
#######################################################
#                                                     #
#                        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   32 (  158),  selected   32 , name T0356TS239_4_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS239_4_2-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    D     314      L      16          1.185
LGA    A     315      E      17          1.283
LGA    -       -      Q      18           -
LGA    I     316      Q      19          4.311
LGA    Y     317      G      20           #
LGA    H     318      E      21           #
LGA    S     319      L      22          4.571
LGA    T     320      K      23          0.568
LGA    Y     321      R      24          3.004
LGA    T     322      -       -           -
LGA    G     323      -       -           -
LGA    R     324      I      25          1.823
LGA    P     325      -       -           -
LGA    P     326      T      26          0.969
LGA    P     329      L      27          1.105
LGA    A     330      P      28          2.035
LGA    V     331      V      29          2.243
LGA    L     332      D      30           #
LGA    G     333      P      31          2.258
LGA    V     334      H      32          3.614
LGA    A     335      L      33          1.040
LGA    L     336      E      34          2.866
LGA    N     337      I      35          1.595
LGA    E     338      T      36          5.000
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    V     339      C      64          3.360
LGA    F     340      N      65          2.762
LGA    V     341      L      66          3.589
LGA    -       -      F      67           -
LGA    P     342      G      68          2.290
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    I     343      V     331          3.828
LGA    L     344      L     332          2.325
LGA    Q     345      -       -           -
LGA    K     346      G     333          2.363
LGA    Q     347      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  124    5.0     24    2.77     8.33     12.252     0.836

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.203280 * X  +  -0.454100 * Y  +   0.867451 * Z  + -18.290056
  Y_new =  -0.565165 * X  +  -0.777876 * Y  +  -0.274767 * Z  + 144.866211
  Z_new =   0.799541 * X  +  -0.434398 * Y  +  -0.414768 * Z  + 138.381699 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.333082    0.808511  [ DEG:  -133.6757     46.3243 ]
  Theta =  -0.926530   -2.215062  [ DEG:   -53.0863   -126.9137 ]
  Phi   =  -1.225521    1.916071  [ DEG:   -70.2172    109.7828 ]
 
# 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: T0356TS239_4_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS239_4_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  124   5.0   24   2.77    8.33  12.252
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS239_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT 1kqf_A
ATOM   1470  N   ASP   314      64.283  83.581  84.539  1.00  9.99
ATOM   1471  CA  ASP   314      65.139  82.807  85.430  1.00  9.99
ATOM   1472  C   ASP   314      64.820  83.088  86.891  1.00  9.99
ATOM   1473  O   ASP   314      64.873  82.190  87.730  1.00  9.99
ATOM   1474  CB  ASP   314      66.605  83.114  85.151  1.00  9.99
ATOM   1475  N   ALA   315      64.481  84.335  87.200  1.00  9.99
