
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0333TS174_1u-D1
# Molecule2: number of CA atoms  206 ( 1581),  selected  206 , name T0333_D1.pdb
# PARAMETERS: T0333TS174_1u-D1.T0333_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      F       3           -
LGA    -       -      V       4           -
LGA    -       -      S       5           -
LGA    -       -      S       6           -
LGA    -       -      P       7           -
LGA    -       -      G       8           -
LGA    -       -      I       9           -
LGA    -       -      G      10           -
LGA    -       -      H      11           -
LGA    -       -      L      12           -
LGA    -       -      F      13           -
LGA    -       -      P      14           -
LGA    -       -      L      15           -
LGA    -       -      I      16           -
LGA    -       -      Q      17           -
LGA    -       -      L      18           -
LGA    -       -      A      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      F      22           -
LGA    -       -      R      23           -
LGA    -       -      T      24           -
LGA    -       -      A      25           -
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    -       -      D      28           -
LGA    -       -      V      29           -
LGA    -       -      L      30           -
LGA    -       -      I      31           -
LGA    -       -      A      32           -
LGA    -       -      V      33           -
LGA    -       -      A      34           -
LGA    -       -      E      35           -
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    -       -      D      38           -
LGA    -       -      R      39           -
LGA    -       -      A      40           -
LGA    -       -      A      41           -
LGA    -       -      A      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      L      45           -
LGA    -       -      E      46           -
LGA    -       -      V      47           -
LGA    -       -      V      48           -
LGA    -       -      D      49           -
LGA    -       -      V      50           -
LGA    -       -      A      51           -
LGA    -       -      P      52           -
LGA    -       -      D      53           -
LGA    -       -      Y      54           -
LGA    -       -      S      55           -
LGA    -       -      A      56           -
LGA    -       -      V      57           -
LGA    -       -      K      58           -
LGA    -       -      V      59           -
LGA    -       -      F      60           -
LGA    -       -      E      61           -
LGA    -       -      Q      62           -
LGA    -       -      V      63           -
LGA    -       -      A      64           -
LGA    -       -      K      65           -
LGA    -       -      D      66           -
LGA    -       -      N      67           -
LGA    -       -      P      68           -
LGA    -       -      R      69           -
LGA    -       -      F      70           -
LGA    -       -      A      71           -
LGA    -       -      E      72           -
LGA    -       -      T      73           -
LGA    -       -      V      74           -
LGA    -       -      A      75           -
LGA    -       -      T      76           -
LGA    -       -      R      77           -
LGA    -       -      P      78           -
LGA    -       -      A      79           -
LGA    -       -      I      80           -
LGA    -       -      D      81           -
LGA    -       -      L      82           -
LGA    -       -      E      83           -
LGA    -       -      E      84           -
LGA    -       -      W      85           -
LGA    -       -      G      86           -
LGA    -       -      V      87           -
LGA    -       -      Q      88           -
LGA    P     361      I      89          2.360
LGA    T     362      A      90          2.644
LGA    -       -      A      91           -
LGA    -       -      V      92           -
LGA    P     363      N      93          2.546
LGA    -       -      R      94           -
LGA    -       -      P      95           -
LGA    -       -      L      96           -
LGA    -       -      V      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      T     100           -
LGA    -       -      M     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      V     104           -
LGA    -       -      D     105           -
