
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_1_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    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
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    R     378      D      99          2.479
LGA    S     379      W     100          2.029
LGA    A     380      S     101          2.769
LGA    R     381      G     102          2.163
LGA    I     382      N     103          2.637
LGA    L     383      C     104          4.027
LGA    M     384      G     105          2.172
LGA    E     385      N     106          3.318
LGA    G     386      L     107          1.307
LGA    W     387      S     108          3.060
LGA    -       -      T     109           -
LGA    -       -      G     110           -
LGA    V     388      A     111          2.754
LGA    R     389      G     112          2.059
LGA    -       -      A     113           -
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     390      V     149          3.749
LGA    P     391      P     150          3.457
LGA    G     392      V     151          3.493
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    D     393      Q     157          1.492
LGA    -       -      E     158           -
LGA    A     394      T     159          2.564
LGA    F     395      G     160          3.732
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    2.84    11.11      5.689     0.612

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.209451 * X  +  -0.950480 * Y  +   0.229602 * Z  +  58.547340
  Y_new =  -0.971792 * X  +   0.228372 * Y  +   0.058885 * Z  +  38.587574
  Z_new =  -0.108404 * X  +  -0.210792 * Y  +  -0.971502 * Z  +  10.857791 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.927929    0.213664  [ DEG:  -167.7580     12.2420 ]
  Theta =   0.108617    3.032975  [ DEG:     6.2233    173.7767 ]
  Phi   =  -1.783080    1.358513  [ DEG:  -102.1630     77.8370 ]
 
# 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_1_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_1_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   2.84   11.11   5.689
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      82.624  28.982  -4.194  1.00  0.00
ATOM   2790  CA  ARG   378      83.159  28.785  -2.851  1.00  0.00
ATOM   2791  C   ARG   378      82.083  28.990  -1.793  1.00  0.00
ATOM   2792  O   ARG   378      81.222  29.859  -1.929  1.00  0.00
ATOM   2793  CB  ARG   378      84.290  29.777  -2.574  1.00  0.00
ATOM   2794  CG  ARG   378      85.530  29.559  -3.428  1.00  0.00
ATOM   2795  CD  ARG   378      86.617  30.566  -3.089  1.00  0.00
ATOM   2796  NE  ARG   378      87.817  30.369  -3.899  1.00  0.00
ATOM   2797  CZ  ARG   378      88.891  31.149  -3.845  1.00  0.00
ATOM   2798  NH1 ARG   378      89.936  30.893  -4.620  1.00  0.00
ATOM   2799  NH2 ARG   378      88.918  32.184  -3.016  1.00  0.00
ATOM   2800  N   SER   379      82.136  28.184  -0.738  1.00  0.00
ATOM   2801  CA  SER   379      81.142  28.247   0.325  1.00  0.00
ATOM   2802  C   SER   379      81.708  27.726   1.640  1.00  0.00
ATOM   2803  O   SER   379      82.791  27.143   1.674  1.00  0.00
ATOM   2804  CB  SER   379      79.918  27.400  -0.032  1.00  0.00
ATOM   2805  OG  SER   379      78.869  27.603   0.897  1.00  0.00
ATOM   2806  N   ALA   380      83.241  25.769  -0.050  1.00  0.00
ATOM   2807  CA  ALA   380      82.336  24.721   0.404  1.00  0.00
ATOM   2808  C   ALA   380      83.085  23.647   1.182  1.00  0.00
ATOM   2809  O   ALA   380      84.232  23.324   0.870  1.00  0.00
ATOM   2810  CB  ALA   380      81.655  24.058  -0.783  1.00  0.00
ATOM   2811  N   ARG   381      82.430  23.093   2.197  1.00  0.00
ATOM   2812  CA  ARG   381      83.011  22.013   2.986  1.00  0.00
ATOM   2813  C   ARG   381      82.204  21.763   4.255  1.00  0.00
ATOM   2814  O   ARG   381      82.069  20.624   4.700  1.00  0.00
ATOM   2815  CB  ARG   381      84.444  22.360   3.396  1.00  0.00
