
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_4-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          2.797
LGA    P     220      E     221          3.107
LGA    -       -      K     222           -
LGA    E     221      I     223          1.252
LGA    K     222      R     224          2.295
LGA    I     223      L     225          3.082
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    R     224      E     228          2.614
LGA    L     225      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    -       -      L     263           -
LGA    L     226      E     264           #
LGA    K     227      G     265          2.236
LGA    E     228      F     266          5.244
LGA    F     229      A     267           -
LGA    -       -      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          1.949
LGA    H     231      I     279          2.107
LGA    T     232      D     280          2.363
LGA    M     233      H     281          1.627
LGA    K     234      L     282          0.248
LGA    N     235      -       -           -
LGA    T     236      -       -           -
LGA    G     237      P     283          2.980
LGA    R     238      P     284          4.012
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     15    2.76     0.00     12.873     0.524

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.342607 * X  +   0.899960 * Y  +   0.269616 * Z  + -41.883587
  Y_new =   0.727589 * X  +  -0.072621 * Y  +  -0.682158 * Z  +  67.647057
  Z_new =  -0.594335 * X  +   0.429882 * Y  +  -0.679682 * Z  +  49.987457 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.577636   -0.563957  [ DEG:   147.6877    -32.3123 ]
  Theta =   0.636439    2.505153  [ DEG:    36.4653    143.5347 ]
  Phi   =   1.130716   -2.010877  [ DEG:    64.7852   -115.2148 ]
 
# 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_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_4-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   15   2.76    0.00  12.873
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_4-D2
PFRMAT TS
TARGET T0386
MODEL  4  REFINED
PARENT 2G03_A
ATOM   1478  N   ASN   219      -1.001  58.871  79.392  1.00  0.00
ATOM   1479  CA  ASN   219      -0.543  59.343  78.047  1.00  0.00
ATOM   1480  C   ASN   219       1.016  58.987  77.755  1.00  0.00
ATOM   1481  O   ASN   219       1.806  59.297  78.636  1.00  0.00
ATOM   1482  CB  ASN   219      -0.893  60.842  77.818  1.00  0.00
ATOM   1483  CG  ASN   219      -0.426  61.319  76.450  1.00  0.00
ATOM   1484  OD1 ASN   219      -0.796  60.784  75.453  1.00  0.00
ATOM   1485  ND2 ASN   219       0.386  62.434  76.533  1.00  0.00
ATOM   1486  N   PRO   220       1.515  58.576  76.509  1.00  0.00
ATOM   1487  CA  PRO   220       2.893  58.056  76.297  1.00  0.00
ATOM   1488  C   PRO   220       4.227  58.861  75.801  1.00  0.00
ATOM   1489  O   PRO   220       5.253  58.426  76.341  1.00  0.00
ATOM   1490  CB  PRO   220       2.595  56.863  75.374  1.00  0.00
ATOM   1491  CG  PRO   220       1.109  56.988  74.737  1.00  0.00
ATOM   1492  CD  PRO   220       0.435  58.082  75.536  1.00  0.00
ATOM   1493  N   GLU   221       4.355  59.914  74.936  1.00  0.00
ATOM   1494  CA  GLU   221       5.730  60.311  74.488  1.00  0.00
ATOM   1495  C   GLU   221       6.280  61.752  74.855  1.00  0.00
ATOM   1496  O   GLU   221       7.437  62.009  74.481  1.00  0.00
