
#######################################################
#                                                     #
#                        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   18 (  144),  selected   18 , name T0301TS193_3_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_3_2-D1.T0301_D1.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    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    R     378      G      60          6.279
LGA    S     379      M      61          0.567
LGA    A     380      G      62          1.018
LGA    R     381      G      63          2.279
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    I     382      T      68          1.416
LGA    L     383      S      69          1.534
LGA    M     384      K      70          1.505
LGA    E     385      C      71          0.852
LGA    G     386      V      72          1.272
LGA    W     387      I      73          4.243
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      T     109           -
LGA    V     388      G     110          3.588
LGA    R     389      A     111          1.995
LGA    V     390      G     112          1.673
LGA    P     391      A     113          0.218
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    G     392      V     156          3.150
LGA    D     393      Q     157          2.672
LGA    A     394      E     158          1.774
LGA    F     395      T     159          2.124
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    -       -      A     172           -
LGA    -       -      E     173           -
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  200    5.0     18    2.55     0.00      6.865     0.678

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.789821 * X  +   0.239507 * Y  +   0.564641 * Z  + 120.243126
  Y_new =  -0.597915 * X  +  -0.505818 * Y  +  -0.621809 * Z  +  39.949623
  Z_new =   0.136678 * X  +  -0.828725 * Y  +   0.542710 * Z  +  -2.693375 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.991003    2.150590  [ DEG:   -56.7803    123.2197 ]
  Theta =  -0.137107   -3.004485  [ DEG:    -7.8557   -172.1443 ]
  Phi   =  -2.493610    0.647983  [ DEG:  -142.8733     37.1267 ]
 
# 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: T0301TS193_3_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_3_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  200   5.0   18   2.55    0.00   6.865
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      78.144  39.182  16.845  1.00  0.00
ATOM   2790  CA  ARG   378      77.209  38.116  16.504  1.00  0.00
ATOM   2791  C   ARG   378      77.158  37.890  14.999  1.00  0.00
ATOM   2792  O   ARG   378      77.160  36.750  14.533  1.00  0.00
ATOM   2793  CB  ARG   378      75.798  38.469  16.979  1.00  0.00
ATOM   2794  CG  ARG   378      75.623  38.425  18.488  1.00  0.00
ATOM   2795  CD  ARG   378      74.223  38.855  18.893  1.00  0.00
ATOM   2796  NE  ARG   378      74.045  38.845  20.344  1.00  0.00
ATOM   2797  CZ  ARG   378      72.940  39.247  20.965  1.00  0.00
ATOM   2798  NH1 ARG   378      72.869  39.202  22.288  1.00  0.00
ATOM   2799  NH2 ARG   378      71.910  39.694  20.260  1.00  0.00
ATOM   2800  N   SER   379      77.113  38.981  14.241  1.00  0.00
ATOM   2801  CA  SER   379      77.071  38.901  12.786  1.00  0.00
ATOM   2802  C   SER   379      78.394  38.396  12.223  1.00  0.00
ATOM   2803  O   SER   379      78.421  37.689  11.217  1.00  0.00
ATOM   2804  CB  SER   379      76.793  40.279  12.182  1.00  0.00
ATOM   2805  OG  SER   379      77.867  41.170  12.430  1.00  0.00
ATOM   2806  N   ALA   380      79.489  38.764  12.879  1.00  0.00
ATOM   2807  CA  ALA   380      80.818  38.358  12.439  1.00  0.00
ATOM   2808  C   ALA   380      80.988  36.846  12.524  1.00  0.00
ATOM   2809  O   ALA   380      81.536  36.222  11.615  1.00  0.00
ATOM   2810  CB  ALA   380      81.884  39.004  13.310  1.00  0.00
ATOM   2811  N   ARG   381      82.753  36.461  13.492  1.00  0.00
ATOM   2812  CA  ARG   381      84.034  36.451  12.797  1.00  0.00
