
#######################################################
#                                                     #
#                        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   16 (  125),  selected   16 , name T0383TS009_1_3
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383TS009_1_3.T0383.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       3           -
LGA    -       -      M       4           -
LGA    -       -      N       5           -
LGA    -       -      L       6           -
LGA    -       -      K       7           -
LGA    -       -      R       8           -
LGA    -       -      E       9           -
LGA    -       -      Q      10           -
LGA    -       -      E      11           -
LGA    -       -      F      12           -
LGA    -       -      V      13           -
LGA    -       -      S      14           -
LGA    -       -      Q      15           -
LGA    -       -      Y      16           -
LGA    -       -      H      17           -
LGA    -       -      F      18           -
LGA    -       -      D      19           -
LGA    -       -      A      20           -
LGA    -       -      R      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      E      24           -
LGA    -       -      W      25           -
LGA    -       -      E      26           -
LGA    -       -      N      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      G      30           -
LGA    -       -      A      31           -
LGA    -       -      P      32           -
LGA    -       -      E      33           -
LGA    -       -      T      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      D      37           -
LGA    -       -      V      38           -
LGA    -       -      N      39           -
LGA    -       -      F      40           -
LGA    -       -      Q      41           -
LGA    -       -      L      42           -
LGA    -       -      L      43           -
LGA    -       -      Q      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      Q      47           -
LGA    -       -      E      48           -
LGA    -       -      N      49           -
LGA    -       -      Q      50           -
LGA    -       -      V      51           -
LGA    -       -      T      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      I      55           -
LGA    -       -      V      56           -
LGA    -       -      I      57           -
LGA    -       -      L      58           -
LGA    -       -      S      59           -
LGA    -       -      F      60           -
LGA    -       -      M      61           -
LGA    -       -      I      62           -
LGA    -       -      V      63           -
LGA    -       -      F      64           -
LGA    -       -      D      65           -
LGA    -       -      K      66           -
LGA    -       -      F      67           -
LGA    -       -      V      68           -
LGA    -       -      I      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      T      72           -
LGA    E     112      I      73          4.736
LGA    -       -      S      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      N      77           -
LGA    -       -      H      78           -
LGA    -       -      I      79           -
LGA    -       -      D      80           -
LGA    -       -      G      81           -
LGA    -       -      R      82           -
LGA    -       -      I      83           -
LGA    -       -      V      84           -
LGA    -       -      N      85           -
LGA    -       -      E      86           -
LGA    -       -      P      87           -
LGA    -       -      S      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      Q      92           -
LGA    -       -      E      93           -
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      E      96           -
LGA    -       -      T      97           -
LGA    -       -      L      98           -
LGA    -       -      A      99           -
LGA    -       -      R     100           -
LGA    V     113      P     101          4.084