ATOM   2816  CG  ARG   381      84.547  23.529   4.363  1.00  0.00
ATOM   2817  CD  ARG   381      85.997  23.855   4.681  1.00  0.00
ATOM   2818  NE  ARG   381      86.115  24.960   5.629  1.00  0.00
ATOM   2819  CZ  ARG   381      87.269  25.479   6.033  1.00  0.00
ATOM   2820  NH1 ARG   381      87.279  26.484   6.898  1.00  0.00
ATOM   2821  NH2 ARG   381      88.412  24.993   5.570  1.00  0.00
ATOM   2822  N   ILE   382      81.671  22.834   4.832  1.00  0.00
ATOM   2823  CA  ILE   382      80.899  22.735   6.065  1.00  0.00
ATOM   2824  C   ILE   382      79.725  21.779   5.905  1.00  0.00
ATOM   2825  O   ILE   382      78.956  21.563   6.842  1.00  0.00
ATOM   2826  CB  ILE   382      80.329  24.103   6.484  1.00  0.00
ATOM   2827  CG1 ILE   382      81.463  25.095   6.750  1.00  0.00
ATOM   2828  CG2 ILE   382      79.500  23.967   7.753  1.00  0.00
ATOM   2829  CD1 ILE   382      80.993  26.517   6.966  1.00  0.00
ATOM   2830  N   LEU   383      79.933  20.305   5.253  1.00  0.00
ATOM   2831  CA  LEU   383      79.799  19.060   5.999  1.00  0.00
ATOM   2832  C   LEU   383      80.707  19.050   7.223  1.00  0.00
ATOM   2833  O   LEU   383      80.368  18.471   8.254  1.00  0.00
ATOM   2834  CB  LEU   383      80.176  17.866   5.120  1.00  0.00
ATOM   2835  CG  LEU   383      79.225  17.549   3.964  1.00  0.00
ATOM   2836  CD1 LEU   383      79.801  16.453   3.080  1.00  0.00
ATOM   2837  CD2 LEU   383      77.879  17.075   4.490  1.00  0.00
ATOM   2838  N   MET   384      81.863  19.696   7.100  1.00  0.00
ATOM   2839  CA  MET   384      82.808  19.788   8.207  1.00  0.00
ATOM   2840  C   MET   384      82.252  20.645   9.337  1.00  0.00
ATOM   2841  O   MET   384      82.268  20.242  10.500  1.00  0.00
ATOM   2842  CB  MET   384      84.122  20.417   7.737  1.00  0.00
ATOM   2843  CG  MET   384      84.931  19.535   6.800  1.00  0.00
ATOM   2844  SD  MET   384      86.418  20.352   6.187  1.00  0.00
ATOM   2845  CE  MET   384      87.420  20.389   7.670  1.00  0.00
ATOM   2846  N   GLU   385      81.762  21.829   8.988  1.00  0.00
ATOM   2847  CA  GLU   385      81.174  22.734   9.969  1.00  0.00
ATOM   2848  C   GLU   385      79.938  22.119  10.614  1.00  0.00
ATOM   2849  O   GLU   385      79.674  22.330  11.798  1.00  0.00
ATOM   2850  CB  GLU   385      80.757  24.048   9.305  1.00  0.00
ATOM   2851  CG  GLU   385      80.187  25.076  10.267  1.00  0.00
ATOM   2852  CD  GLU   385      79.881  26.399   9.592  1.00  0.00
ATOM   2853  OE1 GLU   385      79.097  26.402   8.620  1.00  0.00
ATOM   2854  OE2 GLU   385      80.424  27.432  10.035  1.00  0.00
ATOM   2855  N   GLY   386      78.577  22.431   9.836  1.00  0.00
ATOM   2856  CA  GLY   386      77.299  22.803  10.434  1.00  0.00
ATOM   2857  C   GLY   386      76.590  21.587  11.015  1.00  0.00
ATOM   2858  O   GLY   386      76.667  20.488  10.464  1.00  0.00
ATOM   2859  N   TRP   387      75.899  21.789  12.132  1.00  0.00
ATOM   2860  CA  TRP   387      75.041  20.756  12.699  1.00  0.00
ATOM   2861  C   TRP   387      73.832  20.493  11.810  1.00  0.00
ATOM   2862  O   TRP   387      73.036  21.393  11.546  1.00  0.00
ATOM   2863  CB  TRP   387      74.531  21.181  14.077  1.00  0.00
ATOM   2864  CG  TRP   387      75.592  21.186  15.134  1.00  0.00
ATOM   2865  CD1 TRP   387      76.253  22.274  15.627  1.00  0.00
ATOM   2866  CD2 TRP   387      76.116  20.048  15.830  1.00  0.00
ATOM   2867  NE1 TRP   387      77.157  21.886  16.586  1.00  0.00
ATOM   2868  CE2 TRP   387      77.092  20.522  16.729  1.00  0.00
ATOM   2869  CE3 TRP   387      75.858  18.676  15.780  1.00  0.00
ATOM   2870  CZ2 TRP   387      77.807  19.673  17.571  1.00  0.00
ATOM   2871  CZ3 TRP   387      76.569  17.837  16.617  1.00  0.00
ATOM   2872  CH2 TRP   387      77.533  18.335  17.501  1.00  0.00
ATOM   2873  N   VAL   388      73.702  19.253  11.350  1.00  0.00
