
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS298_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    -       -      P     220           -
LGA    N     219      E     221          2.742
LGA    P     220      K     222          2.265
LGA    E     221      I     223          0.962
LGA    K     222      R     224          1.013
LGA    I     223      L     225          3.080
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          4.545
LGA    L     225      E     264          2.952
LGA    L     226      G     265          3.104
LGA    K     227      F     266          2.814
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          3.753
LGA    H     231      I     279          3.236
LGA    T     232      D     280          2.699
LGA    M     233      H     281          1.978
LGA    K     234      L     282          1.934
LGA    N     235      P     283          2.595
LGA    T     236      P     284          4.111
LGA    G     237      E     285           -
LGA    R     238      Q     286          4.281
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    2.99     0.00     13.436     0.549

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.130091 * X  +   0.907077 * Y  +   0.400360 * Z  + -42.510235
  Y_new =   0.884304 * X  +   0.076475 * Y  +  -0.460607 * Z  +  61.137806
  Z_new =  -0.448423 * X  +   0.413961 * Y  +  -0.792183 * Z  +  53.011417 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.660063   -0.481530  [ DEG:   152.4104    -27.5896 ]
  Theta =   0.465001    2.676592  [ DEG:    26.6426    153.3574 ]
  Phi   =   1.424732   -1.716860  [ DEG:    81.6312    -98.3688 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS298_3-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   2.99    0.00  13.436
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS298_3-D2
PFRMAT TS
TARGET T0386
MODEL  3  REFINED
PARENT 2G03_A
ATOM   1470  N   ASN   219      -0.147  57.790  80.378  1.00  0.00
ATOM   1471  CA  ASN   219       0.369  58.132  78.957  1.00  0.00
ATOM   1472  C   ASN   219       1.928  58.531  78.730  1.00  0.00
ATOM   1473  O   ASN   219       2.500  59.027  79.707  1.00  0.00
ATOM   1474  CB  ASN   219      -0.528  59.280  78.482  1.00  0.00
ATOM   1475  CG  ASN   219      -1.928  58.838  78.014  1.00  0.00
ATOM   1476  OD1 ASN   219      -2.119  58.279  76.923  1.00  0.00
ATOM   1477  ND2 ASN   219      -2.897  59.035  78.895  1.00  0.00
ATOM   1478  N   PRO   220       2.673  58.356  77.536  1.00  0.00
ATOM   1479  CA  PRO   220       4.180  58.539  77.425  1.00  0.00
ATOM   1480  C   PRO   220       5.063  59.883  77.252  1.00  0.00
ATOM   1481  O   PRO   220       5.540  60.369  78.271  1.00  0.00
ATOM   1482  CB  PRO   220       4.611  57.577  76.290  1.00  0.00
ATOM   1483  CG  PRO   220       3.357  57.778  75.309  1.00  0.00
ATOM   1484  CD  PRO   220       2.218  58.254  76.158  1.00  0.00
ATOM   1485  N   GLU   221       5.448  60.410  76.009  1.00  0.00
ATOM   1486  CA  GLU   221       6.420  61.526  75.631  1.00  0.00
ATOM   1487  C   GLU   221       6.557  62.768  76.555  1.00  0.00
ATOM   1488  O   GLU   221       7.657  63.328  76.536  1.00  0.00
ATOM   1489  CB  GLU   221       5.975  62.032  74.242  1.00  0.00
ATOM   1490  CG  GLU   221       5.443  60.925  73.325  1.00  0.00
