
#######################################################
#                                                     #
#                        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   23 (  176),  selected   23 , name T0382TS009_1_3-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_1_3-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K     100      L       4           #
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    W     101      N      38           #
LGA    F     102      R      39          2.940
LGA    P     103      L      40          4.866
LGA    -       -      F      41           -
LGA    Q     104      G      42          2.024
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    A     105      A      45          2.034
LGA    G     106      E      46          3.638
LGA    D     107      I      47          2.474
LGA    A     108      A      48          2.984
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    G     109      K      52          2.266
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    M     110      A      83          4.612
LGA    C     111      V      84          0.551
LGA    L     112      A      85          0.861
LGA    D     113      P      86          3.676
LGA    -       -      V      87           -
LGA    L     114      K      88          1.207
LGA    L     115      A      89          4.079
LGA    -       -      R      90           -
LGA    D     116      E      91          1.099
LGA    D     117      Q      92          3.014
LGA    -       -      L      93           -
LGA    G     118      E      94          0.652
LGA    T     119      A      95          1.939
LGA    F     120      I      96          4.905
LGA    K     121      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    P     122      Q     104           #
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  119    5.0     19    2.96    10.53     10.229     0.621

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.054862 * X  +   0.357418 * Y  +  -0.932332 * Z  +  12.441198
  Y_new =  -0.378293 * X  +   0.856690 * Y  +   0.350680 * Z  +  82.815506
  Z_new =   0.924059 * X  +   0.371934 * Y  +   0.088210 * Z  +  16.032568 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.337934   -1.803659  [ DEG:    76.6580   -103.3420 ]
  Theta =  -1.178566   -1.963027  [ DEG:   -67.5268   -112.4732 ]
  Phi   =  -1.714816    1.426777  [ DEG:   -98.2517     81.7483 ]
 
# 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: T0382TS009_1_3-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_1_3-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  119   5.0   19   2.96   10.53  10.229
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_1_3-D1
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A
ATOM    772  N   LYS   100      -4.897  38.113  -0.136  1.00  0.00              
ATOM    773  CA  LYS   100      -5.854  37.043  -0.392  1.00  0.00              
ATOM    774  C   LYS   100      -5.583  35.836   0.498  1.00  0.00              
ATOM    775  O   LYS   100      -6.437  35.427   1.284  1.00  0.00              
ATOM    776  CB  LYS   100      -7.285  37.542  -0.180  1.00  0.00              
ATOM    777  CG  LYS   100      -8.029  37.858  -1.467  1.00  0.00              
ATOM    778  CD  LYS   100      -9.083  38.931  -1.246  1.00  0.00              
ATOM    779  CE  LYS   100     -10.011  39.048  -2.443  1.00  0.00              
ATOM    780  NZ  LYS   100     -10.739  40.348  -2.458  1.00  0.00              
ATOM    781  N   TRP   101      -4.387  35.269   0.369  1.00  0.00              
ATOM    782  CA  TRP   101      -4.001  34.108   1.162  1.00  0.00              
ATOM    783  C   TRP   101      -3.165  34.517   2.370  1.00  0.00              
ATOM    784  O   TRP   101      -3.697  34.998   3.371  1.00  0.00              
ATOM    785  CB  TRP   101      -5.239  33.333   1.617  1.00  0.00              
ATOM    786  CG  TRP   101      -5.391  31.999   0.953  1.00  0.00              
ATOM    787  CD1 TRP   101      -6.356  31.066   1.197  1.00  0.00              
ATOM    788  CD2 TRP   101      -4.549  31.448  -0.068  1.00  0.00              
ATOM    789  NE1 TRP   101      -6.170  29.967   0.394  1.00  0.00              