ATOM   2813  C   ARG   381      84.357  35.064  12.257  1.00  0.00
ATOM   2814  O   ARG   381      85.014  34.927  11.224  1.00  0.00
ATOM   2815  CB  ARG   381      85.161  36.866  13.745  1.00  0.00
ATOM   2816  CG  ARG   381      85.141  38.336  14.128  1.00  0.00
ATOM   2817  CD  ARG   381      86.233  38.660  15.135  1.00  0.00
ATOM   2818  NE  ARG   381      86.212  40.065  15.531  1.00  0.00
ATOM   2819  CZ  ARG   381      86.987  40.586  16.477  1.00  0.00
ATOM   2820  NH1 ARG   381      86.899  41.876  16.771  1.00  0.00
ATOM   2821  NH2 ARG   381      87.848  39.815  17.128  1.00  0.00
ATOM   2822  N   ILE   382      83.892  34.038  12.960  1.00  0.00
ATOM   2823  CA  ILE   382      84.071  32.661  12.515  1.00  0.00
ATOM   2824  C   ILE   382      83.275  32.382  11.247  1.00  0.00
ATOM   2825  O   ILE   382      83.745  31.685  10.348  1.00  0.00
ATOM   2826  CB  ILE   382      83.604  31.657  13.585  1.00  0.00
ATOM   2827  CG1 ILE   382      84.521  31.717  14.809  1.00  0.00
ATOM   2828  CG2 ILE   382      83.629  30.240  13.033  1.00  0.00
ATOM   2829  CD1 ILE   382      83.989  30.960  16.007  1.00  0.00
ATOM   2830  N   LEU   383      82.068  32.933  11.179  1.00  0.00
ATOM   2831  CA  LEU   383      81.213  32.766  10.010  1.00  0.00
ATOM   2832  C   LEU   383      81.732  33.576   8.828  1.00  0.00
ATOM   2833  O   LEU   383      81.702  33.115   7.687  1.00  0.00
ATOM   2834  CB  LEU   383      79.788  33.233  10.316  1.00  0.00
ATOM   2835  CG  LEU   383      79.070  32.513  11.459  1.00  0.00
ATOM   2836  CD1 LEU   383      77.711  33.143  11.721  1.00  0.00
ATOM   2837  CD2 LEU   383      78.857  31.045  11.120  1.00  0.00
ATOM   2838  N   MET   384      80.722  31.126   8.065  1.00  0.00
ATOM   2839  CA  MET   384      79.926  31.159   6.843  1.00  0.00
ATOM   2840  C   MET   384      78.442  31.000   7.149  1.00  0.00
ATOM   2841  O   MET   384      77.993  29.927   7.554  1.00  0.00
ATOM   2842  CB  MET   384      80.341  30.026   5.902  1.00  0.00
ATOM   2843  CG  MET   384      79.557  29.982   4.601  1.00  0.00
ATOM   2844  SD  MET   384      79.770  31.472   3.609  1.00  0.00
ATOM   2845  CE  MET   384      81.415  31.209   2.952  1.00  0.00
ATOM   2846  N   GLU   385      77.685  32.073   6.950  1.00  0.00
ATOM   2847  CA  GLU   385      76.249  32.054   7.204  1.00  0.00
ATOM   2848  C   GLU   385      75.534  31.100   6.257  1.00  0.00
ATOM   2849  O   GLU   385      75.828  31.059   5.062  1.00  0.00
ATOM   2850  CB  GLU   385      75.652  33.450   7.011  1.00  0.00
ATOM   2851  CG  GLU   385      74.165  33.537   7.314  1.00  0.00
ATOM   2852  CD  GLU   385      73.621  34.943   7.163  1.00  0.00
ATOM   2853  OE1 GLU   385      74.407  35.851   6.819  1.00  0.00
ATOM   2854  OE2 GLU   385      72.408  35.138   7.388  1.00  0.00
ATOM   2855  N   GLY   386      74.594  30.330   6.798  1.00  0.00
ATOM   2856  CA  GLY   386      73.816  29.394   5.996  1.00  0.00
ATOM   2857  C   GLY   386      72.690  28.773   6.813  1.00  0.00
ATOM   2858  O   GLY   386      72.799  28.628   8.031  1.00  0.00
ATOM   2859  N   TRP   387      73.972  26.781   7.506  1.00  0.00
ATOM   2860  CA  TRP   387      72.819  25.892   7.579  1.00  0.00
ATOM   2861  C   TRP   387      73.088  24.716   8.509  1.00  0.00
ATOM   2862  O   TRP   387      73.978  23.905   8.257  1.00  0.00
ATOM   2863  CB  TRP   387      72.483  25.335   6.194  1.00  0.00
ATOM   2864  CG  TRP   387      71.297  24.420   6.187  1.00  0.00
ATOM   2865  CD1 TRP   387      70.187  24.511   6.975  1.00  0.00
ATOM   2866  CD2 TRP   387      71.104  23.273   5.350  1.00  0.00
ATOM   2867  NE1 TRP   387      69.312  23.492   6.683  1.00  0.00
ATOM   2868  CE2 TRP   387      69.853  22.717   5.687  1.00  0.00
ATOM   2869  CE3 TRP   387      71.865  22.661   4.350  1.00  0.00
ATOM   2870  CZ2 TRP   387      69.347  21.581   5.059  1.00  0.00
ATOM   2871  CZ3 TRP   387      71.359  21.533   3.730  1.00  0.00
ATOM   2872  CH2 TRP   387      70.113  21.003   4.084  1.00  0.00