ATOM   1497  CB  GLU   221       5.691  60.204  72.953  1.00  0.00
ATOM   1498  CG  GLU   221       4.718  61.207  72.257  1.00  0.00
ATOM   1499  CD  GLU   221       3.409  60.537  71.805  1.00  0.00
ATOM   1500  OE1 GLU   221       3.190  60.350  70.570  1.00  0.00
ATOM   1501  OE2 GLU   221       2.512  60.210  72.632  1.00  0.00
ATOM   1502  N   LYS   222       5.647  62.539  75.723  1.00  0.00
ATOM   1503  CA  LYS   222       6.135  63.888  76.026  1.00  0.00
ATOM   1504  C   LYS   222       7.438  63.827  76.887  1.00  0.00
ATOM   1505  O   LYS   222       7.518  63.040  77.833  1.00  0.00
ATOM   1506  CB  LYS   222       5.025  64.706  76.699  1.00  0.00
ATOM   1507  CG  LYS   222       5.466  66.155  76.984  1.00  0.00
ATOM   1508  CD  LYS   222       5.552  67.003  75.711  1.00  0.00
ATOM   1509  CE  LYS   222       5.909  68.464  75.995  1.00  0.00
ATOM   1510  NZ  LYS   222       6.142  69.247  74.775  1.00  0.00
ATOM   1511  N   ILE   223       8.497  64.536  76.448  1.00  0.00
ATOM   1512  CA  ILE   223       9.767  64.667  77.197  1.00  0.00
ATOM   1513  C   ILE   223       9.466  64.965  78.722  1.00  0.00
ATOM   1514  O   ILE   223      10.140  64.343  79.542  1.00  0.00
ATOM   1515  CB  ILE   223      10.606  65.728  76.524  1.00  0.00
ATOM   1516  CG1 ILE   223      12.040  65.764  77.124  1.00  0.00
ATOM   1517  CG2 ILE   223       9.942  67.150  76.520  1.00  0.00
ATOM   1518  CD1 ILE   223      12.446  66.803  78.217  1.00  0.00
ATOM   1519  N   ARG   224       8.751  66.050  79.074  1.00  0.00
ATOM   1520  CA  ARG   224       8.336  66.382  80.452  1.00  0.00
ATOM   1521  C   ARG   224       7.631  65.165  81.132  1.00  0.00
ATOM   1522  O   ARG   224       7.912  64.956  82.309  1.00  0.00
ATOM   1523  CB  ARG   224       7.448  67.639  80.426  1.00  0.00
ATOM   1524  CG  ARG   224       6.881  68.054  81.779  1.00  0.00
ATOM   1525  CD  ARG   224       5.959  69.283  81.686  1.00  0.00
ATOM   1526  NE  ARG   224       5.399  69.598  83.008  1.00  0.00
ATOM   1527  CZ  ARG   224       4.081  69.719  83.258  1.00  0.00
ATOM   1528  NH1 ARG   224       3.187  69.534  82.268  1.00  0.00
ATOM   1529  NH2 ARG   224       3.651  70.005  84.501  1.00  0.00
ATOM   1530  N   LEU   225       6.573  64.570  80.546  1.00  0.00
ATOM   1531  CA  LEU   225       5.921  63.362  81.060  1.00  0.00
ATOM   1532  C   LEU   225       6.934  62.197  81.385  1.00  0.00
ATOM   1533  O   LEU   225       6.563  61.386  82.222  1.00  0.00
ATOM   1534  CB  LEU   225       4.952  62.927  79.950  1.00  0.00
ATOM   1535  CG  LEU   225       3.663  63.701  79.692  1.00  0.00
ATOM   1536  CD1 LEU   225       2.774  62.932  78.708  1.00  0.00
ATOM   1537  CD2 LEU   225       2.874  63.939  80.982  1.00  0.00
ATOM   1538  N   LEU   226       7.960  61.927  80.550  1.00  0.00
ATOM   1539  CA  LEU   226       8.937  60.850  80.679  1.00  0.00
ATOM   1540  C   LEU   226      10.018  61.232  81.765  1.00  0.00
ATOM   1541  O   LEU   226      10.248  60.376  82.616  1.00  0.00
ATOM   1542  CB  LEU   226       9.587  60.753  79.314  1.00  0.00
ATOM   1543  CG  LEU   226       8.856  60.106  78.176  1.00  0.00
ATOM   1544  CD1 LEU   226       9.723  60.108  76.924  1.00  0.00
ATOM   1545  CD2 LEU   226       8.576  58.663  78.478  1.00  0.00
ATOM   1546  N   LYS   227      10.652  62.434  81.740  1.00  0.00