ATOM    790  CE2 TRP   101      -5.065  30.179  -0.393  1.00  0.00              
ATOM    791  CE3 TRP   101      -3.410  31.907  -0.738  1.00  0.00              
ATOM    792  CZ2 TRP   101      -4.482  29.360  -1.360  1.00  0.00              
ATOM    793  CZ3 TRP   101      -2.834  31.094  -1.696  1.00  0.00              
ATOM    794  CH2 TRP   101      -3.369  29.833  -2.000  1.00  0.00              
ATOM    795  N   PHE   102      -1.854  34.323   2.270  1.00  0.00              
ATOM    796  CA  PHE   102      -0.944  34.672   3.353  1.00  0.00              
ATOM    797  C   PHE   102      -1.380  35.957   4.049  1.00  0.00              
ATOM    798  O   PHE   102      -1.321  36.070   5.274  1.00  0.00              
ATOM    799  CB  PHE   102      -0.854  33.530   4.368  1.00  0.00              
ATOM    800  CG  PHE   102       0.436  32.762   4.305  1.00  0.00              
ATOM    801  CD1 PHE   102       1.146  32.670   3.120  1.00  0.00              
ATOM    802  CD2 PHE   102       0.940  32.135   5.430  1.00  0.00              
ATOM    803  CE1 PHE   102       2.332  31.964   3.062  1.00  0.00              
ATOM    804  CE2 PHE   102       2.127  31.429   5.372  1.00  0.00              
ATOM    805  CZ  PHE   102       2.823  31.343   4.195  1.00  0.00              
ATOM    806  N   PRO   103      -1.827  36.950   3.265  1.00  0.00              
ATOM    807  CA  PRO   103      -2.278  38.237   3.802  1.00  0.00              
ATOM    808  C   PRO   103      -3.767  38.463   3.556  1.00  0.00              
ATOM    809  O   PRO   103      -4.598  37.629   3.915  1.00  0.00              
ATOM    810  CB  PRO   103      -2.007  38.100   5.300  1.00  0.00              
ATOM    811  CG  PRO   103      -2.781  36.893   5.711  1.00  0.00              
ATOM    812  CD  PRO   103      -1.926  36.887   1.797  1.00  0.00              
ATOM    813  N   GLN   104      -4.095  39.595   2.943  1.00  0.00              
ATOM    814  CA  GLN   104      -5.482  39.933   2.650  1.00  0.00              
ATOM    815  C   GLN   104      -5.580  40.873   1.453  1.00  0.00              
ATOM    816  O   GLN   104      -4.621  41.567   1.117  1.00  0.00              
ATOM    817  CB  GLN   104      -6.299  38.665   2.391  1.00  0.00              
ATOM    818  CG  GLN   104      -7.576  38.571   3.209  1.00  0.00              
ATOM    819  CD  GLN   104      -8.459  37.415   2.781  1.00  0.00              
ATOM    820  OE1 GLN   104      -9.640  37.365   3.122  1.00  0.00              
ATOM    821  NE2 GLN   104      -7.886  36.481   2.031  1.00  0.00              
ATOM    822  N   ALA   105      -6.745  40.890   0.813  1.00  0.00              
ATOM    823  CA  ALA   105      -6.970  41.744  -0.346  1.00  0.00              
ATOM    824  C   ALA   105      -8.150  41.250  -1.175  1.00  0.00              
ATOM    825  O   ALA   105      -9.061  40.605  -0.654  1.00  0.00              
ATOM    826  CB  ALA   105      -7.203  43.182   0.091  1.00  0.00              
ATOM    827  N   GLY   106      -8.128  41.554  -2.469  1.00  0.00              
ATOM    828  CA  GLY   106      -9.204  41.131  -3.347  1.00  0.00              
ATOM    829  C   GLY   106      -9.397  42.069  -4.521  1.00  0.00              
ATOM    830  O   GLY   106     -10.493  42.581  -4.746  1.00  0.00              
ATOM    831  N   ASP   107      -8.327  42.297  -5.277  1.00  0.00              
ATOM    832  CA  ASP   107      -8.383  43.178  -6.437  1.00  0.00              
ATOM    833  C   ASP   107      -8.279  44.642  -6.022  1.00  0.00              
ATOM    834  O   ASP   107      -7.538  44.985  -5.100  1.00  0.00              
ATOM    835  CB  ASP   107      -7.268  42.833  -7.428  1.00  0.00              
ATOM    836  CG  ASP   107      -7.803  42.388  -8.773  1.00  0.00              
ATOM    837  OD1 ASP   107      -7.003  42.288  -9.728  1.00  0.00              
ATOM    838  OD2 ASP   107      -9.022  42.138  -8.876  1.00  0.00              
ATOM    839  N   ALA   108      -9.028  45.501  -6.707  1.00  0.00              
ATOM    840  CA  ALA   108      -9.022  46.928  -6.410  1.00  0.00              
ATOM    841  C   ALA   108     -10.317  47.591  -6.865  1.00  0.00              
ATOM    842  O   ALA   108     -11.230  46.924  -7.352  1.00  0.00              