ATOM   2873  N   VAL   388      72.312  24.628   9.583  1.00  0.00
ATOM   2874  CA  VAL   388      72.479  23.562  10.564  1.00  0.00
ATOM   2875  C   VAL   388      71.362  22.531  10.452  1.00  0.00
ATOM   2876  O   VAL   388      70.182  22.881  10.426  1.00  0.00
ATOM   2877  CB  VAL   388      72.461  24.110  12.002  1.00  0.00
ATOM   2878  CG1 VAL   388      72.587  22.975  13.007  1.00  0.00
ATOM   2879  CG2 VAL   388      73.618  25.074  12.219  1.00  0.00
ATOM   2880  N   ARG   389      71.742  21.260  10.387  1.00  0.00
ATOM   2881  CA  ARG   389      70.772  20.173  10.320  1.00  0.00
ATOM   2882  C   ARG   389      71.206  18.993  11.179  1.00  0.00
ATOM   2883  O   ARG   389      72.212  18.343  10.895  1.00  0.00
ATOM   2884  CB  ARG   389      70.618  19.680   8.880  1.00  0.00
ATOM   2885  CG  ARG   389      71.900  19.138   8.270  1.00  0.00
ATOM   2886  CD  ARG   389      71.663  18.614   6.862  1.00  0.00
ATOM   2887  NE  ARG   389      72.873  18.039   6.281  1.00  0.00
ATOM   2888  CZ  ARG   389      73.814  18.744   5.661  1.00  0.00
ATOM   2889  NH1 ARG   389      74.882  18.134   5.164  1.00  0.00
ATOM   2890  NH2 ARG   389      73.684  20.058   5.539  1.00  0.00
ATOM   2891  N   VAL   390      72.611  17.906  13.067  1.00  0.00
ATOM   2892  CA  VAL   390      71.201  17.822  13.426  1.00  0.00
ATOM   2893  C   VAL   390      70.831  18.883  14.455  1.00  0.00
ATOM   2894  O   VAL   390      71.364  18.898  15.565  1.00  0.00
ATOM   2895  CB  VAL   390      70.853  16.449  14.030  1.00  0.00
ATOM   2896  CG1 VAL   390      69.402  16.420  14.486  1.00  0.00
ATOM   2897  CG2 VAL   390      71.056  15.348  13.000  1.00  0.00
ATOM   2898  N   PRO   391      69.914  19.769  14.080  1.00  0.00
ATOM   2899  CA  PRO   391      69.402  20.777  15.002  1.00  0.00
ATOM   2900  C   PRO   391      68.382  20.179  15.961  1.00  0.00
ATOM   2901  O   PRO   391      67.373  19.615  15.537  1.00  0.00
ATOM   2902  CB  PRO   391      68.762  21.823  14.087  1.00  0.00
ATOM   2903  CG  PRO   391      68.346  21.057  12.876  1.00  0.00
ATOM   2904  CD  PRO   391      69.360  19.960  12.708  1.00  0.00
ATOM   2905  N   GLY   392      68.649  20.306  17.256  1.00  0.00
ATOM   2906  CA  GLY   392      67.797  19.708  18.278  1.00  0.00
ATOM   2907  C   GLY   392      67.519  20.691  19.407  1.00  0.00
ATOM   2908  O   GLY   392      68.214  21.696  19.554  1.00  0.00
ATOM   2909  N   ASP   393      68.658  19.751  20.594  1.00  0.00
ATOM   2910  CA  ASP   393      68.029  20.149  21.848  1.00  0.00
ATOM   2911  C   ASP   393      69.067  20.628  22.856  1.00  0.00
ATOM   2912  O   ASP   393      70.116  20.006  23.024  1.00  0.00
ATOM   2913  CB  ASP   393      67.275  18.970  22.467  1.00  0.00
ATOM   2914  CG  ASP   393      65.997  18.639  21.720  1.00  0.00
ATOM   2915  OD1 ASP   393      65.596  19.438  20.847  1.00  0.00
ATOM   2916  OD2 ASP   393      65.398  17.582  22.007  1.00  0.00
ATOM   2917  N   ALA   394      68.766  21.736  23.524  1.00  0.00
ATOM   2918  CA  ALA   394      69.677  22.307  24.509  1.00  0.00
ATOM   2919  C   ALA   394      69.146  22.117  25.924  1.00  0.00
ATOM   2920  O   ALA   394      67.992  22.434  26.213  1.00  0.00
ATOM   2921  CB  ALA   394      69.855  23.798  24.266  1.00  0.00
ATOM   2922  N   PHE   395      69.997  21.600  26.805  1.00  0.00
ATOM   2923  CA  PHE   395      69.616  21.375  28.195  1.00  0.00
ATOM   2924  C   PHE   395      70.711  21.837  29.147  1.00  0.00
ATOM   2925  O   PHE   395      71.848  22.071  28.735  1.00  0.00
ATOM   2926  CB  PHE   395      69.364  19.887  28.447  1.00  0.00
ATOM   2927  CG  PHE   395      68.314  19.291  27.554  1.00  0.00
ATOM   2928  CD1 PHE   395      68.671  18.599  26.410  1.00  0.00
ATOM   2929  CD2 PHE   395      66.970  19.421  27.858  1.00  0.00
ATOM   2930  CE1 PHE   395      67.705  18.049  25.588  1.00  0.00
ATOM   2931  CE2 PHE   395      66.005  18.872  27.037  1.00  0.00
ATOM   2932  CZ  PHE   395      66.366  18.189  25.905  1.00  0.00
TER
END