LGA    T     114      C     102          1.066
LGA    E     115      L     103          2.131
LGA    I     116      N     104          4.618
LGA    -       -      M     105           -
LGA    A     117      L     106          1.420
LGA    L     118      N     107          2.268
LGA    D     119      R     108          0.320
LGA    L     120      L     109          2.617
LGA    P     121      T     110          2.636
LGA    G     122      Y     111          1.539
LGA    I     123      E     112          0.790
LGA    N     124      V     113          2.470
LGA    L     125      T     114          2.731
LGA    E     126      E     115          1.731
LGA    -       -      I     116           -
LGA    -       -      A     117           -
LGA    -       -      L     118           -
LGA    -       -      D     119           -
LGA    -       -      L     120           -
LGA    F     127      P     121          2.019
LGA    -       -      G     122           -
LGA    -       -      I     123           -
LGA    -       -      N     124           -
LGA    -       -      L     125           -
LGA    -       -      E     126           -
LGA    -       -      F     127           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  125    5.0     16    2.63    12.50      9.583     0.586

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.245629 * X  +   0.516662 * Y  +  -0.820199 * Z  +  -8.752001
  Y_new =   0.816865 * X  +   0.345240 * Y  +   0.462105 * Z  +  25.128565
  Z_new =   0.521918 * X  +  -0.783498 * Y  +  -0.337242 * Z  +  50.282547 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.977258    1.164334  [ DEG:  -113.2886     66.7114 ]
  Theta =  -0.549098   -2.592495  [ DEG:   -31.4610   -148.5390 ]
  Phi   =   1.278700   -1.862892  [ DEG:    73.2641   -106.7359 ]
 
# 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: T0383TS009_1_3                                
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_1_3.T0383.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  125   5.0   16   2.63   12.50   9.583
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_1_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    910  N   GLU   112      14.498  26.970   7.576  1.00  0.00              
ATOM    911  CA  GLU   112      13.937  28.316   7.614  1.00  0.00              
ATOM    912  C   GLU   112      14.496  29.114   8.788  1.00  0.00              
ATOM    913  O   GLU   112      14.054  30.229   9.059  1.00  0.00              
ATOM    914  CB  GLU   112      14.215  29.049   6.300  1.00  0.00              
ATOM    915  CG  GLU   112      13.007  29.770   5.725  1.00  0.00              
ATOM    916  CD  GLU   112      13.104  29.965   4.225  1.00  0.00              
ATOM    917  OE1 GLU   112      12.246  29.422   3.498  1.00  0.00              
ATOM    918  OE2 GLU   112      14.039  30.662   3.775  1.00  0.00              
ATOM    919  N   VAL   113      15.470  28.532   9.482  1.00  0.00              
ATOM    920  CA  VAL   113      16.105  29.202  10.652  1.00  0.00              
ATOM    921  C   VAL   113      15.822  30.701  10.650  1.00  0.00              
ATOM    922  O   VAL   113      16.722  31.512  10.427  1.00  0.00              
ATOM    923  CB  VAL   113      15.614  28.599  11.981  1.00  0.00              
ATOM    924  CG1 VAL   113      16.649  27.638  12.545  1.00  0.00              
ATOM    925  CG2 VAL   113      14.276  27.901  11.788  1.00  0.00              
ATOM    926  N   THR   114      14.568  31.062  10.901  1.00  0.00              
ATOM    927  CA  THR   114      14.157  32.495  10.929  1.00  0.00              
ATOM    928  C   THR   114      15.037  33.340  10.014  1.00  0.00              
ATOM    929  O   THR   114      14.538  34.137   9.219  1.00  0.00              
ATOM    930  CB  THR   114      12.684  32.668  10.512  1.00  0.00              
ATOM    931  OG1 THR   114      12.325  31.641   9.578  1.00  0.00              
ATOM    932  CG2 THR   114      11.773  32.583  11.727  1.00  0.00              
ATOM    933  N   GLU   115      16.348  33.159  10.130  1.00  0.00              