LGA    -       -      D     106           -
LGA    -       -      Y     107           -
LGA    -       -      R     108           -
LGA    -       -      P     109           -
LGA    -       -      D     110           -
LGA    -       -      L     111           -
LGA    -       -      V     112           -
LGA    -       -      V     113           -
LGA    -       -      Y     114           -
LGA    -       -      E     115           -
LGA    -       -      Q     116           -
LGA    -       -      G     117           -
LGA    A     364      A     118          1.675
LGA    E     365      T     119          2.190
LGA    T     366      V     120          1.610
LGA    V     367      G     121          1.656
LGA    R     368      L     122          0.970
LGA    R     369      L     123          0.585
LGA    I     370      A     124          0.863
LGA    V     371      A     125          0.948
LGA    E     372      D     126          1.183
LGA    R     373      R     127          1.123
LGA    I     374      A     128          0.510
LGA    S     375      G     129          1.331
LGA    -       -      V     130           -
LGA    -       -      P     131           -
LGA    -       -      A     132           -
LGA    -       -      V     133           -
LGA    -       -      Q     134           -
LGA    -       -      R     135           -
LGA    -       -      N     136           -
LGA    -       -      Q     137           -
LGA    -       -      S     138           -
LGA    -       -      A     139           -
LGA    -       -      W     140           -
LGA    -       -      R     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      G     144           -
LGA    -       -      M     145           -
LGA    -       -      H     146           -
LGA    -       -      R     147           -
LGA    -       -      S     148           -
LGA    -       -      I     149           -
LGA    -       -      A     150           -
LGA    -       -      S     151           -
LGA    -       -      F     152           -
LGA    -       -      L     153           -
LGA    -       -      T     154           -
LGA    -       -      D     155           -
LGA    -       -      L     156           -
LGA    -       -      M     157           -
LGA    -       -      D     158           -
LGA    -       -      K     159           -
LGA    -       -      H     160           -
LGA    -       -      Q     161           -
LGA    -       -      V     162           -
LGA    -       -      S     163           -
LGA    -       -      L     164           -
LGA    -       -      P     165           -
LGA    -       -      E     166           -
LGA    -       -      P     167           -
LGA    -       -      V     168           -
LGA    -       -      A     169           -
LGA    -       -      T     170           -
LGA    -       -      I     171           -
LGA    -       -      E     172           -
LGA    -       -      S     173           -
LGA    -       -      F     174           -
LGA    -       -      P     175           -
LGA    -       -      P     176           -
LGA    -       -      S     177           -
LGA    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      L     180           -
LGA    -       -      E     181           -
LGA    -       -      A     182           -
LGA    -       -      E     183           -
LGA    -       -      P     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      W     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     360           -
LGA    -       -      P     361           -
LGA    -       -      T     362           -
LGA    -       -      P     363           -
LGA    -       -      A     364           -
LGA    -       -      E     365           -
LGA    -       -      T     366           -
LGA    -       -      V     367           -
LGA    -       -      R     368           -
LGA    -       -      R     369           -
LGA    -       -      I     370           -
LGA    -       -      V     371           -
LGA    -       -      E     372           -
LGA    -       -      R     373           -
LGA    -       -      I     374           -
LGA    -       -      S     375           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  206    5.0     15    1.62    13.33      6.917     0.870

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.233902 * X  +  -0.926842 * Y  +  -0.293691 * Z  + 113.954681
