
#######################################################
#                                                     #
#                        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   24 (  179),  selected   24 , name T0347TS671_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS671_4-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    D     134      D     172          2.639
LGA    P     135      L     173          1.741
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    F     136      D     176          2.362
LGA    R     137      S     177          2.824
LGA    -       -      F     178           -
LGA    S     138      D     179          1.970
LGA    L     139      D     180          1.319
LGA    A     140      A     181          0.997
LGA    G     141      L     182          0.724
LGA    A     142      A     183          0.917
LGA    L     143      E     184          1.484
LGA    R     144      A     185          0.911
LGA    M     145      M     186          1.570
LGA    A     146      K     187          1.282
LGA    G     147      L     188          1.764
LGA    G     148      A     189          2.296
LGA    Y     149      K     190          2.479
LGA    A     150      S     191          1.490
LGA    K     151      R     192          4.439
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    V     152      V     203          6.042
LGA    I     153      E     204          2.346
LGA    I     154      -       -           -
LGA    P     155      -       -           -
LGA    F     156      -       -           -
LGA    S     157      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   71    5.0     20    2.42    25.00     23.451     0.794

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.911587 * X  +   0.291781 * Y  +  -0.289608 * Z  +  42.668961
  Y_new =   0.385614 * X  +   0.362662 * Y  +  -0.848397 * Z  +  85.374336
  Z_new =  -0.142517 * X  +  -0.885065 * Y  +  -0.443113 * Z  + -14.936080 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.034968    1.106625  [ DEG:  -116.5951     63.4049 ]
  Theta =   0.143004    2.998589  [ DEG:     8.1935    171.8065 ]
  Phi   =   2.741405   -0.400187  [ DEG:   157.0710    -22.9290 ]
 
# 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: T0347TS671_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS671_4-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   71   5.0   20   2.42   25.00  23.451
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS671_4-D2
PFRMAT TS
TARGET T0347
MODEL  4  REFINED
PARENT 1VZ0_A 1A04_B 1HLV_A 1R71_B 1RXX_C 1VK1_A 1YZS_A 1ZX4_A
ATOM    870  N   ASP   134       9.941  70.309   1.404  1.00  0.00
ATOM    871  CA  ASP   134       8.726  70.190   0.546  1.00  0.00
ATOM    872  C   ASP   134       9.189  69.549  -0.790  1.00  0.00
ATOM    873  O   ASP   134       9.812  70.276  -1.592  1.00  0.00
ATOM    874  CB  ASP   134       8.092  71.587   0.388  1.00  0.00
ATOM    875  CG  ASP   134       6.753  71.542  -0.290  1.00  0.00
ATOM    876  OD1 ASP   134       6.155  72.638  -0.422  1.00  0.00
ATOM    877  OD2 ASP   134       6.302  70.455  -0.714  1.00  0.00
ATOM    878  N   PRO   135       9.051  68.196  -0.994  1.00  0.00
ATOM    879  CA  PRO   135       9.568  67.569  -2.184  1.00  0.00
ATOM    880  C   PRO   135       9.385  68.316  -3.483  1.00  0.00
ATOM    881  O   PRO   135       8.548  69.206  -3.664  1.00  0.00
ATOM    882  CB  PRO   135       9.246  66.024  -2.225  1.00  0.00
ATOM    883  CG  PRO   135       8.584  65.781  -0.828  1.00  0.00
ATOM    884  CD  PRO   135       8.427  67.139  -0.128  1.00  0.00
ATOM    885  N   PHE   136      10.573  68.244  -4.060  1.00  0.00
ATOM    886  CA  PHE   136      11.012  68.614  -5.338  1.00  0.00
ATOM    887  C   PHE   136      12.002  67.447  -5.664  1.00  0.00
ATOM    888  O   PHE   136      13.146  67.555  -5.275  1.00  0.00
ATOM    889  CB  PHE   136      11.655  69.986  -5.399  1.00  0.00
ATOM    890  CG  PHE   136      10.898  71.253  -5.250  1.00  0.00
ATOM    891  CD1 PHE   136      10.515  71.732  -4.023  1.00  0.00
ATOM    892  CD2 PHE   136      10.488  71.917  -6.419  1.00  0.00
