
#######################################################
#                                                     #
#                        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 (  158),  selected   19 , name T0386TS028_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS028_2-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     219      N     239          3.124
LGA    P     220      V     240          1.212
LGA    E     221      N     241          2.583
LGA    -       -      D     242           -
LGA    K     222      R     243          1.171
LGA    I     223      P     244          2.577
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          4.910
LGA    L     225      G     272           #
LGA    L     226      A     273          4.690
LGA    K     227      Y     274          3.380
LGA    E     228      -       -           -
LGA    F     229      I     275          3.629
LGA    M     230      I     276          1.575
LGA    H     231      G     277          3.558
LGA    T     232      -       -           -
LGA    M     233      -       -           -
LGA    K     234      -       -           -
LGA    N     235      N     278          3.866
LGA    T     236      I     279          0.620
LGA    G     237      D     280          2.429
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)   19   81    5.0     14    3.08    14.29     11.009     0.440

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.698556 * X  +  -0.499460 * Y  +  -0.512405 * Z  +  51.216393
  Y_new =  -0.548773 * X  +  -0.833495 * Y  +   0.064301 * Z  + 108.072350
  Z_new =  -0.459203 * X  +   0.236276 * Y  +  -0.856333 * Z  +  55.867786 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.872375   -0.269218  [ DEG:   164.5750    -15.4250 ]
  Theta =   0.477098    2.664495  [ DEG:    27.3357    152.6643 ]
  Phi   =  -0.665887    2.475705  [ DEG:   -38.1525    141.8475 ]
 
# 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_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS028_2-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   14   3.08   14.29  11.009
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS028_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2g03-A
ATOM   1470  N   ASN   219      23.051  70.381  71.748  1.00  9.00
ATOM   1471  CA  ASN   219      23.362  69.130  71.035  1.00  9.00
ATOM   1472  C   ASN   219      22.159  68.183  71.084  1.00  9.00
ATOM   1473  O   ASN   219      22.168  67.233  71.877  1.00  9.00
ATOM   1474  CB  ASN   219      24.533  68.433  71.733  1.00  9.00
ATOM   1475  CG  ASN   219      25.743  69.347  71.941  1.00  9.00
ATOM   1476  OD1 ASN   219      25.998  70.284  71.176  1.00  9.00
ATOM   1477  ND2 ASN   219      26.476  69.056  73.003  1.00  9.00
ATOM   1478  N   PRO   220      21.241  68.306  70.134  1.00  9.00
ATOM   1479  CA  PRO   220      19.899  67.736  70.318  1.00  9.00
ATOM   1480  C   PRO   220      19.805  66.245  69.985  1.00  9.00
ATOM   1481  O   PRO   220      18.886  65.555  70.433  1.00  9.00
ATOM   1482  CB  PRO   220      19.030  68.510  69.379  1.00  9.00
ATOM   1483  CG  PRO   220      19.914  69.259  68.395  1.00  9.00
ATOM   1484  CD  PRO   220      21.332  69.124  68.919  1.00  9.00