ATOM   1476  CA  ALA   315      64.170  84.686  88.578  1.00  9.99
ATOM   1477  C   ALA   315      62.808  84.136  89.014  1.00  9.99
ATOM   1478  O   ALA   315      62.585  83.909  90.205  1.00  9.99
ATOM   1479  CB  ALA   315      64.242  86.212  88.756  1.00  9.99
ATOM   1480  N   ILE   316      61.899  83.920  88.060  1.00  9.99
ATOM   1481  CA  ILE   316      60.589  83.347  88.392  1.00  9.99
ATOM   1482  C   ILE   316      60.865  81.981  89.002  1.00  9.99
ATOM   1483  O   ILE   316      60.355  81.634  90.067  1.00  9.99
ATOM   1484  CB  ILE   316      59.724  83.109  87.139  1.00  9.99
ATOM   1485  N   TYR   317      61.692  81.215  88.303  1.00  9.99
ATOM   1486  CA  TYR   317      62.046  79.865  88.708  1.00  9.99
ATOM   1487  C   TYR   317      62.855  79.825  90.001  1.00  9.99
ATOM   1488  O   TYR   317      62.674  78.923  90.822  1.00  9.99
ATOM   1489  CB  TYR   317      62.769  79.177  87.540  1.00  9.99
ATOM   1490  N   HIS   318      63.731  80.808  90.193  1.00  9.99
ATOM   1491  CA  HIS   318      64.524  80.893  91.420  1.00  9.99
ATOM   1492  C   HIS   318      63.589  80.914  92.623  1.00  9.99
ATOM   1493  O   HIS   318      63.779  80.179  93.595  1.00  9.99
ATOM   1494  CB  HIS   318      65.368  82.178  91.432  1.00  9.99
ATOM   1495  N   SER   319      62.562  81.752  92.544  1.00  9.99
ATOM   1496  CA  SER   319      61.622  81.888  93.651  1.00  9.99
ATOM   1497  C   SER   319      60.911  80.587  94.008  1.00  9.99
ATOM   1498  O   SER   319      60.749  80.270  95.185  1.00  9.99
ATOM   1499  CB  SER   319      60.560  82.972  93.364  1.00  9.99
ATOM   1500  N   THR   320      60.476  79.834  93.003  1.00  9.99
ATOM   1501  CA  THR   320      59.791  78.571  93.267  1.00  9.99
ATOM   1502  C   THR   320      60.754  77.533  93.846  1.00  9.99
ATOM   1503  O   THR   320      60.396  76.769  94.745  1.00  9.99
ATOM   1504  CB  THR   320      59.133  78.048  91.981  1.00  9.99
ATOM   1505  N   TYR   321      61.981  77.516  93.336  1.00  9.99
ATOM   1506  CA  TYR   321      62.978  76.566  93.818  1.00  9.99
ATOM   1507  C   TYR   321      63.272  76.824  95.290  1.00  9.99
ATOM   1508  O   TYR   321      63.498  75.896  96.067  1.00  9.99
ATOM   1509  CB  TYR   321      64.259  76.688  92.995  1.00  9.99
ATOM   1510  N   THR   322      63.289  78.098  95.666  1.00  9.99
ATOM   1511  CA  THR   322      63.545  78.471  97.048  1.00  9.99
ATOM   1512  C   THR   322      62.412  77.944  97.925  1.00  9.99
ATOM   1513  O   THR   322      62.641  77.479  99.042  1.00  9.99
ATOM   1514  CB  THR   322      63.660  79.991  97.160  1.00  9.99
ATOM   1515  N   GLY   323      61.190  78.011  97.404  1.00  9.99
ATOM   1516  CA  GLY   323      60.031  77.521  98.139  1.00  9.99
ATOM   1517  C   GLY   323      60.180  76.029  98.411  1.00  9.99
ATOM   1518  O   GLY   323      59.956  75.567  99.534  1.00  9.99
ATOM   1519  N   ARG   324      60.578  75.271  97.393  1.00  9.99
ATOM   1520  CA  ARG   324      60.745  73.837  97.572  1.00  9.99
ATOM   1521  C   ARG   324      61.858  73.493  98.561  1.00  9.99
ATOM   1522  O   ARG   324      61.820  72.443  99.197  1.00  9.99
ATOM   1523  CB  ARG   324      60.995  73.157  96.221  1.00  9.99
ATOM   1524  N   PRO   325      62.849  74.369  98.699  1.00  9.99
ATOM   1525  CA  PRO   325      63.926  74.107  99.650  1.00  9.99
ATOM   1526  C   PRO   325      63.419  74.366 101.071  1.00  9.99