ATOM    893  CE1 PHE   136       9.777  72.936  -3.922  1.00  0.00
ATOM    894  CE2 PHE   136       9.720  73.125  -6.340  1.00  0.00
ATOM    895  CZ  PHE   136       9.345  73.591  -5.095  1.00  0.00
ATOM    896  N   ARG   137      11.672  66.607  -6.662  1.00  0.00
ATOM    897  CA  ARG   137      12.417  65.399  -7.060  1.00  0.00
ATOM    898  C   ARG   137      13.986  65.594  -7.093  1.00  0.00
ATOM    899  O   ARG   137      14.662  64.759  -6.499  1.00  0.00
ATOM    900  CB  ARG   137      11.820  65.001  -8.421  1.00  0.00
ATOM    901  CG  ARG   137      12.237  63.646  -8.875  1.00  0.00
ATOM    902  CD  ARG   137      11.392  63.219 -10.042  1.00  0.00
ATOM    903  NE  ARG   137      12.073  62.061 -10.584  1.00  0.00
ATOM    904  CZ  ARG   137      11.772  61.466 -11.719  1.00  0.00
ATOM    905  NH1 ARG   137      10.776  61.906 -12.526  1.00  0.00
ATOM    906  NH2 ARG   137      12.498  60.381 -12.016  1.00  0.00
ATOM    907  N   SER   138      14.532  66.477  -7.969  1.00  0.00
ATOM    908  CA  SER   138      15.992  66.792  -7.987  1.00  0.00
ATOM    909  C   SER   138      16.415  67.149  -6.513  1.00  0.00
ATOM    910  O   SER   138      17.486  66.695  -6.095  1.00  0.00
ATOM    911  CB  SER   138      16.358  67.894  -8.985  1.00  0.00
ATOM    912  OG  SER   138      15.775  69.185  -8.693  1.00  0.00
ATOM    913  N   LEU   139      15.776  68.139  -5.917  1.00  0.00
ATOM    914  CA  LEU   139      15.985  68.515  -4.529  1.00  0.00
ATOM    915  C   LEU   139      15.408  67.330  -3.669  1.00  0.00
ATOM    916  O   LEU   139      15.148  66.243  -4.250  1.00  0.00
ATOM    917  CB  LEU   139      15.255  69.809  -4.226  1.00  0.00
ATOM    918  CG  LEU   139      15.760  71.000  -4.992  1.00  0.00
ATOM    919  CD1 LEU   139      15.067  72.351  -4.605  1.00  0.00
ATOM    920  CD2 LEU   139      17.302  71.113  -5.020  1.00  0.00
ATOM    921  N   ALA   140      15.769  67.286  -2.436  1.00  0.00
ATOM    922  CA  ALA   140      15.429  66.211  -1.482  1.00  0.00
ATOM    923  C   ALA   140      16.336  64.940  -1.739  1.00  0.00
ATOM    924  O   ALA   140      16.410  64.131  -0.839  1.00  0.00
ATOM    925  CB  ALA   140      13.908  65.970  -1.486  1.00  0.00
ATOM    926  N   GLY   141      16.992  64.780  -2.922  1.00  0.00
ATOM    927  CA  GLY   141      17.942  63.700  -3.245  1.00  0.00
ATOM    928  C   GLY   141      19.225  64.060  -2.398  1.00  0.00
ATOM    929  O   GLY   141      20.011  63.150  -2.163  1.00  0.00
ATOM    930  N   ALA   142      19.643  65.356  -2.513  1.00  0.00
ATOM    931  CA  ALA   142      20.718  65.989  -1.782  1.00  0.00
ATOM    932  C   ALA   142      20.141  66.294  -0.409  1.00  0.00
ATOM    933  O   ALA   142      19.082  66.935  -0.287  1.00  0.00
ATOM    934  CB  ALA   142      21.231  67.220  -2.543  1.00  0.00
ATOM    935  N   LEU   143      20.938  65.989   0.552  1.00  0.00
ATOM    936  CA  LEU   143      20.648  66.062   1.994  1.00  0.00
ATOM    937  C   LEU   143      19.870  64.761   2.425  1.00  0.00
ATOM    938  O   LEU   143      19.729  64.562   3.646  1.00  0.00
ATOM    939  CB  LEU   143      19.853  67.345   2.308  1.00  0.00
ATOM    940  CG  LEU   143      20.477  68.732   2.367  1.00  0.00
ATOM    941  CD1 LEU   143      21.984  68.866   2.461  1.00  0.00
ATOM    942  CD2 LEU   143      19.945  69.570   1.237  1.00  0.00
ATOM    943  N   ARG   144      19.227  63.988   1.522  1.00  0.00
ATOM    944  CA  ARG   144      18.652  62.656   1.782  1.00  0.00
ATOM    945  C   ARG   144      19.881  61.684   1.591  1.00  0.00
ATOM    946  O   ARG   144      20.159  60.900   2.515  1.00  0.00
ATOM    947  CB  ARG   144      17.512  62.276   0.866  1.00  0.00
ATOM    948  CG  ARG   144      16.880  60.985   1.214  1.00  0.00
ATOM    949  CD  ARG   144      15.398  61.150   1.018  1.00  0.00
ATOM    950  NE  ARG   144      15.240  61.616  -0.332  1.00  0.00
ATOM    951  CZ  ARG   144      14.229  62.427  -0.621  1.00  0.00
ATOM    952  NH1 ARG   144      13.370  62.834   0.294  1.00  0.00
ATOM    953  NH2 ARG   144      14.107  62.869  -1.842  1.00  0.00