ATOM   1485  N   GLU   221      20.797  65.735  69.280  1.00  9.00
ATOM   1486  CA  GLU   221      20.756  64.349  68.820  1.00  9.00
ATOM   1487  C   GLU   221      21.838  63.480  69.453  1.00  9.00
ATOM   1488  O   GLU   221      22.100  62.378  68.960  1.00  9.00
ATOM   1489  CB  GLU   221      20.887  64.349  67.303  1.00  9.00
ATOM   1490  CG  GLU   221      19.660  64.983  66.654  1.00  9.00
ATOM   1491  CD  GLU   221      19.863  65.099  65.148  1.00  9.00
ATOM   1492  OE1 GLU   221      20.944  65.522  64.765  1.00  9.00
ATOM   1493  OE2 GLU   221      18.897  64.904  64.426  1.00  9.00
ATOM   1494  N   LYS   222      22.490  63.983  70.487  1.00  9.00
ATOM   1495  CA  LYS   222      23.548  63.200  71.134  1.00  9.00
ATOM   1496  C   LYS   222      22.940  62.021  71.895  1.00  9.00
ATOM   1497  O   LYS   222      22.101  62.212  72.783  1.00  9.00
ATOM   1498  CB  LYS   222      24.320  64.117  72.077  1.00  9.00
ATOM   1499  CG  LYS   222      25.497  63.405  72.736  1.00  9.00
ATOM   1500  CD  LYS   222      26.238  64.322  73.699  1.00  9.00
ATOM   1501  CE  LYS   222      27.347  63.577  74.429  1.00  9.00
ATOM   1502  NZ  LYS   222      27.997  64.446  75.421  1.00  9.00
ATOM   1503  N   ILE   223      23.486  60.838  71.653  1.00  9.00
ATOM   1504  CA  ILE   223      22.944  59.591  72.214  1.00  9.00
ATOM   1505  C   ILE   223      23.041  59.499  73.736  1.00  9.00
ATOM   1506  O   ILE   223      22.037  59.156  74.375  1.00  9.00
ATOM   1507  CB  ILE   223      23.728  58.438  71.599  1.00  9.00
ATOM   1508  CG1 ILE   223      23.554  58.411  70.086  1.00  9.00
ATOM   1509  CG2 ILE   223      23.313  57.104  72.209  1.00  9.00
ATOM   1510  CD1 ILE   223      24.349  57.269  69.465  1.00  9.00
ATOM   1511  N   ARG   224      24.096  60.062  74.310  1.00  9.00
ATOM   1512  CA  ARG   224      24.236  60.046  75.770  1.00  9.00
ATOM   1513  C   ARG   224      23.228  60.975  76.414  1.00  9.00
ATOM   1514  O   ARG   224      22.566  60.581  77.382  1.00  9.00
ATOM   1515  CB  ARG   224      25.618  60.536  76.170  1.00  9.00
ATOM   1516  CG  ARG   224      26.722  59.582  75.749  1.00  9.00
ATOM   1517  CD  ARG   224      28.064  60.115  76.227  1.00  9.00
ATOM   1518  NE  ARG   224      29.154  59.188  75.902  1.00  9.00
ATOM   1519  CZ  ARG   224      30.436  59.487  76.117  1.00  9.00
ATOM   1520  NH1 ARG   224      31.384  58.586  75.850  1.00  9.00
ATOM   1521  NH2 ARG   224      30.765  60.672  76.635  1.00  9.00
ATOM   1522  N   LEU   225      22.919  62.049  75.709  1.00  9.00
ATOM   1523  CA  LEU   225      21.939  62.993  76.206  1.00  9.00
ATOM   1524  C   LEU   225      20.563  62.349  76.156  1.00  9.00
ATOM   1525  O   LEU   225      20.054  62.003  77.227  1.00  9.00
ATOM   1526  CB  LEU   225      21.973  64.264  75.364  1.00  9.00
ATOM   1527  CG  LEU   225      23.278  65.039  75.536  1.00  9.00
ATOM   1528  CD1 LEU   225      23.206  66.372  74.802  1.00  9.00
ATOM   1529  CD2 LEU   225      23.614  65.279  77.005  1.00  9.00
ATOM   1530  N   LEU   226      20.191  61.840  74.994  1.00  9.00
ATOM   1531  CA  LEU   226      18.842  61.288  74.802  1.00  9.00
