
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0316TS307_5u-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS307_5u-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    G     220      D     226          2.768
LGA    R     221      G     227          3.788
LGA    M     222      R     228          2.474
LGA    M     223      D     229          4.095
LGA    T     224      -       -           -
LGA    V     225      M     230          2.236
LGA    D     226      G     231           #
LGA    G     227      E     232           #
LGA    R     228      H     233          2.779
LGA    D     229      A     234           #
LGA    M     230      -       -           -
LGA    G     231      G     235          4.078
LGA    M     237      L     236          3.133
LGA    Y     238      -       -           -
LGA    Y     239      M     237          4.378
LGA    T     240      Y     238          4.239
LGA    I     241      Y     239          3.623
LGA    G     242      T     240          3.178
LGA    Q     243      -       -           -
LGA    R     244      -       -           -
LGA    G     245      -       -           -
LGA    G     246      -       -           -
LGA    L     247      I     241          2.563
LGA    G     248      G     242          4.629
LGA    I     249      Q     243          1.788
LGA    G     250      R     244          3.062
LGA    G     251      -       -           -
LGA    Q     252      -       -           -
LGA    H     253      G     245          1.212
LGA    G     254      G     246          4.186
LGA    G     255      L     247          2.559
LGA    D     256      G     248          4.100
LGA    N     257      I     249          1.375
LGA    -       -      G     250           -
LGA    A     258      G     251          3.577
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    P     259      A     258          4.890
LGA    W     260      P     259          4.990
LGA    F     261      W     260          4.175
LGA    V     262      F     261          2.207
LGA    N     270      -       -           -
LGA    I     271      V     262           #
LGA    L     272      V     263          3.048
LGA    Y     273      G     264          4.603
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    D     281      D     281          4.592
LGA    S     282      S     282          2.344
LGA    L     283      L     283           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   60    5.0     30    3.51    16.67     27.617     0.830

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.095311 * X  +   0.995063 * Y  +   0.027663 * Z  +  43.460217
  Y_new =   0.019192 * X  +   0.025948 * Y  +  -0.999479 * Z  +   3.596917
  Z_new =  -0.995263 * X  +   0.095792 * Y  +  -0.016624 * Z  + -20.905107 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.742628   -1.398965  [ DEG:    99.8452    -80.1548 ]
  Theta =   1.473419    1.668174  [ DEG:    84.4207     95.5793 ]
  Phi   =   0.198704   -2.942889  [ DEG:    11.3849   -168.6151 ]
 
# 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: T0316TS307_5u-D2                              
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS307_5u-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   60   5.0   30   3.51   16.67  27.617
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS307_5u-D2
PFRMAT   TS
TARGET   T0316
MODEL    5  UNREFINED
PARENT   1xng_A
ATOM   1517  N   GLY   220      32.834  12.788 -29.673  1.00 34.19           N  
ATOM   1518  CA  GLY   220      32.251  13.858 -30.462  1.00 34.57           C  