ATOM   2874  CA  VAL   388      72.665  18.898  10.387  1.00  0.00
ATOM   2875  C   VAL   388      71.486  18.222  11.072  1.00  0.00
ATOM   2876  O   VAL   388      70.330  18.469  10.728  1.00  0.00
ATOM   2877  CB  VAL   388      73.198  17.928   9.316  1.00  0.00
ATOM   2878  CG1 VAL   388      72.070  17.472   8.403  1.00  0.00
ATOM   2879  CG2 VAL   388      74.261  18.606   8.465  1.00  0.00
ATOM   2880  N   ARG   389      71.783  17.366  12.044  1.00  0.00
ATOM   2881  CA  ARG   389      70.747  16.647  12.775  1.00  0.00
ATOM   2882  C   ARG   389      71.235  16.233  14.158  1.00  0.00
ATOM   2883  O   ARG   389      72.438  16.107  14.391  1.00  0.00
ATOM   2884  CB  ARG   389      70.336  15.382  12.018  1.00  0.00
ATOM   2885  CG  ARG   389      71.471  14.394  11.800  1.00  0.00
ATOM   2886  CD  ARG   389      71.000  13.176  11.023  1.00  0.00
ATOM   2887  NE  ARG   389      70.080  12.350  11.804  1.00  0.00
ATOM   2888  CZ  ARG   389      69.414  11.309  11.316  1.00  0.00
ATOM   2889  NH1 ARG   389      68.599  10.616  12.100  1.00  0.00
ATOM   2890  NH2 ARG   389      69.563  10.962  10.044  1.00  0.00
ATOM   2891  N   VAL   390      70.741  17.268  15.307  1.00  0.00
ATOM   2892  CA  VAL   390      71.391  17.408  16.605  1.00  0.00
ATOM   2893  C   VAL   390      70.484  16.923  17.730  1.00  0.00
ATOM   2894  O   VAL   390      69.270  16.817  17.559  1.00  0.00
ATOM   2895  CB  VAL   390      71.752  18.876  16.900  1.00  0.00
ATOM   2896  CG1 VAL   390      72.726  19.405  15.858  1.00  0.00
ATOM   2897  CG2 VAL   390      70.504  19.746  16.878  1.00  0.00
ATOM   2898  N   PRO   391      71.082  16.630  18.879  1.00  0.00
ATOM   2899  CA  PRO   391      70.329  16.160  20.036  1.00  0.00
ATOM   2900  C   PRO   391      69.221  17.138  20.406  1.00  0.00
ATOM   2901  O   PRO   391      69.428  18.352  20.417  1.00  0.00
ATOM   2902  CB  PRO   391      71.379  16.060  21.145  1.00  0.00
ATOM   2903  CG  PRO   391      72.670  15.874  20.420  1.00  0.00
ATOM   2904  CD  PRO   391      72.577  16.717  19.179  1.00  0.00
ATOM   2905  N   GLY   392      68.043  16.603  20.709  1.00  0.00
ATOM   2906  CA  GLY   392      66.898  17.427  21.077  1.00  0.00
ATOM   2907  C   GLY   392      66.722  17.482  22.589  1.00  0.00
ATOM   2908  O   GLY   392      67.354  16.724  23.325  1.00  0.00
ATOM   2909  N   ASP   393      66.122  17.535  25.023  1.00  0.00
ATOM   2910  CA  ASP   393      66.427  18.929  24.728  1.00  0.00
ATOM   2911  C   ASP   393      67.705  19.373  25.430  1.00  0.00
ATOM   2912  O   ASP   393      68.162  20.502  25.254  1.00  0.00
ATOM   2913  CB  ASP   393      65.288  19.838  25.195  1.00  0.00
ATOM   2914  CG  ASP   393      65.126  19.839  26.702  1.00  0.00
ATOM   2915  OD1 ASP   393      65.962  19.220  27.391  1.00  0.00
ATOM   2916  OD2 ASP   393      64.160  20.462  27.195  1.00  0.00
ATOM   2917  N   ALA   394      68.276  18.477  26.228  1.00  0.00
ATOM   2918  CA  ALA   394      69.496  18.779  26.969  1.00  0.00
ATOM   2919  C   ALA   394      70.626  17.836  26.578  1.00  0.00
ATOM   2920  O   ALA   394      71.737  18.273  26.281  1.00  0.00
ATOM   2921  CB  ALA   394      69.257  18.636  28.465  1.00  0.00
ATOM   2922  N   PHE   395      70.335  16.539  26.581  1.00  0.00
ATOM   2923  CA  PHE   395      71.348  15.527  26.309  1.00  0.00
ATOM   2924  C   PHE   395      71.245  15.013  24.879  1.00  0.00
ATOM   2925  O   PHE   395      70.212  14.479  24.473  1.00  0.00
ATOM   2926  CB  PHE   395      71.181  14.335  27.254  1.00  0.00
ATOM   2927  CG  PHE   395      71.440  14.664  28.697  1.00  0.00
ATOM   2928  CD1 PHE   395      70.389  14.863  29.575  1.00  0.00
ATOM   2929  CD2 PHE   395      72.734  14.775  29.175  1.00  0.00
ATOM   2930  CE1 PHE   395      70.627  15.166  30.902  1.00  0.00
ATOM   2931  CE2 PHE   395      72.972  15.078  30.502  1.00  0.00
ATOM   2932  CZ  PHE   395      71.926  15.273  31.365  1.00  0.00
TER
END