ATOM   1491  CD  GLU   221       5.178  61.021  71.861  1.00  0.00
ATOM   1492  OE1 GLU   221       4.658  60.092  71.237  1.00  0.00
ATOM   1493  OE2 GLU   221       5.528  62.107  71.333  1.00  0.00
ATOM   1494  N   LYS   222       5.550  63.274  77.250  1.00  0.00
ATOM   1495  CA  LYS   222       5.748  64.519  78.021  1.00  0.00
ATOM   1496  C   LYS   222       7.046  64.525  78.906  1.00  0.00
ATOM   1497  O   LYS   222       7.338  63.596  79.673  1.00  0.00
ATOM   1498  CB  LYS   222       4.524  64.736  78.922  1.00  0.00
ATOM   1499  CG  LYS   222       4.574  66.074  79.696  1.00  0.00
ATOM   1500  CD  LYS   222       4.354  67.297  78.800  1.00  0.00
ATOM   1501  CE  LYS   222       4.347  68.611  79.585  1.00  0.00
ATOM   1502  NZ  LYS   222       4.290  69.798  78.720  1.00  0.00
ATOM   1503  N   ILE   223       7.796  65.637  78.711  1.00  0.00
ATOM   1504  CA  ILE   223       9.054  65.979  79.387  1.00  0.00
ATOM   1505  C   ILE   223       8.829  66.029  80.932  1.00  0.00
ATOM   1506  O   ILE   223       9.717  65.518  81.624  1.00  0.00
ATOM   1507  CB  ILE   223       9.587  67.323  78.826  1.00  0.00
ATOM   1508  CG1 ILE   223       9.666  67.366  77.305  1.00  0.00
ATOM   1509  CG2 ILE   223      10.945  67.661  79.472  1.00  0.00
ATOM   1510  CD1 ILE   223      10.277  66.132  76.633  1.00  0.00
ATOM   1511  N   ARG   224       7.913  66.865  81.494  1.00  0.00
ATOM   1512  CA  ARG   224       7.597  66.880  82.940  1.00  0.00
ATOM   1513  C   ARG   224       7.271  65.429  83.431  1.00  0.00
ATOM   1514  O   ARG   224       7.804  65.070  84.461  1.00  0.00
ATOM   1515  CB  ARG   224       6.452  67.877  83.142  1.00  0.00
ATOM   1516  CG  ARG   224       6.534  68.533  84.497  1.00  0.00
ATOM   1517  CD  ARG   224       5.565  69.651  84.587  1.00  0.00
ATOM   1518  NE  ARG   224       6.056  70.926  84.046  1.00  0.00
ATOM   1519  CZ  ARG   224       5.236  72.001  84.202  1.00  0.00
ATOM   1520  NH1 ARG   224       4.054  71.941  84.822  1.00  0.00
ATOM   1521  NH2 ARG   224       5.613  73.179  83.704  1.00  0.00
ATOM   1522  N   LEU   225       6.257  64.732  82.893  1.00  0.00
ATOM   1523  CA  LEU   225       5.936  63.348  83.208  1.00  0.00
ATOM   1524  C   LEU   225       7.235  62.462  83.336  1.00  0.00
ATOM   1525  O   LEU   225       7.157  61.523  84.112  1.00  0.00
ATOM   1526  CB  LEU   225       5.040  62.843  82.077  1.00  0.00
ATOM   1527  CG  LEU   225       3.591  63.292  81.971  1.00  0.00
ATOM   1528  CD1 LEU   225       2.861  62.465  80.906  1.00  0.00
ATOM   1529  CD2 LEU   225       2.853  63.133  83.303  1.00  0.00
ATOM   1530  N   LEU   226       8.179  62.470  82.366  1.00  0.00
ATOM   1531  CA  LEU   226       9.423  61.689  82.352  1.00  0.00
ATOM   1532  C   LEU   226      10.438  62.192  83.422  1.00  0.00
ATOM   1533  O   LEU   226      11.065  61.324  84.007  1.00  0.00
ATOM   1534  CB  LEU   226      10.053  61.745  80.965  1.00  0.00
ATOM   1535  CG  LEU   226       9.407  61.030  79.826  1.00  0.00
ATOM   1536  CD1 LEU   226      10.197  61.288  78.549  1.00  0.00
ATOM   1537  CD2 LEU   226       9.485  59.551  80.064  1.00  0.00
ATOM   1538  N   LYS   227      10.896  63.481  83.405  1.00  0.00
ATOM   1539  CA  LYS   227      11.790  64.073  84.413  1.00  0.00
ATOM   1540  C   LYS   227      11.209  63.892  85.844  1.00  0.00