ATOM   1547  CA  LYS   227      11.609  62.929  82.716  1.00  0.00
ATOM   1548  C   LYS   227      10.954  63.254  84.097  1.00  0.00
ATOM   1549  O   LYS   227      11.645  62.975  85.095  1.00  0.00
ATOM   1550  CB  LYS   227      12.344  64.084  82.104  1.00  0.00
ATOM   1551  CG  LYS   227      13.218  63.891  80.929  1.00  0.00
ATOM   1552  CD  LYS   227      13.936  65.164  80.491  1.00  0.00
ATOM   1553  CE  LYS   227      14.971  65.652  81.472  1.00  0.00
ATOM   1554  NZ  LYS   227      16.084  64.657  81.608  1.00  0.00
ATOM   1555  N   GLU   228       9.954  64.162  84.197  1.00  0.00
ATOM   1556  CA  GLU   228       9.307  64.347  85.493  1.00  0.00
ATOM   1557  C   GLU   228       8.971  62.927  86.040  1.00  0.00
ATOM   1558  O   GLU   228       9.446  62.645  87.138  1.00  0.00
ATOM   1559  CB  GLU   228       8.008  65.143  85.430  1.00  0.00
ATOM   1560  CG  GLU   228       8.018  66.547  84.962  1.00  0.00
ATOM   1561  CD  GLU   228       9.036  67.283  85.690  1.00  0.00
ATOM   1562  OE1 GLU   228      10.126  67.654  85.228  1.00  0.00
ATOM   1563  OE2 GLU   228       8.630  67.420  86.985  1.00  0.00
ATOM   1564  N   PHE   229       8.231  62.044  85.310  1.00  0.00
ATOM   1565  CA  PHE   229       7.937  60.640  85.677  1.00  0.00
ATOM   1566  C   PHE   229       9.151  59.904  86.283  1.00  0.00
ATOM   1567  O   PHE   229       8.924  59.151  87.229  1.00  0.00
ATOM   1568  CB  PHE   229       7.572  59.896  84.361  1.00  0.00
ATOM   1569  CG  PHE   229       7.626  58.356  84.551  1.00  0.00
ATOM   1570  CD1 PHE   229       6.797  57.704  85.451  1.00  0.00
ATOM   1571  CD2 PHE   229       8.528  57.637  83.795  1.00  0.00
ATOM   1572  CE1 PHE   229       6.873  56.335  85.584  1.00  0.00
ATOM   1573  CE2 PHE   229       8.596  56.263  83.937  1.00  0.00
ATOM   1574  CZ  PHE   229       7.769  55.610  84.830  1.00  0.00
ATOM   1575  N   MET   230      10.324  59.881  85.586  1.00  0.00
ATOM   1576  CA  MET   230      11.541  59.258  86.030  1.00  0.00
ATOM   1577  C   MET   230      11.915  59.797  87.434  1.00  0.00
ATOM   1578  O   MET   230      12.362  58.964  88.224  1.00  0.00
ATOM   1579  CB  MET   230      12.674  59.461  84.980  1.00  0.00
ATOM   1580  CG  MET   230      12.379  58.559  83.741  1.00  0.00
ATOM   1581  SD  MET   230      13.742  58.672  82.607  1.00  0.00
ATOM   1582  CE  MET   230      13.768  60.433  82.217  1.00  0.00
ATOM   1583  N   HIS   231      12.133  61.118  87.623  1.00  0.00
ATOM   1584  CA  HIS   231      12.402  61.752  88.921  1.00  0.00
ATOM   1585  C   HIS   231      11.373  61.251  89.989  1.00  0.00
ATOM   1586  O   HIS   231      11.841  60.988  91.098  1.00  0.00
ATOM   1587  CB  HIS   231      12.347  63.256  88.763  1.00  0.00
ATOM   1588  CG  HIS   231      13.506  63.905  88.148  1.00  0.00
ATOM   1589  ND1 HIS   231      13.498  65.216  87.799  1.00  0.00
ATOM   1590  CD2 HIS   231      14.724  63.488  87.834  1.00  0.00
ATOM   1591  CE1 HIS   231      14.646  65.611  87.335  1.00  0.00
ATOM   1592  NE2 HIS   231      15.433  64.544  87.342  1.00  0.00
ATOM   1593  N   THR   232      10.032  61.416  89.794  1.00  0.00
ATOM   1594  CA  THR   232       9.028  60.906  90.723  1.00  0.00
ATOM   1595  C   THR   232       9.323  59.403  91.083  1.00  0.00
ATOM   1596  O   THR   232       9.110  59.056  92.253  1.00  0.00
ATOM   1597  CB  THR   232       7.550  61.238  90.325  1.00  0.00