ATOM   1532  C   LEU   226      18.526  60.100  75.717  1.00  9.00
ATOM   1533  O   LEU   226      17.518  60.146  76.435  1.00  9.00
ATOM   1534  CB  LEU   226      18.723  60.842  73.348  1.00  9.00
ATOM   1535  CG  LEU   226      18.842  62.014  72.379  1.00  9.00
ATOM   1536  CD1 LEU   226      18.989  61.525  70.944  1.00  9.00
ATOM   1537  CD2 LEU   226      17.659  62.967  72.511  1.00  9.00
ATOM   1538  N   LYS   227      19.474  59.193  75.888  1.00  9.00
ATOM   1539  CA  LYS   227      19.203  58.009  76.711  1.00  9.00
ATOM   1540  C   LYS   227      19.286  58.275  78.214  1.00  9.00
ATOM   1541  O   LYS   227      18.443  57.758  78.960  1.00  9.00
ATOM   1542  CB  LYS   227      20.182  56.908  76.330  1.00  9.00
ATOM   1543  CG  LYS   227      19.938  56.440  74.901  1.00  9.00
ATOM   1544  CD  LYS   227      20.837  55.261  74.547  1.00  9.00
ATOM   1545  CE  LYS   227      20.536  54.740  73.146  1.00  9.00
ATOM   1546  NZ  LYS   227      21.399  53.595  72.815  1.00  9.00
ATOM   1547  N   GLU   228      20.091  59.241  78.626  1.00  9.00
ATOM   1548  CA  GLU   228      20.156  59.561  80.056  1.00  9.00
ATOM   1549  C   GLU   228      19.022  60.499  80.452  1.00  9.00
ATOM   1550  O   GLU   228      18.531  60.431  81.585  1.00  9.00
ATOM   1551  CB  GLU   228      21.492  60.223  80.365  1.00  9.00
ATOM   1552  CG  GLU   228      22.662  59.268  80.166  1.00  9.00
ATOM   1553  CD  GLU   228      23.973  60.037  80.293  1.00  9.00
ATOM   1554  OE1 GLU   228      23.911  61.252  80.438  1.00  9.00
ATOM   1555  OE2 GLU   228      25.016  59.401  80.232  1.00  9.00
ATOM   1556  N   PHE   229      18.462  61.181  79.466  1.00  9.00
ATOM   1557  CA  PHE   229      17.322  62.066  79.718  1.00  9.00
ATOM   1558  C   PHE   229      16.058  61.249  79.842  1.00  9.00
ATOM   1559  O   PHE   229      15.242  61.520  80.727  1.00  9.00
ATOM   1560  CB  PHE   229      17.109  63.029  78.556  1.00  9.00
ATOM   1561  CG  PHE   229      18.223  64.027  78.276  1.00  9.00
ATOM   1562  CD1 PHE   229      19.309  64.149  79.135  1.00  9.00
ATOM   1563  CD2 PHE   229      18.152  64.809  77.135  1.00  9.00
ATOM   1564  CE1 PHE   229      20.325  65.046  78.851  1.00  9.00
ATOM   1565  CE2 PHE   229      19.165  65.712  76.854  1.00  9.00
ATOM   1566  CZ  PHE   229      20.249  65.831  77.712  1.00  9.00
ATOM   1567  N   MET   230      16.015  60.142  79.121  1.00  9.00
ATOM   1568  CA  MET   230      14.873  59.238  79.206  1.00  9.00
ATOM   1569  C   MET   230      14.895  58.469  80.519  1.00  9.00
ATOM   1570  O   MET   230      13.858  58.370  81.191  1.00  9.00
ATOM   1571  CB  MET   230      14.964  58.249  78.054  1.00  9.00
ATOM   1572  CG  MET   230      13.820  57.247  78.111  1.00  9.00
ATOM   1573  SD  MET   230      13.941  55.882  76.938  1.00  9.00
ATOM   1574  CE  MET   230      15.485  55.146  77.523  1.00  9.00
ATOM   1575  N   HIS   231      16.093  58.174  80.995  1.00  9.00
ATOM   1576  CA  HIS   231      16.230  57.495  82.280  1.00  9.00
ATOM   1577  C   HIS   231      15.846  58.423  83.429  1.00  9.00
ATOM   1578  O   HIS   231      14.951  58.063  84.202  1.00  9.00
ATOM   1579  CB  HIS   231      17.677  57.044  82.433  1.00  9.00