ATOM   1527  O   PRO   325      63.721  73.607 101.985  1.00  9.99
ATOM   1528  CB  PRO   325      65.148  74.982  99.336  1.00  9.99
ATOM   1529  N   PRO   326      62.635  75.428 101.246  1.00  9.99
ATOM   1530  CA  PRO   326      62.084  75.747 102.560  1.00  9.99
ATOM   1531  C   PRO   326      61.132  74.650 103.033  1.00  9.99
ATOM   1532  O   PRO   326      61.089  74.334 104.218  1.00  9.99
ATOM   1533  CB  PRO   326      61.334  77.086 102.525  1.00  9.99
ATOM   1534  N   PRO   329      60.377  74.072 102.103  1.00  9.99
ATOM   1535  CA  PRO   329      59.419  73.021 102.437  1.00  9.99
ATOM   1536  C   PRO   329      60.065  71.642 102.591  1.00  9.99
ATOM   1537  O   PRO   329      59.428  70.703 103.062  1.00  9.99
ATOM   1538  CB  PRO   329      58.315  72.965 101.373  1.00  9.99
ATOM   1539  N   ALA   330      61.329  71.527 102.190  1.00  9.99
ATOM   1540  CA  ALA   330      62.033  70.255 102.296  1.00  9.99
ATOM   1541  C   ALA   330      61.532  69.219 101.311  1.00  9.99
ATOM   1542  O   ALA   330      61.521  68.025 101.608  1.00  9.99
ATOM   1543  CB  ALA   330      61.907  69.736 103.739  1.00  9.99
ATOM   1544  N   VAL   331      61.143  69.670 100.123  1.00  9.99
ATOM   1545  CA  VAL   331      60.608  68.763  99.114  1.00  9.99
ATOM   1546  C   VAL   331      61.550  68.304  97.997  1.00  9.99
ATOM   1547  O   VAL   331      61.158  67.488  97.165  1.00  9.99
ATOM   1548  CB  VAL   331      59.345  69.367  98.495  1.00  9.99
ATOM   1549  N   LEU   332      62.777  68.813  97.963  1.00  9.99
ATOM   1550  CA  LEU   332      63.711  68.382  96.922  1.00  9.99
ATOM   1551  C   LEU   332      64.311  67.022  97.278  1.00  9.99
ATOM   1552  O   LEU   332      64.640  66.766  98.437  1.00  9.99
ATOM   1553  CB  LEU   332      64.828  69.411  96.723  1.00  9.99
ATOM   1554  N   GLY   333      64.448  66.155  96.276  1.00  9.99
ATOM   1555  CA  GLY   333      64.999  64.828  96.500  1.00  9.99
ATOM   1556  C   GLY   333      63.959  63.812  96.938  1.00  9.99
ATOM   1557  O   GLY   333      64.269  62.632  97.091  1.00  9.99
ATOM   1558  N   VAL   334      62.726  64.273  97.127  1.00  9.99
ATOM   1559  CA  VAL   334      61.617  63.424  97.566  1.00  9.99
ATOM   1560  C   VAL   334      60.758  62.856  96.446  1.00  9.99
ATOM   1561  O   VAL   334      60.499  63.524  95.437  1.00  9.99
ATOM   1562  CB  VAL   334      60.693  64.211  98.497  1.00  9.99
ATOM   1563  N   ALA   335      60.302  61.622  96.637  1.00  9.99
ATOM   1564  CA  ALA   335      59.421  60.996  95.668  1.00  9.99
ATOM   1565  C   ALA   335      58.120  61.771  95.840  1.00  9.99
ATOM   1566  O   ALA   335      57.619  61.902  96.958  1.00  9.99
ATOM   1567  CB  ALA   335      59.206  59.524  96.010  1.00  9.99
ATOM   1568  N   LEU   336      57.585  62.307  94.749  1.00  9.99
ATOM   1569  CA  LEU   336      56.354  63.073  94.850  1.00  9.99
ATOM   1570  C   LEU   336      56.611  64.547  95.124  1.00  9.99
ATOM   1571  O   LEU   336      55.679  65.320  95.348  1.00  9.99
ATOM   1572  CB  LEU   336      55.474  62.455  95.949  1.00  9.99
ATOM   1573  N   ASN   337      57.881  64.935  95.111  1.00  9.99
ATOM   1574  CA  ASN   337      58.234  66.325  95.345  1.00  9.99
ATOM   1575  C   ASN   337      59.035  66.845  94.167  1.00  9.99
ATOM   1576  O   ASN   337      58.696  66.570  93.013  1.00  9.99
ATOM   1577  CB  ASN   337      59.019  66.448  96.662  1.00  9.99