  Y_new =  -0.683917 * X  +  -0.057853 * Y  +   0.727263 * Z  +  25.582972
  Z_new =  -0.691048 * X  +   0.370968 * Y  +  -0.620350 * Z  +  56.173756 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.602647   -0.538946  [ DEG:   149.1207    -30.8793 ]
  Theta =   0.762938    2.378654  [ DEG:    43.7131    136.2868 ]
  Phi   =  -1.900330    1.241263  [ DEG:  -108.8809     71.1191 ]
 
# 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: T0333TS174_1u-D1                              
REMARK     2: T0333_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS174_1u-D1.T0333_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  206   5.0   15   1.62   13.33   6.917
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS174_1u-D1
PFRMAT TS
TARGET T0333
MODEL 1  UNREFINED
PARENT 1iir_A 
ATOM   2717  N   PRO   361      28.755  35.114  14.591  1.00  1.00
ATOM   2718  CA  PRO   361      30.204  35.014  14.717  1.00  1.00
ATOM   2719  C   PRO   361      30.722  35.218  16.134  1.00  1.00
ATOM   2720  O   PRO   361      31.909  35.469  16.331  1.00  1.00
ATOM   2721  CB  PRO   361      30.861  36.031  13.771  1.00  1.00
ATOM   2722  CG  PRO   361      29.760  37.102  13.794  1.00  1.00
ATOM   2723  CD  PRO   361      28.493  36.413  13.842  1.00  1.00
ATOM   2724  N   THR   362      29.839  35.088  17.117  1.00  1.00
ATOM   2725  CA  THR   362      30.236  35.294  18.501  1.00  1.00
ATOM   2726  C   THR   362      31.406  34.466  19.000  1.00  1.00
ATOM   2727  O   THR   362      32.247  34.967  19.751  1.00  1.00
ATOM   2728  CB  THR   362      29.293  35.080  19.624  1.00  1.00
ATOM   2729  OG1 THR   362      29.769  35.435  20.926  1.00  1.00
ATOM   2730  CG2 THR   362      28.895  33.626  19.566  1.00  1.00
ATOM   2731  N   PRO   363      31.459  33.197  18.613  1.00  1.00
ATOM   2732  CA  PRO   363      32.550  32.335  19.053  1.00  1.00
ATOM   2733  C   PRO   363      33.871  32.829  18.463  1.00  1.00
ATOM   2734  O   PRO   363      34.910  32.797  19.131  1.00  1.00
ATOM   2735  CB  PRO   363      32.281  30.884  18.640  1.00  1.00
ATOM   2736  CG  PRO   363      31.477  31.189  17.367  1.00  1.00
ATOM   2737  CD  PRO   363      30.687  32.366  17.630  1.00  1.00
ATOM   2738  N   ALA   364      33.827  33.297  17.216  1.00  1.00
ATOM   2739  CA  ALA   364      35.024  33.809  16.554  1.00  1.00
ATOM   2740  C   ALA   364      35.453  35.109  17.233  1.00  1.00
ATOM   2741  O   ALA   364      36.647  35.366  17.415  1.00  1.00
ATOM   2742  CB  ALA   364      34.741  34.048  15.068  1.00  1.00
ATOM   2743  N   GLU   365      34.475  35.932  17.600  1.00  1.00
ATOM   2744  CA  GLU   365      34.754  37.190  18.284  1.00  1.00
ATOM   2745  C   GLU   365      35.470  36.886  19.600  1.00  1.00
ATOM   2746  O   GLU   365      36.465  37.528  19.946  1.00  1.00
ATOM   2747  CB  GLU   365      33.443  37.957  18.580  1.00  1.00
ATOM   2748  CG  GLU   365      32.739  38.451  17.340  1.00  1.00
ATOM   2749  CD  GLU   365      31.462  39.204  17.649  1.00  1.00
ATOM   2750  OE1 GLU   365      31.433  40.194  18.314  1.00  1.00
ATOM   2751  OE2 GLU   365      30.416  38.636  17.117  1.00  1.00
ATOM   2752  N   THR   366      34.962  35.901  20.334  1.00  1.00
ATOM   2753  CA  THR   366      35.565  35.531  21.610  1.00  1.00
ATOM   2754  C   THR   366      36.956  34.933  21.409  1.00  1.00
ATOM   2755  O   THR   366      37.879  35.224  22.171  1.00  1.00
ATOM   2756  CB  THR   366      34.667  34.537  22.346  1.00  1.00
ATOM   2757  OG1 THR   366      33.479  35.274  22.641  1.00  1.00
ATOM   2758  CG2 THR   366      35.319  34.044  23.610  1.00  1.00
ATOM   2759  N   VAL   367      37.101  34.096  20.388  1.00  1.00
ATOM   2760  CA  VAL   367      38.383  33.459  20.107  1.00  1.00
ATOM   2761  C   VAL   367      39.468  34.508  19.888  1.00  1.00
ATOM   2762  O   VAL   367      40.587  34.364  20.379  1.00  1.00
ATOM   2763  CB  VAL   367      38.266  32.560  18.883  1.00  1.00
ATOM   2764  CG1 VAL   367      37.239  31.461  19.082  1.00  1.00
ATOM   2765  CG2 VAL   367      39.629  31.984  18.571  1.00  1.00
ATOM   2766  N   ARG   368      39.134  35.565  19.152  1.00  1.00
ATOM   2767  CA  ARG   368      40.094  36.631  18.882  1.00  1.00
ATOM   2768  C   ARG   368      40.455  37.395  20.151  1.00  1.00
ATOM   2769  O   ARG   368      41.627  37.691  20.396  1.00  1.00
ATOM   2770  CB  ARG   368      39.538  37.600  17.828  1.00  1.00