ATOM   1541  O   LYS   227      12.011  63.537  86.698  1.00  0.00
ATOM   1542  CB  LYS   227      12.025  65.554  84.105  1.00  0.00
ATOM   1543  CG  LYS   227      12.751  65.887  82.840  1.00  0.00
ATOM   1544  CD  LYS   227      12.985  67.389  82.696  1.00  0.00
ATOM   1545  CE  LYS   227      13.943  67.960  83.710  1.00  0.00
ATOM   1546  NZ  LYS   227      15.314  67.377  83.531  1.00  0.00
ATOM   1547  N   GLU   228       9.994  64.417  86.196  1.00  0.00
ATOM   1548  CA  GLU   228       9.368  64.170  87.515  1.00  0.00
ATOM   1549  C   GLU   228       9.434  62.626  87.836  1.00  0.00
ATOM   1550  O   GLU   228       9.725  62.323  88.970  1.00  0.00
ATOM   1551  CB  GLU   228       7.933  64.614  87.619  1.00  0.00
ATOM   1552  CG  GLU   228       7.557  66.034  87.441  1.00  0.00
ATOM   1553  CD  GLU   228       8.413  66.848  88.285  1.00  0.00
ATOM   1554  OE1 GLU   228       9.346  67.563  87.888  1.00  0.00
ATOM   1555  OE2 GLU   228       8.075  66.628  89.588  1.00  0.00
ATOM   1556  N   PHE   229       8.994  61.732  86.930  1.00  0.00
ATOM   1557  CA  PHE   229       9.038  60.238  86.950  1.00  0.00
ATOM   1558  C   PHE   229      10.397  59.683  87.469  1.00  0.00
ATOM   1559  O   PHE   229      10.402  58.746  88.249  1.00  0.00
ATOM   1560  CB  PHE   229       8.714  59.795  85.475  1.00  0.00
ATOM   1561  CG  PHE   229       9.121  58.356  85.171  1.00  0.00
ATOM   1562  CD1 PHE   229       8.468  57.279  85.764  1.00  0.00
ATOM   1563  CD2 PHE   229      10.212  58.120  84.356  1.00  0.00
ATOM   1564  CE1 PHE   229       8.912  55.989  85.548  1.00  0.00
ATOM   1565  CE2 PHE   229      10.645  56.827  84.154  1.00  0.00
ATOM   1566  CZ  PHE   229      10.004  55.764  84.745  1.00  0.00
ATOM   1567  N   MET   230      11.515  60.125  86.812  1.00  0.00
ATOM   1568  CA  MET   230      12.895  59.826  87.178  1.00  0.00
ATOM   1569  C   MET   230      13.113  60.355  88.648  1.00  0.00
ATOM   1570  O   MET   230      13.856  59.674  89.360  1.00  0.00
ATOM   1571  CB  MET   230      13.804  60.453  86.111  1.00  0.00
ATOM   1572  CG  MET   230      13.763  59.611  84.817  1.00  0.00
ATOM   1573  SD  MET   230      14.984  60.210  83.672  1.00  0.00
ATOM   1574  CE  MET   230      14.484  61.928  83.448  1.00  0.00
ATOM   1575  N   HIS   231      12.750  61.618  89.008  1.00  0.00
ATOM   1576  CA  HIS   231      12.836  62.118  90.376  1.00  0.00
ATOM   1577  C   HIS   231      12.055  61.193  91.391  1.00  0.00
ATOM   1578  O   HIS   231      12.673  60.869  92.401  1.00  0.00
ATOM   1579  CB  HIS   231      12.341  63.569  90.358  1.00  0.00
ATOM   1580  CG  HIS   231      12.553  64.303  91.647  1.00  0.00
ATOM   1581  ND1 HIS   231      11.828  64.194  92.777  1.00  0.00
ATOM   1582  CD2 HIS   231      13.547  65.245  91.842  1.00  0.00
ATOM   1583  CE1 HIS   231      12.348  65.037  93.640  1.00  0.00
ATOM   1584  NE2 HIS   231      13.376  65.662  93.070  1.00  0.00
ATOM   1585  N   THR   232      10.727  60.948  91.254  1.00  0.00
ATOM   1586  CA  THR   232       9.959  60.018  92.130  1.00  0.00
ATOM   1587  C   THR   232      10.613  58.614  92.230  1.00  0.00
ATOM   1588  O   THR   232      10.621  58.095  93.324  1.00  0.00
ATOM   1589  CB  THR   232       8.422  60.025  91.892  1.00  0.00
ATOM   1590  OG1 THR   232       7.629  58.842  92.094  1.00  0.00