ATOM   1519  C   GLY   220      33.166  15.048 -30.677  1.00 35.24           C  
ATOM   1520  O   GLY   220      32.932  15.862 -31.574  1.00 35.01           O  
ATOM   1521  N   ARG   221      34.209  15.156 -29.860  1.00 34.83           N  
ATOM   1522  CA  ARG   221      35.149  16.263 -29.974  1.00 35.27           C  
ATOM   1523  C   ARG   221      36.587  15.782 -29.796  1.00 34.69           C  
ATOM   1524  O   ARG   221      36.830  14.756 -29.158  1.00 34.75           O  
ATOM   1533  N   MET   222      37.557  16.510 -30.377  1.00 33.18           N  
ATOM   1534  CA  MET   222      38.976  16.152 -30.267  1.00 32.48           C  
ATOM   1535  C   MET   222      39.501  16.603 -28.903  1.00 30.93           C  
ATOM   1536  O   MET   222      38.957  17.530 -28.305  1.00 30.80           O  
ATOM   1540  N   MET   223      40.556  15.962 -28.413  1.00 30.31           N  
ATOM   1541  CA  MET   223      41.104  16.323 -27.108  1.00 29.80           C  
ATOM   1542  C   MET   223      41.622  17.760 -27.052  1.00 30.93           C  
ATOM   1543  O   MET   223      41.841  18.309 -25.970  1.00 28.69           O  
ATOM   1552  N   THR   224      41.806  18.373 -28.216  1.00 30.15           N  
ATOM   1553  CA  THR   224      42.277  19.753 -28.268  1.00 30.30           C  
ATOM   1554  C   THR   224      41.157  20.691 -27.809  1.00 29.69           C  
ATOM   1555  O   THR   224      41.408  21.831 -27.405  1.00 29.74           O  
ATOM   1558  N   VAL   225      39.923  20.197 -27.874  1.00 28.67           N  
ATOM   1559  CA  VAL   225      38.745  20.963 -27.472  1.00 27.97           C  
ATOM   1560  C   VAL   225      38.218  20.502 -26.111  1.00 26.02           C  
ATOM   1561  O   VAL   225      37.716  21.305 -25.325  1.00 26.95           O  
ATOM   1565  N   ASP   226      38.336  19.207 -25.841  1.00 23.84           N  
ATOM   1566  CA  ASP   226      37.860  18.641 -24.584  1.00 22.58           C  
ATOM   1567  C   ASP   226      38.759  18.976 -23.404  1.00 21.25           C  
ATOM   1568  O   ASP   226      38.280  19.402 -22.354  1.00 21.35           O  
ATOM   1573  N   GLY   227      40.063  18.793 -23.584  1.00 20.56           N  
ATOM   1574  CA  GLY   227      41.023  19.032 -22.511  1.00 19.83           C  
ATOM   1575  C   GLY   227      41.009  20.410 -21.857  1.00 19.78           C  
ATOM   1576  O   GLY   227      41.147  20.520 -20.639  1.00 17.80           O  
ATOM   1581  N   ARG   228      40.865  21.484 -22.643  1.00 19.00           N  
ATOM   1582  CA  ARG   228      40.843  22.792 -21.986  1.00 20.19           C  
ATOM   1583  C   ARG   228      39.666  22.887 -21.004  1.00 18.42           C  
ATOM   1584  O   ARG   228      39.797  23.453 -19.918  1.00 18.30           O  
ATOM   1588  N   ASP   229      38.528  22.313 -21.387  1.00 18.02           N  
ATOM   1589  CA  ASP   229      37.337  22.314 -20.543  1.00 19.11           C  
ATOM   1590  C   ASP   229      37.540  21.401 -19.339  1.00 18.98           C  
ATOM   1591  O   ASP   229      37.203  21.761 -18.211  1.00 19.50           O  
ATOM   1596  N   MET   230      38.091  20.214 -19.577  1.00 18.86           N  
ATOM   1597  CA  MET   230      38.333  19.299 -18.473  1.00 18.50           C  
ATOM   1598  C   MET   230      39.297  19.916 -17.456  1.00 18.37           C  
ATOM   1599  O   MET   230      39.156  19.708 -16.251  1.00 16.83           O  
ATOM   1604  N   GLY   231      40.276  20.680 -17.932  1.00 18.48           N  
ATOM   1605  CA  GLY   231      41.225  21.303 -17.015  1.00 17.57           C  
ATOM   1606  C   GLY   231      40.537  22.309 -16.088  1.00 18.68           C  