ATOM   1580  CG  HIS   231      17.947  56.250  83.693  1.00  9.00
ATOM   1581  ND1 HIS   231      17.292  55.147  84.106  1.00  9.00
ATOM   1582  CD2 HIS   231      18.915  56.513  84.633  1.00  9.00
ATOM   1583  CE1 HIS   231      17.822  54.721  85.270  1.00  9.00
ATOM   1584  NE2 HIS   231      18.825  55.567  85.596  1.00  9.00
ATOM   1585  N   THR   232      16.247  59.683  83.348  1.00  9.00
ATOM   1586  CA  THR   232      15.923  60.632  84.422  1.00  9.00
ATOM   1587  C   THR   232      14.455  61.060  84.387  1.00  9.00
ATOM   1588  O   THR   232      13.825  61.159  85.446  1.00  9.00
ATOM   1589  CB  THR   232      16.803  61.868  84.283  1.00  9.00
ATOM   1590  OG1 THR   232      18.164  61.459  84.294  1.00  9.00
ATOM   1591  CG2 THR   232      16.582  62.823  85.450  1.00  9.00
ATOM   1592  N   MET   233      13.874  61.035  83.198  1.00  9.00
ATOM   1593  CA  MET   233      12.453  61.327  83.008  1.00  9.00
ATOM   1594  C   MET   233      11.579  60.248  83.633  1.00  9.00
ATOM   1595  O   MET   233      10.721  60.559  84.470  1.00  9.00
ATOM   1596  CB  MET   233      12.221  61.360  81.501  1.00  9.00
ATOM   1597  CG  MET   233      10.757  61.518  81.124  1.00  9.00
ATOM   1598  SD  MET   233      10.419  61.554  79.355  1.00  9.00
ATOM   1599  CE  MET   233      10.805  59.829  78.992  1.00  9.00
ATOM   1600  N   LYS   234      12.002  59.004  83.472  1.00  9.00
ATOM   1601  CA  LYS   234      11.260  57.881  84.044  1.00  9.00
ATOM   1602  C   LYS   234      11.444  57.801  85.561  1.00  9.00
ATOM   1603  O   LYS   234      10.449  57.614  86.276  1.00  9.00
ATOM   1604  CB  LYS   234      11.777  56.608  83.391  1.00  9.00
ATOM   1605  CG  LYS   234      11.043  55.377  83.902  1.00  9.00
ATOM   1606  CD  LYS   234      11.646  54.107  83.321  1.00  9.00
ATOM   1607  CE  LYS   234      10.956  52.868  83.873  1.00  9.00
ATOM   1608  NZ  LYS   234      11.646  51.646  83.429  1.00  9.00
ATOM   1609  N   ASN   235      12.583  58.288  86.032  1.00  9.00
ATOM   1610  CA  ASN   235      12.864  58.341  87.474  1.00  9.00
ATOM   1611  C   ASN   235      12.122  59.460  88.201  1.00  9.00
ATOM   1612  O   ASN   235      12.105  59.459  89.437  1.00  9.00
ATOM   1613  CB  ASN   235      14.344  58.625  87.698  1.00  9.00
ATOM   1614  CG  ASN   235      15.260  57.525  87.181  1.00  9.00
ATOM   1615  OD1 ASN   235      14.859  56.375  86.965  1.00  9.00
ATOM   1616  ND2 ASN   235      16.525  57.892  87.073  1.00  9.00
ATOM   1617  N   THR   236      11.475  60.359  87.478  1.00  9.00
ATOM   1618  CA  THR   236      10.759  61.453  88.133  1.00  9.00
ATOM   1619  C   THR   236       9.349  61.036  88.558  1.00  9.00
ATOM   1620  O   THR   236       8.776  61.643  89.472  1.00  9.00
ATOM   1621  CB  THR   236      10.679  62.621  87.157  1.00  9.00
ATOM   1622  OG1 THR   236      11.992  62.920  86.702  1.00  9.00
ATOM   1623  CG2 THR   236      10.096  63.871  87.804  1.00  9.00
ATOM   1624  N   GLY   237       8.860  59.932  88.015  1.00  9.00
ATOM   1625  CA  GLY   237       7.513  59.471  88.364  1.00  9.00
ATOM   1626  C   GLY   237       7.500  58.011  88.805  1.00  9.00
ATOM   1627  O   GLY   237       6.603  57.305  88.367  1.00  9.00
TER
END
