.630  90.802  1.00  0.00
ATOM   1607  CE  LYS   234      17.873  57.529  90.065  1.00  0.00
ATOM   1608  NZ  LYS   234      18.003  56.147  89.521  1.00  0.00
ATOM   1609  N   ASN   235      13.169  58.734  94.799  1.00  0.00
ATOM   1610  CA  ASN   235      12.528  58.972  96.079  1.00  0.00
ATOM   1611  C   ASN   235      12.042  57.679  96.795  1.00  0.00
ATOM   1612  O   ASN   235      12.300  57.611  97.997  1.00  0.00
ATOM   1613  CB  ASN   235      11.373  59.963  95.855  1.00  0.00
ATOM   1614  CG  ASN   235      10.457  60.229  97.063  1.00  0.00
ATOM   1615  OD1 ASN   235       9.926  59.283  97.702  1.00  0.00
ATOM   1616  ND2 ASN   235      10.184  61.498  97.346  1.00  0.00
ATOM   1617  N   THR   236      11.290  56.771  96.150  1.00  0.00
ATOM   1618  CA  THR   236      10.803  55.526  96.791  1.00  0.00
ATOM   1619  C   THR   236      11.941  54.778  97.576  1.00  0.00
ATOM   1620  O   THR   236      11.647  54.353  98.705  1.00  0.00
ATOM   1621  CB  THR   236      10.063  54.597  95.775  1.00  0.00
ATOM   1622  OG1 THR   236      10.781  53.415  95.321  1.00  0.00
ATOM   1623  CG2 THR   236       9.630  55.267  94.431  1.00  0.00
ATOM   1624  N   GLY   237      13.050  54.370  96.941  1.00  0.00
ATOM   1625  CA  GLY   237      14.195  53.751  97.617  1.00  0.00
ATOM   1626  C   GLY   237      14.774  54.630  98.768  1.00  0.00
ATOM   1627  O   GLY   237      14.975  54.077  99.850  1.00  0.00
ATOM   1628  N   ARG   238      15.227  55.867  98.497  1.00  0.00
ATOM   1629  CA  ARG   238      15.797  56.808  99.474  1.00  0.00
ATOM   1630  C   ARG   238      16.030  58.158  98.770  1.00  0.00
ATOM   1631  O   ARG   238      15.447  59.171  99.142  1.00  0.00
ATOM   1632  CB  ARG   238      17.076  56.234 100.083  1.00  0.00
ATOM   1633  CG  ARG   238      18.193  56.032  99.043  1.00  0.00
ATOM   1634  CD  ARG   238      19.466  55.679  99.736  1.00  0.00
ATOM   1635  NE  ARG   238      20.506  55.428  98.688  1.00  0.00
ATOM   1636  CZ  ARG   238      21.763  55.296  99.136  1.00  0.00
ATOM   1637  NH1 ARG   238      22.217  55.213 100.396  1.00  0.00
ATOM   1638  NH2 ARG   238      22.627  55.332  98.138  1.00  0.00
ATOM   1639  OXT ARG   238      16.583  58.101  97.649  1.00  0.00
TER
END