ATOM   2771  CG  ARG   368      40.403  38.839  17.597  1.00  1.00
ATOM   2772  CD  ARG   368      41.857  38.467  17.336  1.00  1.00
ATOM   2773  NE  ARG   368      42.011  37.672  16.123  1.00  1.00
ATOM   2774  CZ  ARG   368      43.137  37.060  15.767  1.00  1.00
ATOM   2775  NH1 ARG   368      44.215  37.149  16.534  1.00  1.00
ATOM   2776  NH2 ARG   368      43.185  36.363  14.640  1.00  1.00
ATOM   2777  N   ARG   369      39.451  37.717  20.959  1.00  1.00
ATOM   2778  CA  ARG   369      39.694  38.438  22.201  1.00  1.00
ATOM   2779  C   ARG   369      40.562  37.602  23.135  1.00  1.00
ATOM   2780  O   ARG   369      41.397  38.136  23.867  1.00  1.00
ATOM   2781  CB  ARG   369      38.372  38.779  22.894  1.00  1.00
ATOM   2782  CG  ARG   369      37.704  37.609  23.224  1.00  1.00
ATOM   2783  CD  ARG   369      36.382  37.916  23.927  1.00  1.00
ATOM   2784  NE  ARG   369      36.498  38.505  25.099  1.00  1.00
ATOM   2785  CZ  ARG   369      36.689  37.846  26.265  1.00  1.00
ATOM   2786  NH1 ARG   369      36.792  38.538  27.379  1.00  1.00
ATOM   2787  NH2 ARG   369      36.761  36.387  26.043  1.00  1.00
ATOM   2788  N   ILE   370      40.361  36.288  23.104  1.00  1.00
ATOM   2789  CA  ILE   370      41.120  35.375  23.948  1.00  1.00
ATOM   2790  C   ILE   370      42.597  35.352  23.553  1.00  1.00
ATOM   2791  O   ILE   370      43.480  35.542  24.395  1.00  1.00
ATOM   2792  CB  ILE   370      40.538  33.963  23.844  1.00  1.00
ATOM   2793  CG1 ILE   370      39.134  33.901  24.425  1.00  1.00
ATOM   2794  CG2 ILE   370      41.439  33.039  24.638  1.00  1.00
ATOM   2795  CD1 ILE   370      38.401  32.582  24.204  1.00  1.00
ATOM   2796  N   VAL   371      42.864  35.119  22.271  1.00  1.00
ATOM   2797  CA  VAL   371      44.242  35.071  21.795  1.00  1.00
ATOM   2798  C   VAL   371      44.971  36.390  22.015  1.00  1.00
ATOM   2799  O   VAL   371      46.152  36.397  22.362  1.00  1.00
ATOM   2800  CB  VAL   371      44.291  34.690  20.315  1.00  1.00
ATOM   2801  CG1 VAL   371      43.602  35.722  19.443  1.00  1.00
ATOM   2802  CG2 VAL   371      43.675  33.321  20.139  1.00  1.00
ATOM   2803  N   GLU   372      44.280  37.507  21.815  1.00  1.00
ATOM   2804  CA  GLU   372      44.915  38.802  22.031  1.00  1.00
ATOM   2805  C   GLU   372      45.273  38.947  23.507  1.00  1.00
ATOM   2806  O   GLU   372      46.331  39.473  23.854  1.00  1.00
ATOM   2807  CB  GLU   372      43.988  39.948  21.619  1.00  1.00
ATOM   2808  CG  GLU   372      42.707  40.005  22.411  1.00  1.00
ATOM   2809  CD  GLU   372      41.802  41.139  21.985  1.00  1.00
ATOM   2810  OE1 GLU   372      42.129  42.289  22.031  1.00  1.00
ATOM   2811  OE2 GLU   372      40.646  40.705  21.568  1.00  1.00
ATOM   2812  N   ARG   373      44.384  38.479  24.379  1.00  1.00
ATOM   2813  CA  ARG   373      44.623  38.557  25.816  1.00  1.00
ATOM   2814  C   ARG   373      45.814  37.689  26.208  1.00  1.00
ATOM   2815  O   ARG   373      46.658  38.099  27.005  1.00  1.00
ATOM   2816  CB  ARG   373      43.380  38.112  26.578  1.00  1.00
ATOM   2817  CG  ARG   373      42.353  39.033  26.384  1.00  1.00
ATOM   2818  CD  ARG   373      41.098  38.627  27.153  1.00  1.00
ATOM   2819  NE  ARG   373      40.538  37.501  26.748  1.00  1.00
ATOM   2820  CZ  ARG   373      40.624  36.327  27.416  1.00  1.00
ATOM   2821  NH1 ARG   373      40.016  35.264  26.924  1.00  1.00
ATOM   2822  NH2 ARG   373      41.422  36.477  28.656  1.00  1.00
ATOM   2823  N   ILE   374      45.877  36.487  25.645  1.00  1.00
ATOM   2824  CA  ILE   374      46.963  35.562  25.945  1.00  1.00
ATOM   2825  C   ILE   374      48.292  36.115  25.438  1.00  1.00
ATOM   2826  O   ILE   374      49.345  35.859  26.021  1.00  1.00
ATOM   2827  CB  ILE   374      46.704  34.182  25.308  1.00  1.00
ATOM   2828  CG1 ILE   374      46.654  34.288  23.793  1.00  1.00
ATOM   2829  CG2 ILE   374      45.398  33.590  25.796  1.00  1.00
ATOM   2830  CD1 ILE   374      47.946  33.914  23.072  1.00  1.00
ATOM   2831  N   SER   375      48.233  36.881  24.356  1.00  1.00
ATOM   2832  CA  SER   375      49.434  37.475  23.782  1.00  1.00
ATOM   2833  C   SER   375      49.964  38.603  24.661  1.00  1.00
ATOM   2834  O   SER   375      51.104  39.042  24.499  1.00  1.00
ATOM   2835  CB  SER   375      49.142  38.006  22.378  1.00  1.00
ATOM   2836  OG  SER   375      48.752  36.952  21.516  1.00  1.00
TER
END