ATOM    934  CA  GLU   115      17.299  33.904   9.314  1.00  0.00              
ATOM    935  C   GLU   115      16.945  33.815   7.834  1.00  0.00              
ATOM    936  O   GLU   115      17.487  32.984   7.105  1.00  0.00              
ATOM    937  CB  GLU   115      17.353  35.368   9.756  1.00  0.00              
ATOM    938  CG  GLU   115      18.639  35.756  10.468  1.00  0.00              
ATOM    939  CD  GLU   115      18.594  37.165  11.026  1.00  0.00              
ATOM    940  OE1 GLU   115      17.903  37.378  12.044  1.00  0.00              
ATOM    941  OE2 GLU   115      19.248  38.054  10.445  1.00  0.00              
ATOM    942  N   ILE   116      16.032  34.675   7.396  1.00  0.00              
ATOM    943  CA  ILE   116      15.593  34.697   5.972  1.00  0.00              
ATOM    944  C   ILE   116      15.716  33.315   5.337  1.00  0.00              
ATOM    945  O   ILE   116      15.927  33.192   4.130  1.00  0.00              
ATOM    946  CB  ILE   116      14.140  35.185   5.835  1.00  0.00              
ATOM    947  CG2 ILE   116      14.106  36.678   5.541  1.00  0.00              
ATOM    948  CG1 ILE   116      13.348  34.867   7.105  1.00  0.00              
ATOM    949  CD1 ILE   116      12.488  36.013   7.593  1.00  0.00              
ATOM    950  N   ALA   117      15.583  32.278   6.158  1.00  0.00              
ATOM    951  CA  ALA   117      15.679  30.904   5.678  1.00  0.00              
ATOM    952  C   ALA   117      17.015  30.653   4.988  1.00  0.00              
ATOM    953  O   ALA   117      17.145  29.732   4.181  1.00  0.00              
ATOM    954  CB  ALA   117      15.492  29.927   6.829  1.00  0.00              
ATOM    955  N   LEU   118      18.007  31.478   5.310  1.00  0.00              
ATOM    956  CA  LEU   118      19.334  31.347   4.721  1.00  0.00              
ATOM    957  C   LEU   118      19.392  30.175   3.745  1.00  0.00              
ATOM    958  O   LEU   118      18.769  30.208   2.684  1.00  0.00              
ATOM    959  CB  LEU   118      19.736  32.642   4.013  1.00  0.00              
ATOM    960  CG  LEU   118      20.693  33.562   4.774  1.00  0.00              
ATOM    961  CD1 LEU   118      21.269  34.623   3.851  1.00  0.00              
ATOM    962  CD2 LEU   118      21.803  32.757   5.433  1.00  0.00              
ATOM    963  N   ASP   119      20.143  29.144   4.112  1.00  0.00              
ATOM    964  CA  ASP   119      20.284  27.961   3.271  1.00  0.00              
ATOM    965  C   ASP   119      19.098  27.017   3.443  1.00  0.00              
ATOM    966  O   ASP   119      18.856  26.149   2.605  1.00  0.00              
ATOM    967  CB  ASP   119      20.427  28.363   1.801  1.00  0.00              
ATOM    968  CG  ASP   119      21.599  27.682   1.123  1.00  0.00              
ATOM    969  OD1 ASP   119      21.592  27.589  -0.124  1.00  0.00              
ATOM    970  OD2 ASP   119      22.524  27.242   1.835  1.00  0.00              
ATOM    971  N   LEU   120      18.362  27.194   4.535  1.00  0.00              
ATOM    972  CA  LEU   120      17.200  26.360   4.819  1.00  0.00              
ATOM    973  C   LEU   120      16.652  25.724   3.546  1.00  0.00              
ATOM    974  O   LEU   120      16.243  24.563   3.541  1.00  0.00              
ATOM    975  CB  LEU   120      17.556  25.275   5.838  1.00  0.00              
ATOM    976  CG  LEU   120      16.515  24.996   6.924  1.00  0.00              
ATOM    977  CD1 LEU   120      16.667  23.582   7.463  1.00  0.00              
ATOM    978  CD2 LEU   120      15.109  25.224   6.391  1.00  0.00              
ATOM    979  N   PRO   121      16.641  26.487   2.443  1.00  0.00              
ATOM    980  CA  PRO   121      16.143  26.003   1.153  1.00  0.00              
ATOM    981  C   PRO   121      17.073  26.385   0.007  1.00  0.00              
ATOM    982  O   PRO   121      17.046  25.770  -1.060  1.00  0.00              
ATOM    983  CB  PRO   121      16.131  24.484   1.336  1.00  0.00              
ATOM    984  CG  PRO   121      16.946  24.250   2.563  1.00  0.00              