ATOM   1607  O   GLY   231      40.831  22.360 -14.890  1.00 17.02           O  
ATOM   1613  N   MET   237      39.624  23.108 -16.630  1.00 19.84           N  
ATOM   1614  CA  MET   237      38.907  24.069 -15.798  1.00 21.61           C  
ATOM   1615  C   MET   237      37.972  23.358 -14.825  1.00 21.65           C  
ATOM   1616  O   MET   237      37.799  23.795 -13.687  1.00 20.86           O  
ATOM   1621  N   TYR   238      37.368  22.263 -15.272  1.00 21.45           N  
ATOM   1622  CA  TYR   238      36.476  21.500 -14.411  1.00 20.15           C  
ATOM   1623  C   TYR   238      37.276  20.876 -13.266  1.00 20.73           C  
ATOM   1624  O   TYR   238      36.835  20.874 -12.117  1.00 21.28           O  
ATOM   1629  N   TYR   239      38.468  20.367 -13.563  1.00 18.13           N  
ATOM   1630  CA  TYR   239      39.276  19.760 -12.515  1.00 18.27           C  
ATOM   1631  C   TYR   239      39.749  20.802 -11.503  1.00 18.43           C  
ATOM   1632  O   TYR   239      39.856  20.514 -10.310  1.00 19.98           O  
ATOM   1638  N   THR   240      40.025  22.012 -11.979  1.00 19.56           N  
ATOM   1639  CA  THR   240      40.511  23.076 -11.104  1.00 20.12           C  
ATOM   1640  C   THR   240      39.403  23.708 -10.275  1.00 22.76           C  
ATOM   1641  O   THR   240      39.591  24.011  -9.094  1.00 22.37           O  
ATOM   1643  N   ILE   241      38.248  23.889 -10.902  1.00 23.13           N  
ATOM   1644  CA  ILE   241      37.106  24.518 -10.251  1.00 25.61           C  
ATOM   1645  C   ILE   241      36.221  23.576  -9.452  1.00 26.23           C  
ATOM   1646  O   ILE   241      35.785  23.917  -8.350  1.00 26.40           O  
ATOM   1651  N   GLY   242      35.952  22.397 -10.005  1.00 26.70           N  
ATOM   1652  CA  GLY   242      35.078  21.435  -9.347  1.00 29.27           C  
ATOM   1653  C   GLY   242      35.695  20.047  -9.220  1.00 32.03           C  
ATOM   1654  O   GLY   242      35.210  19.088  -9.824  1.00 34.86           O  
ATOM   1662  N   GLN   243      36.754  19.933  -8.433  1.00 33.77           N  
ATOM   1663  CA  GLN   243      37.399  18.643  -8.252  1.00 35.95           C  
ATOM   1664  C   GLN   243      36.659  17.826  -7.199  1.00 37.44           C  
ATOM   1665  O   GLN   243      36.514  16.612  -7.335  1.00 37.68           O  
ATOM   1671  N   ARG   244      36.186  18.501  -6.156  1.00 38.93           N  
ATOM   1672  CA  ARG   244      35.470  17.830  -5.075  1.00 41.09           C  
ATOM   1673  C   ARG   244      34.112  18.483  -4.820  1.00 40.50           C  
ATOM   1674  O   ARG   244      33.542  18.349  -3.738  1.00 41.10           O  
ATOM   1678  N   GLY   245      33.603  19.194  -5.820  1.00 39.06           N  
ATOM   1679  CA  GLY   245      32.315  19.865  -5.705  1.00 37.94           C  
ATOM   1680  C   GLY   245      31.545  19.702  -7.013  1.00 36.95           C  
ATOM   1681  O   GLY   245      32.130  19.398  -8.053  1.00 37.44           O  
ATOM   1683  N   GLY   246      30.219  19.900  -6.977  1.00 35.33           N  
ATOM   1684  CA  GLY   246      29.390  19.765  -8.179  1.00 33.50           C  
ATOM   1685  C   GLY   246      29.728  20.771  -9.274  1.00 31.35           C  
ATOM   1686  O   GLY   246      30.030  21.930  -8.999  1.00 31.28           O  
ATOM   1690  N   LEU   247      29.669  20.318 -10.520  1.00 29.08           N  
ATOM   1691  CA  LEU   247      29.968  21.180 -11.655  1.00 28.00           C  
ATOM   1692  C   LEU   247      28.885  22.239 -11.867  1.00 28.68           C  