ATOM    843  CB  ALA   108      -8.808  47.160  -4.922  1.00  0.00              
ATOM    844  N   GLY   109     -10.392  48.907  -6.701  1.00  0.00              
ATOM    845  CA  GLY   109     -11.582  49.636  -7.100  1.00  0.00              
ATOM    846  C   GLY   109     -12.001  50.670  -6.075  1.00  0.00              
ATOM    847  O   GLY   109     -11.345  50.841  -5.046  1.00  0.00              
ATOM    848  N   MET   110     -13.099  51.366  -6.351  1.00  0.00              
ATOM    849  CA  MET   110     -13.605  52.390  -5.445  1.00  0.00              
ATOM    850  C   MET   110     -14.638  53.276  -6.135  1.00  0.00              
ATOM    851  O   MET   110     -14.715  53.313  -7.363  1.00  0.00              
ATOM    852  CB  MET   110     -14.215  51.747  -4.197  1.00  0.00              
ATOM    853  CG  MET   110     -13.601  52.223  -2.891  1.00  0.00              
ATOM    854  SD  MET   110     -13.983  51.134  -1.505  1.00  0.00              
ATOM    855  CE  MET   110     -13.047  51.916  -0.193  1.00  0.00              
ATOM    856  N   CYS   111     -15.429  53.985  -5.338  1.00  0.00              
ATOM    857  CA  CYS   111     -16.458  54.871  -5.870  1.00  0.00              
ATOM    858  C   CYS   111     -17.698  54.872  -4.984  1.00  0.00              
ATOM    859  O   CYS   111     -18.684  54.196  -5.278  1.00  0.00              
ATOM    860  CB  CYS   111     -15.915  56.294  -6.018  1.00  0.00              
ATOM    861  SG  CYS   111     -15.703  56.845  -7.740  1.00  0.00              
ATOM    862  N   LEU   112     -17.642  55.634  -3.897  1.00  0.00              
ATOM    863  CA  LEU   112     -18.760  55.724  -2.965  1.00  0.00              
ATOM    864  C   LEU   112     -18.366  55.223  -1.580  1.00  0.00              
ATOM    865  O   LEU   112     -17.194  54.960  -1.315  1.00  0.00              
ATOM    866  CB  LEU   112     -19.271  57.164  -2.878  1.00  0.00              
ATOM    867  CG  LEU   112     -20.713  57.400  -3.333  1.00  0.00              
ATOM    868  CD1 LEU   112     -21.441  58.313  -2.358  1.00  0.00              
ATOM    869  CD2 LEU   112     -21.451  56.080  -3.489  1.00  0.00              
ATOM    870  N   ASP   113     -19.354  55.092  -0.700  1.00  0.00              
ATOM    871  CA  ASP   113     -19.112  54.623   0.659  1.00  0.00              
ATOM    872  C   ASP   113     -20.272  54.982   1.581  1.00  0.00              
ATOM    873  O   ASP   113     -20.067  55.394   2.722  1.00  0.00              
ATOM    874  CB  ASP   113     -18.879  53.111   0.670  1.00  0.00              
ATOM    875  CG  ASP   113     -17.492  52.739   1.155  1.00  0.00              
ATOM    876  OD1 ASP   113     -17.288  51.563   1.524  1.00  0.00              
ATOM    877  OD2 ASP   113     -16.610  53.622   1.165  1.00  0.00              
ATOM    878  N   LEU   114     -21.492  54.822   1.079  1.00  0.00              
ATOM    879  CA  LEU   114     -22.687  55.129   1.855  1.00  0.00              
ATOM    880  C   LEU   114     -22.382  56.132   2.962  1.00  0.00              
ATOM    881  O   LEU   114     -23.229  56.410   3.812  1.00  0.00              
ATOM    882  CB  LEU   114     -23.794  55.668   0.946  1.00  0.00              
ATOM    883  CG  LEU   114     -25.226  55.286   1.323  1.00  0.00              
ATOM    884  CD1 LEU   114     -26.156  56.482   1.184  1.00  0.00              
ATOM    885  CD2 LEU   114     -25.279  54.722   2.735  1.00  0.00              
ATOM    886  N   LEU   115     -21.168  56.672   2.948  1.00  0.00              
ATOM    887  CA  LEU   115     -20.750  57.644   3.950  1.00  0.00              
ATOM    888  C   LEU   115     -21.428  57.383   5.291  1.00  0.00              
ATOM    889  O   LEU   115     -20.840  57.603   6.349  1.00  0.00              
ATOM    890  CB  LEU   115     -19.229  57.621   4.116  1.00  0.00              
ATOM    891  CG  LEU   115     -18.534  58.984   4.180  1.00  0.00              
ATOM    892  CD1 LEU   115     -17.678  59.092   5.433  1.00  0.00              
ATOM    893  CD2 LEU   115     -19.553  60.110   4.121  1.00  0.00              
ATOM    894  N   ASP   116     -22.669  56.909   5.237  1.00  0.00              
ATOM    895  CA  ASP   116     -23.429  56.616   6.447  1.00  0.00              