ATOM    985  CD  PRO   121      17.114  27.881   2.376  1.00  0.00              
ATOM    986  N   GLY   122      17.896  27.404   0.234  1.00  0.00              
ATOM    987  CA  GLY   122      18.822  27.848  -0.792  1.00  0.00              
ATOM    988  C   GLY   122      19.117  26.768  -1.813  1.00  0.00              
ATOM    989  O   GLY   122      19.064  27.010  -3.020  1.00  0.00              
ATOM    990  N   ILE   123      19.432  25.570  -1.333  1.00  0.00              
ATOM    991  CA  ILE   123      19.745  24.422  -2.233  1.00  0.00              
ATOM    992  C   ILE   123      18.742  24.331  -3.378  1.00  0.00              
ATOM    993  O   ILE   123      18.825  23.434  -4.217  1.00  0.00              
ATOM    994  CB  ILE   123      21.166  24.532  -2.815  1.00  0.00              
ATOM    995  CG2 ILE   123      22.180  23.918  -1.861  1.00  0.00              
ATOM    996  CG1 ILE   123      21.513  25.994  -3.103  1.00  0.00              
ATOM    997  CD1 ILE   123      22.960  26.342  -2.835  1.00  0.00              
ATOM    998  N   ASN   124      17.797  25.265  -3.407  1.00  0.00              
ATOM    999  CA  ASN   124      16.779  25.292  -4.450  1.00  0.00              
ATOM   1000  C   ASN   124      16.972  24.148  -5.440  1.00  0.00              
ATOM   1001  O   ASN   124      17.024  22.981  -5.052  1.00  0.00              
ATOM   1002  CB  ASN   124      15.379  25.222  -3.833  1.00  0.00              
ATOM   1003  CG  ASN   124      14.387  26.125  -4.539  1.00  0.00              
ATOM   1004  OD1 ASN   124      13.181  26.037  -4.309  1.00  0.00              
ATOM   1005  ND2 ASN   124      14.892  26.997  -5.403  1.00  0.00              
ATOM   1006  N   LEU   125      17.079  24.492  -6.720  1.00  0.00              
ATOM   1007  CA  LEU   125      17.267  23.495  -7.767  1.00  0.00              
ATOM   1008  C   LEU   125      18.726  23.423  -8.204  1.00  0.00              
ATOM   1009  O   LEU   125      19.246  22.344  -8.488  1.00  0.00              
ATOM   1010  CB  LEU   125      16.791  22.121  -7.291  1.00  0.00              
ATOM   1011  CG  LEU   125      16.037  21.272  -8.317  1.00  0.00              
ATOM   1012  CD1 LEU   125      16.201  19.791  -8.013  1.00  0.00              
ATOM   1013  CD2 LEU   125      16.507  21.591  -9.728  1.00  0.00              
ATOM   1014  N   GLU   126      19.382  24.578  -8.254  1.00  0.00              
ATOM   1015  CA  GLU   126      20.782  24.647  -8.655  1.00  0.00              
ATOM   1016  C   GLU   126      21.603  25.455  -7.656  1.00  0.00              
ATOM   1017  O   GLU   126      21.611  25.160  -6.461  1.00  0.00              
ATOM   1018  CB  GLU   126      21.368  23.242  -8.802  1.00  0.00              
ATOM   1019  CG  GLU   126      22.408  23.115  -9.903  1.00  0.00              
ATOM   1020  CD  GLU   126      22.525  21.698 -10.433  1.00  0.00              
ATOM   1021  OE1 GLU   126      22.156  21.471 -11.604  1.00  0.00              
ATOM   1022  OE2 GLU   126      22.986  20.817  -9.677  1.00  0.00              
ATOM   1023  N   PHE   127      22.292  26.478  -8.153  1.00  0.00              
ATOM   1024  CA  PHE   127      23.117  27.330  -7.306  1.00  0.00              
ATOM   1025  C   PHE   127      22.321  27.864  -6.120  1.00  0.00              
ATOM   1026  O   PHE   127      22.946  28.541  -5.276  1.00  0.00              
ATOM   1027  CB  PHE   127      24.347  26.566  -6.812  1.00  0.00              
ATOM   1028  CG  PHE   127      25.642  27.062  -7.392  1.00  0.00              
ATOM   1029  CD1 PHE   127      25.647  28.035  -8.376  1.00  0.00              
ATOM   1030  CD2 PHE   127      26.852  26.556  -6.953  1.00  0.00              
ATOM   1031  CE1 PHE   127      26.838  28.492  -8.909  1.00  0.00              
ATOM   1032  CE2 PHE   127      28.043  27.012  -7.486  1.00  0.00              
ATOM   1033  CZ  PHE   127      28.039  27.976  -8.460  1.00  0.00              
ATOM   1034  OXT PHE   127      21.105  27.585  -6.081  1.00  0.00              
TER
END