ATOM   1578  N   GLU   338      60.086  67.608  94.454  1.00  9.99
ATOM   1579  CA  GLU   338      60.945  68.134  93.403  1.00  9.99
ATOM   1580  C   GLU   338      60.403  69.238  92.515  1.00  9.99
ATOM   1581  O   GLU   338      59.323  69.786  92.753  1.00  9.99
ATOM   1582  CB  GLU   338      61.376  66.944  92.529  1.00  9.99
ATOM   1583  N   VAL   339      61.179  69.568  91.486  1.00  9.99
ATOM   1584  CA  VAL   339      60.814  70.600  90.523  1.00  9.99
ATOM   1585  C   VAL   339      60.706  69.965  89.160  1.00  9.99
ATOM   1586  O   VAL   339      61.714  69.656  88.523  1.00  9.99
ATOM   1587  CB  VAL   339      61.872  71.717  90.453  1.00  9.99
ATOM   1588  N   PHE   340      59.477  69.753  88.710  1.00  9.99
ATOM   1589  CA  PHE   340      59.289  69.146  87.413  1.00  9.99
ATOM   1590  C   PHE   340      59.108  70.200  86.339  1.00  9.99
ATOM   1591  O   PHE   340      57.991  70.570  85.970  1.00  9.99
ATOM   1592  CB  PHE   340      58.139  68.137  87.470  1.00  9.99
ATOM   1593  N   VAL   341      60.255  70.701  85.882  1.00  9.99
ATOM   1594  CA  VAL   341      60.334  71.697  84.827  1.00  9.99
ATOM   1595  C   VAL   341      60.099  70.885  83.565  1.00  9.99
ATOM   1596  O   VAL   341      61.021  70.268  83.028  1.00  9.99
ATOM   1597  CB  VAL   341      61.733  72.321  84.803  1.00  9.99
ATOM   1598  N   PRO   342      58.857  70.881  83.105  1.00  9.99
ATOM   1599  CA  PRO   342      58.465  70.094  81.944  1.00  9.99
ATOM   1600  C   PRO   342      59.021  70.590  80.613  1.00  9.99
ATOM   1601  O   PRO   342      58.652  71.655  80.124  1.00  9.99
ATOM   1602  CB  PRO   342      56.935  70.008  81.892  1.00  9.99
ATOM   1603  N   ILE   343      59.918  69.795  80.038  1.00  9.99
ATOM   1604  CA  ILE   343      60.553  70.111  78.765  1.00  9.99
ATOM   1605  C   ILE   343      59.561  70.138  77.604  1.00  9.99
ATOM   1606  O   ILE   343      58.463  69.576  77.684  1.00  9.99
ATOM   1607  CB  ILE   343      61.668  69.101  78.490  1.00  9.99
ATOM   1608  N   LEU   344      59.957  70.792  76.519  1.00  9.99
ATOM   1609  CA  LEU   344      59.077  70.907  75.372  1.00  9.99
ATOM   1610  C   LEU   344      59.184  69.875  74.276  1.00  9.99
ATOM   1611  O   LEU   344      58.484  68.865  74.294  1.00  9.99
ATOM   1612  CB  LEU   344      59.293  72.307  74.773  1.00  9.99
ATOM   1613  N   GLN   345      60.043  70.155  73.300  1.00  9.99
ATOM   1614  CA  GLN   345      60.255  69.245  72.184  1.00  9.99
ATOM   1615  C   GLN   345      60.678  67.877  72.686  1.00  9.99
ATOM   1616  O   GLN   345      61.294  67.754  73.747  1.00  9.99
ATOM   1617  CB  GLN   345      61.345  69.788  71.253  1.00  9.99
ATOM   1618  N   LYS   346      60.355  66.860  71.897  1.00  9.99
ATOM   1619  CA  LYS   346      60.686  65.477  72.206  1.00  9.99
ATOM   1620  C   LYS   346      62.155  65.298  72.566  1.00  9.99
ATOM   1621  O   LYS   346      62.486  64.453  73.396  1.00  9.99
ATOM   1622  CB  LYS   346      60.346  64.591  71.011  1.00  9.99
ATOM   1623  N   GLN   347      63.042  66.077  71.951  1.00  9.99
ATOM   1624  CA  GLN   347      64.456  65.938  72.276  1.00  9.99
ATOM   1625  C   GLN   347      65.188  67.228  72.580  1.00  9.99
ATOM   1626  O   GLN   347      66.382  67.346  72.313  1.00  9.99
ATOM   1627  CB  GLN   347      65.209  65.183  71.174  1.00  9.99
TER
END