ATOM    896  C   ASP   116     -22.786  55.485   7.242  1.00  0.00              
ATOM    897  O   ASP   116     -23.359  54.992   8.213  1.00  0.00              
ATOM    898  CB  ASP   116     -23.554  57.868   7.318  1.00  0.00              
ATOM    899  CG  ASP   116     -24.992  58.321   7.485  1.00  0.00              
ATOM    900  OD1 ASP   116     -25.382  58.652   8.624  1.00  0.00              
ATOM    901  OD2 ASP   116     -25.728  58.343   6.476  1.00  0.00              
ATOM    902  N   ASP   117     -21.591  55.080   6.824  1.00  0.00              
ATOM    903  CA  ASP   117     -20.867  54.007   7.496  1.00  0.00              
ATOM    904  C   ASP   117     -21.510  53.664   8.836  1.00  0.00              
ATOM    905  O   ASP   117     -21.867  52.513   9.088  1.00  0.00              
ATOM    906  CB  ASP   117     -20.808  52.763   6.608  1.00  0.00              
ATOM    907  CG  ASP   117     -19.544  51.954   6.824  1.00  0.00              
ATOM    908  OD1 ASP   117     -19.610  50.711   6.719  1.00  0.00              
ATOM    909  OD2 ASP   117     -18.488  52.563   7.098  1.00  0.00              
ATOM    910  N   GLY   118     -21.653  54.671   9.693  1.00  0.00              
ATOM    911  CA  GLY   118     -22.253  54.451  10.996  1.00  0.00              
ATOM    912  C   GLY   118     -23.568  53.704  10.910  1.00  0.00              
ATOM    913  O   GLY   118     -24.091  53.232  11.920  1.00  0.00              
ATOM    914  N   THR   119     -24.109  53.595   9.702  1.00  0.00              
ATOM    915  CA  THR   119     -25.401  52.885   9.483  1.00  0.00              
ATOM    916  C   THR   119     -25.730  51.963  10.652  1.00  0.00              
ATOM    917  O   THR   119     -25.575  52.340  11.814  1.00  0.00              
ATOM    918  CB  THR   119     -26.563  53.876   9.280  1.00  0.00              
ATOM    919  OG1 THR   119     -26.104  55.211   9.524  1.00  0.00              
ATOM    920  CG2 THR   119     -27.102  53.781   7.861  1.00  0.00              
ATOM    921  N   PHE   120     -26.184  50.754  10.338  1.00  0.00              
ATOM    922  CA  PHE   120     -26.535  49.778  11.362  1.00  0.00              
ATOM    923  C   PHE   120     -26.015  48.390  11.001  1.00  0.00              
ATOM    924  O   PHE   120     -25.276  47.774  11.770  1.00  0.00              
ATOM    925  CB  PHE   120     -25.986  50.208  12.723  1.00  0.00              
ATOM    926  CG  PHE   120     -27.000  50.888  13.598  1.00  0.00              
ATOM    927  CD1 PHE   120     -28.250  51.219  13.104  1.00  0.00              
ATOM    928  CD2 PHE   120     -26.704  51.198  14.914  1.00  0.00              
ATOM    929  CE1 PHE   120     -29.183  51.845  13.910  1.00  0.00              
ATOM    930  CE2 PHE   120     -27.637  51.823  15.719  1.00  0.00              
ATOM    931  CZ  PHE   120     -28.872  52.147  15.222  1.00  0.00              
ATOM    932  N   LYS   121     -26.404  47.905   9.827  1.00  0.00              
ATOM    933  CA  LYS   121     -25.979  46.590   9.362  1.00  0.00              
ATOM    934  C   LYS   121     -24.462  46.446   9.430  1.00  0.00              
ATOM    935  O   LYS   121     -23.782  47.195  10.131  1.00  0.00              
ATOM    936  CB  LYS   121     -26.649  45.488  10.185  1.00  0.00              
ATOM    937  CG  LYS   121     -27.760  44.755   9.453  1.00  0.00              
ATOM    938  CD  LYS   121     -28.368  43.665  10.321  1.00  0.00              
ATOM    939  CE  LYS   121     -29.717  43.217   9.780  1.00  0.00              
ATOM    940  NZ  LYS   121     -30.336  42.166  10.633  1.00  0.00              
ATOM    941  N   PRO   122     -23.912  45.470   8.692  1.00  0.00              
ATOM    942  CA  PRO   122     -22.467  45.220   8.664  1.00  0.00              
ATOM    943  C   PRO   122     -22.137  43.879   8.019  1.00  0.00              
ATOM    944  O   PRO   122     -22.639  43.557   6.942  1.00  0.00              
ATOM    945  CB  PRO   122     -21.937  46.366   7.799  1.00  0.00              
ATOM    946  CG  PRO   122     -23.074  46.707   6.895  1.00  0.00              
ATOM    947  CD  PRO   122     -24.659  44.537   7.832  1.00  0.00              
TER
END