ATOM   1598  OG1 THR   232       6.480  60.325  90.652  1.00  0.00
ATOM   1599  CG2 THR   232       7.389  61.973  89.040  1.00  0.00
ATOM   1600  N   MET   233       9.463  58.496  90.105  1.00  0.00
ATOM   1601  CA  MET   233       9.829  57.091  90.259  1.00  0.00
ATOM   1602  C   MET   233      11.013  56.868  91.230  1.00  0.00
ATOM   1603  O   MET   233      10.833  56.067  92.146  1.00  0.00
ATOM   1604  CB  MET   233      10.174  56.603  88.832  1.00  0.00
ATOM   1605  CG  MET   233      10.333  55.035  88.864  1.00  0.00
ATOM   1606  SD  MET   233      12.152  54.805  88.866  1.00  0.00
ATOM   1607  CE  MET   233      12.434  54.259  87.165  1.00  0.00
ATOM   1608  N   LYS   234      12.191  57.518  91.070  1.00  0.00
ATOM   1609  CA  LYS   234      13.311  57.433  91.998  1.00  0.00
ATOM   1610  C   LYS   234      12.881  57.899  93.428  1.00  0.00
ATOM   1611  O   LYS   234      13.277  57.230  94.392  1.00  0.00
ATOM   1612  CB  LYS   234      14.394  58.347  91.466  1.00  0.00
ATOM   1613  CG  LYS   234      15.470  57.770  90.628  1.00  0.00
ATOM   1614  CD  LYS   234      15.127  56.557  89.817  1.00  0.00
ATOM   1615  CE  LYS   234      16.390  55.981  89.137  1.00  0.00
ATOM   1616  NZ  LYS   234      16.131  54.550  88.813  1.00  0.00
ATOM   1617  N   ASN   235      12.355  59.125  93.604  1.00  0.00
ATOM   1618  CA  ASN   235      11.834  59.673  94.846  1.00  0.00
ATOM   1619  C   ASN   235      10.985  58.654  95.656  1.00  0.00
ATOM   1620  O   ASN   235      11.141  58.688  96.879  1.00  0.00
ATOM   1621  CB  ASN   235      11.006  60.932  94.518  1.00  0.00
ATOM   1622  CG  ASN   235      10.232  61.568  95.675  1.00  0.00
ATOM   1623  OD1 ASN   235       9.451  60.884  96.387  1.00  0.00
ATOM   1624  ND2 ASN   235      10.350  62.881  95.840  1.00  0.00
ATOM   1625  N   THR   236      10.114  57.801  95.038  1.00  0.00
ATOM   1626  CA  THR   236       9.330  56.802  95.771  1.00  0.00
ATOM   1627  C   THR   236      10.194  55.938  96.765  1.00  0.00
ATOM   1628  O   THR   236       9.821  55.910  97.948  1.00  0.00
ATOM   1629  CB  THR   236       8.503  55.904  94.809  1.00  0.00
ATOM   1630  OG1 THR   236       7.664  56.621  93.854  1.00  0.00
ATOM   1631  CG2 THR   236       7.479  55.105  95.693  1.00  0.00
ATOM   1632  N   GLY   237      11.354  55.357  96.370  1.00  0.00
ATOM   1633  CA  GLY   237      12.112  54.502  97.278  1.00  0.00
ATOM   1634  C   GLY   237      12.767  55.255  98.457  1.00  0.00
ATOM   1635  O   GLY   237      12.697  54.726  99.590  1.00  0.00
ATOM   1636  N   ARG   238      13.648  56.165  98.161  1.00  0.00
ATOM   1637  CA  ARG   238      14.387  56.844  99.247  1.00  0.00
ATOM   1638  C   ARG   238      14.044  58.365  99.277  1.00  0.00
ATOM   1639  O   ARG   238      13.162  58.793 100.013  1.00  0.00
ATOM   1640  CB  ARG   238      15.879  56.500  99.004  1.00  0.00
ATOM   1641  CG  ARG   238      16.502  57.261  97.843  1.00  0.00
ATOM   1642  CD  ARG   238      15.558  57.309  96.691  1.00  0.00
ATOM   1643  NE  ARG   238      16.207  57.723  95.449  1.00  0.00
ATOM   1644  CZ  ARG   238      16.883  58.873  95.332  1.00  0.00
ATOM   1645  NH1 ARG   238      17.035  59.707  96.359  1.00  0.00
ATOM   1646  NH2 ARG   238      17.385  59.177  94.138  1.00  0.00
ATOM   1647  OXT ARG   238      14.617  59.050  98.419  1.00  0.00
TER
END