ATOM   1693  O   LEU   247      27.691  21.937 -11.828  1.00 27.97           O  
ATOM   1698  N   GLY   248      29.313  23.482 -12.075  1.00 29.42           N  
ATOM   1699  CA  GLY   248      28.394  24.594 -12.311  1.00 31.40           C  
ATOM   1700  C   GLY   248      28.490  24.955 -13.788  1.00 31.19           C  
ATOM   1701  O   GLY   248      29.403  25.669 -14.206  1.00 30.56           O  
ATOM   1706  N   ILE   249      27.546  24.450 -14.576  1.00 32.19           N  
ATOM   1707  CA  ILE   249      27.537  24.696 -16.011  1.00 34.31           C  
ATOM   1708  C   ILE   249      27.454  26.175 -16.362  1.00 35.87           C  
ATOM   1709  O   ILE   249      27.932  26.599 -17.414  1.00 36.08           O  
ATOM   1713  N   GLY   250      26.849  26.960 -15.477  1.00 38.54           N  
ATOM   1714  CA  GLY   250      26.713  28.388 -15.715  1.00 40.66           C  
ATOM   1715  C   GLY   250      28.080  29.058 -15.632  1.00 39.75           C  
ATOM   1716  O   GLY   250      28.393  29.947 -16.422  1.00 40.80           O  
ATOM   1722  N   GLY   251      28.892  28.622 -14.676  1.00 39.18           N  
ATOM   1723  CA  GLY   251      30.229  29.175 -14.507  1.00 37.39           C  
ATOM   1724  C   GLY   251      31.060  28.851 -15.742  1.00 37.48           C  
ATOM   1725  O   GLY   251      31.795  29.698 -16.246  1.00 37.53           O  
ATOM   1729  N   GLN   252      30.935  27.621 -16.230  1.00 37.39           N  
ATOM   1730  CA  GLN   252      31.674  27.195 -17.412  1.00 36.75           C  
ATOM   1731  C   GLN   252      31.209  27.987 -18.632  1.00 38.47           C  
ATOM   1732  O   GLN   252      31.998  28.287 -19.530  1.00 37.46           O  
ATOM   1737  N   HIS   253      29.924  28.327 -18.651  1.00 39.55           N  
ATOM   1738  CA  HIS   253      29.349  29.091 -19.751  1.00 41.27           C  
ATOM   1739  C   HIS   253      29.982  30.477 -19.805  1.00 42.37           C  
ATOM   1740  O   HIS   253      30.252  31.008 -20.882  1.00 42.94           O  
ATOM   1742  N   GLY   254      30.222  31.054 -18.633  1.00 43.67           N  
ATOM   1743  CA  GLY   254      30.822  32.378 -18.536  1.00 45.19           C  
ATOM   1744  C   GLY   254      32.271  32.378 -19.009  1.00 44.55           C  
ATOM   1745  O   GLY   254      32.790  33.407 -19.441  1.00 43.84           O  
ATOM   1751  N   GLY   255      32.923  31.223 -18.925  1.00 43.18           N  
ATOM   1752  CA  GLY   255      34.310  31.108 -19.354  1.00 42.40           C  
ATOM   1753  C   GLY   255      34.417  31.118 -20.873  1.00 41.87           C  
ATOM   1754  O   GLY   255      35.518  31.160 -21.426  1.00 42.31           O  
ATOM   1759  N   ASP   256      33.270  31.070 -21.542  1.00 41.18           N  
ATOM   1760  CA  ASP   256      33.260  31.093 -22.993  1.00 40.74           C  
ATOM   1761  C   ASP   256      33.133  29.741 -23.668  1.00 40.22           C  
ATOM   1762  O   ASP   256      33.396  29.624 -24.865  1.00 40.78           O  
ATOM   1763  N   ASN   257      32.734  28.718 -22.917  1.00 39.47           N  
ATOM   1764  CA  ASN   257      32.583  27.385 -23.491  1.00 38.72           C  
ATOM   1765  C   ASN   257      31.208  27.187 -24.111  1.00 40.22           C  
ATOM   1766  O   ASN   257      30.207  27.677 -23.594  1.00 40.01           O  
ATOM   1775  N   ALA   258      31.176  26.462 -25.225  1.00 42.95           N  
ATOM   1776  CA  ALA   258      29.937  26.173 -25.939  1.00 46.18           C  
ATOM   1777  C   ALA   258      28.940  25.491 -25.011  1.00 47.03           C  
ATOM   1778  O   ALA   258      29.298  24.575 -24.270  1.00 47.66           O  