ATOM   1591  CG2 THR   232       7.960  60.902  90.756  1.00  0.00
ATOM   1592  N   MET   233      10.860  57.897  91.090  1.00  0.00
ATOM   1593  CA  MET   233      11.637  56.645  91.059  1.00  0.00
ATOM   1594  C   MET   233      12.861  56.694  91.935  1.00  0.00
ATOM   1595  O   MET   233      13.176  55.646  92.500  1.00  0.00
ATOM   1596  CB  MET   233      12.112  56.476  89.621  1.00  0.00
ATOM   1597  CG  MET   233      11.033  55.788  88.709  1.00  0.00
ATOM   1598  SD  MET   233      11.749  55.583  87.057  1.00  0.00
ATOM   1599  CE  MET   233      12.635  53.999  87.078  1.00  0.00
ATOM   1600  N   LYS   234      13.797  57.669  91.793  1.00  0.00
ATOM   1601  CA  LYS   234      14.949  57.833  92.661  1.00  0.00
ATOM   1602  C   LYS   234      14.556  57.791  94.157  1.00  0.00
ATOM   1603  O   LYS   234      15.311  57.188  94.923  1.00  0.00
ATOM   1604  CB  LYS   234      15.650  59.122  92.358  1.00  0.00
ATOM   1605  CG  LYS   234      16.765  59.148  91.387  1.00  0.00
ATOM   1606  CD  LYS   234      16.780  58.092  90.325  1.00  0.00
ATOM   1607  CE  LYS   234      18.103  58.137  89.528  1.00  0.00
ATOM   1608  NZ  LYS   234      18.309  56.806  88.892  1.00  0.00
ATOM   1609  N   ASN   235      13.668  58.746  94.535  1.00  0.00
ATOM   1610  CA  ASN   235      13.143  58.833  95.855  1.00  0.00
ATOM   1611  C   ASN   235      12.655  57.465  96.469  1.00  0.00
ATOM   1612  O   ASN   235      12.744  57.349  97.701  1.00  0.00
ATOM   1613  CB  ASN   235      11.976  59.848  95.805  1.00  0.00
ATOM   1614  CG  ASN   235      11.140  59.994  97.101  1.00  0.00
ATOM   1615  OD1 ASN   235      10.643  58.988  97.671  1.00  0.00
ATOM   1616  ND2 ASN   235      10.895  61.227  97.531  1.00  0.00
ATOM   1617  N   THR   236      11.982  56.555  95.704  1.00  0.00
ATOM   1618  CA  THR   236      11.514  55.273  96.224  1.00  0.00
ATOM   1619  C   THR   236      12.592  54.587  97.147  1.00  0.00
ATOM   1620  O   THR   236      12.288  54.409  98.336  1.00  0.00
ATOM   1621  CB  THR   236      10.942  54.350  95.130  1.00  0.00
ATOM   1622  OG1 THR   236      11.809  53.243  94.696  1.00  0.00
ATOM   1623  CG2 THR   236      10.593  55.035  93.768  1.00  0.00
ATOM   1624  N   GLY   237      13.831  54.345  96.648  1.00  0.00
ATOM   1625  CA  GLY   237      14.969  53.758  97.369  1.00  0.00
ATOM   1626  C   GLY   237      15.499  54.681  98.492  1.00  0.00
ATOM   1627  O   GLY   237      15.903  54.145  99.529  1.00  0.00
ATOM   1628  N   ARG   238      15.894  55.917  98.153  1.00  0.00
ATOM   1629  CA  ARG   238      16.360  56.957  99.052  1.00  0.00
ATOM   1630  C   ARG   238      15.338  58.113  99.104  1.00  0.00
ATOM   1631  O   ARG   238      14.632  58.288 100.078  1.00  0.00
ATOM   1632  CB  ARG   238      17.645  57.446  98.485  1.00  0.00
ATOM   1633  CG  ARG   238      18.929  56.728  98.674  1.00  0.00
ATOM   1634  CD  ARG   238      19.740  56.757  99.937  1.00  0.00
ATOM   1635  NE  ARG   238      20.682  55.578  99.845  1.00  0.00
ATOM   1636  CZ  ARG   238      21.632  55.323 100.771  1.00  0.00
ATOM   1637  NH1 ARG   238      21.709  56.193 101.791  1.00  0.00
ATOM   1638  NH2 ARG   238      22.476  54.282 100.711  1.00  0.00
ATOM   1639  OXT ARG   238      15.323  58.917  98.116  1.00  0.00
TER
END