ATOM   1783  N   PRO   259      27.689  25.935 -25.062  1.00 48.08           N  
ATOM   1784  CA  PRO   259      26.632  25.376 -24.227  1.00 48.78           C  
ATOM   1785  C   PRO   259      26.505  23.866 -24.420  1.00 48.00           C  
ATOM   1786  O   PRO   259      26.504  23.099 -23.454  1.00 47.52           O  
ATOM   1792  N   TRP   260      26.398  23.448 -25.676  1.00 47.04           N  
ATOM   1793  CA  TRP   260      26.265  22.036 -26.015  1.00 46.05           C  
ATOM   1794  C   TRP   260      27.458  21.215 -25.524  1.00 44.34           C  
ATOM   1795  O   TRP   260      27.290  20.122 -24.983  1.00 43.95           O  
ATOM   1800  N   PHE   261      28.658  21.753 -25.714  1.00 41.08           N  
ATOM   1801  CA  PHE   261      29.879  21.073 -25.302  1.00 39.05           C  
ATOM   1802  C   PHE   261      29.881  20.816 -23.799  1.00 36.12           C  
ATOM   1803  O   PHE   261      30.160  19.703 -23.354  1.00 34.12           O  
ATOM   1808  N   VAL   262      29.561  21.845 -23.020  1.00 34.29           N  
ATOM   1809  CA  VAL   262      29.526  21.726 -21.563  1.00 31.76           C  
ATOM   1810  C   VAL   262      28.494  20.699 -21.107  1.00 32.31           C  
ATOM   1811  O   VAL   262      28.764  19.880 -20.231  1.00 30.82           O  
ATOM   1815  N   ASN   270      27.308  20.752 -21.706  1.00 31.73           N  
ATOM   1816  CA  ASN   270      26.238  19.828 -21.352  1.00 32.69           C  
ATOM   1817  C   ASN   270      26.651  18.388 -21.631  1.00 32.34           C  
ATOM   1818  O   ASN   270      26.372  17.483 -20.841  1.00 32.86           O  
ATOM   1820  N   ILE   271      27.328  18.180 -22.754  1.00 31.90           N  
ATOM   1821  CA  ILE   271      27.772  16.849 -23.138  1.00 31.76           C  
ATOM   1822  C   ILE   271      28.888  16.321 -22.235  1.00 29.38           C  
ATOM   1823  O   ILE   271      28.808  15.198 -21.735  1.00 28.63           O  
ATOM   1828  N   LEU   272      29.923  17.126 -22.033  1.00 27.27           N  
ATOM   1829  CA  LEU   272      31.049  16.725 -21.196  1.00 25.16           C  
ATOM   1830  C   LEU   272      30.641  16.583 -19.730  1.00 25.23           C  
ATOM   1831  O   LEU   272      31.059  15.640 -19.057  1.00 22.82           O  
ATOM   1836  N   TYR   273      29.826  17.511 -19.235  1.00 24.98           N  
ATOM   1837  CA  TYR   273      29.369  17.440 -17.847  1.00 24.70           C  
ATOM   1838  C   TYR   273      28.564  16.165 -17.598  1.00 25.56           C  
ATOM   1839  O   TYR   273      28.730  15.507 -16.570  1.00 22.97           O  
ATOM   1843  N   ASP   281      27.693  15.821 -18.544  1.00 25.86           N  
ATOM   1844  CA  ASP   281      26.868  14.622 -18.432  1.00 27.54           C  
ATOM   1845  C   ASP   281      27.728  13.363 -18.350  1.00 25.99           C  
ATOM   1846  O   ASP   281      27.459  12.465 -17.551  1.00 25.03           O  
ATOM   1849  N   SER   282      28.756  13.299 -19.188  1.00 25.90           N  
ATOM   1850  CA  SER   282      29.663  12.155 -19.204  1.00 25.89           C  
ATOM   1851  C   SER   282      30.380  12.016 -17.865  1.00 23.22           C  
ATOM   1852  O   SER   282      30.463  10.921 -17.306  1.00 23.68           O  
ATOM   1860  N   LEU   283      30.899  13.129 -17.359  1.00 21.10           N  
ATOM   1861  CA  LEU   283      31.618  13.123 -16.090  1.00 20.82           C  
ATOM   1862  C   LEU   283      30.751  12.668 -14.917  1.00 21.38           C  
ATOM   1863  O   LEU   283      31.142  11.783 -14.154  1.00 22.41           O  
TER
END