ATOM    954  N   MET   145      20.593  61.747   0.428  1.00  0.00
ATOM    955  CA  MET   145      21.822  61.043   0.178  1.00  0.00
ATOM    956  C   MET   145      22.867  61.690   1.144  1.00  0.00
ATOM    957  O   MET   145      23.754  60.954   1.568  1.00  0.00
ATOM    958  CB  MET   145      22.365  61.195  -1.232  1.00  0.00
ATOM    959  CG  MET   145      21.541  60.634  -2.325  1.00  0.00
ATOM    960  SD  MET   145      22.603  59.605  -3.354  1.00  0.00
ATOM    961  CE  MET   145      21.831  58.134  -2.745  1.00  0.00
ATOM    962  N   ALA   146      22.954  63.053   1.217  1.00  0.00
ATOM    963  CA  ALA   146      23.797  63.728   2.135  1.00  0.00
ATOM    964  C   ALA   146      23.356  63.280   3.507  1.00  0.00
ATOM    965  O   ALA   146      22.164  63.385   3.834  1.00  0.00
ATOM    966  CB  ALA   146      23.855  65.246   1.907  1.00  0.00
ATOM    967  N   GLY   147      24.256  63.315   4.431  1.00  0.00
ATOM    968  CA  GLY   147      23.972  62.687   5.756  1.00  0.00
ATOM    969  C   GLY   147      24.761  61.307   5.747  1.00  0.00
ATOM    970  O   GLY   147      24.637  60.608   6.755  1.00  0.00
ATOM    971  N   GLY   148      24.889  60.689   4.542  1.00  0.00
ATOM    972  CA  GLY   148      25.696  59.561   4.245  1.00  0.00
ATOM    973  C   GLY   148      27.170  60.050   4.439  1.00  0.00
ATOM    974  O   GLY   148      28.026  59.169   4.418  1.00  0.00
ATOM    975  N   TYR   149      27.451  61.233   3.809  1.00  0.00
ATOM    976  CA  TYR   149      28.756  61.875   4.128  1.00  0.00
ATOM    977  C   TYR   149      28.802  62.093   5.702  1.00  0.00
ATOM    978  O   TYR   149      29.840  61.760   6.256  1.00  0.00
ATOM    979  CB  TYR   149      28.923  63.144   3.273  1.00  0.00
ATOM    980  CG  TYR   149      28.499  64.498   3.816  1.00  0.00
ATOM    981  CD1 TYR   149      29.179  65.195   4.829  1.00  0.00
ATOM    982  CD2 TYR   149      27.391  65.116   3.271  1.00  0.00
ATOM    983  CE1 TYR   149      28.732  66.446   5.267  1.00  0.00
ATOM    984  CE2 TYR   149      26.925  66.362   3.692  1.00  0.00
ATOM    985  CZ  TYR   149      27.611  67.039   4.684  1.00  0.00
ATOM    986  OH  TYR   149      27.118  68.276   5.054  1.00  0.00
ATOM    987  N   ALA   150      27.627  61.989   6.373  1.00  0.00
ATOM    988  CA  ALA   150      27.446  62.044   7.761  1.00  0.00
ATOM    989  C   ALA   150      27.458  60.553   8.240  1.00  0.00
ATOM    990  O   ALA   150      26.476  60.196   8.902  1.00  0.00
ATOM    991  CB  ALA   150      26.146  62.805   7.976  1.00  0.00
ATOM    992  N   LYS   151      28.162  59.590   7.565  1.00  0.00
ATOM    993  CA  LYS   151      28.216  58.281   8.264  1.00  0.00
ATOM    994  C   LYS   151      28.975  58.673   9.550  1.00  0.00
ATOM    995  O   LYS   151      30.006  58.066   9.764  1.00  0.00
ATOM    996  CB  LYS   151      28.816  57.164   7.458  1.00  0.00
ATOM    997  CG  LYS   151      28.617  57.076   5.945  1.00  0.00
ATOM    998  CD  LYS   151      28.355  55.607   5.648  1.00  0.00
ATOM    999  CE  LYS   151      27.671  55.228   4.437  1.00  0.00
ATOM   1000  NZ  LYS   151      26.828  54.052   4.446  1.00  0.00
ATOM   1001  N   VAL   152      28.072  58.842  10.512  1.00  0.00
ATOM   1002  CA  VAL   152      28.289  59.411  11.858  1.00  0.00
ATOM   1003  C   VAL   152      29.750  59.718  12.152  1.00  0.00
ATOM   1004  O   VAL   152      30.057  60.910  12.122  1.00  0.00
ATOM   1005  CB  VAL   152      27.629  58.492  12.907  1.00  0.00
ATOM   1006  CG1 VAL   152      27.982  58.869  14.355  1.00  0.00
ATOM   1007  CG2 VAL   152      26.123  58.463  12.780  1.00  0.00
ATOM   1008  N   ILE   153      30.649  58.744  12.319  1.00  0.00
ATOM   1009  CA  ILE   153      32.046  59.100  12.493  1.00  0.00
ATOM   1010  C   ILE   153      32.726  59.732  11.202  1.00  0.00
ATOM   1011  O   ILE   153      33.808  60.280  11.389  1.00  0.00
ATOM   1012  CB  ILE   153      32.866  57.874  13.003  1.00  0.00
ATOM   1013  CG1 ILE   153      32.378  57.507  14.430  1.00  0.00
ATOM   1014  CG2 ILE   153      34.429  58.068  13.024  1.00  0.00
ATOM   1015  CD1 ILE   153      32.933  56.233  15.125  1.00  0.00
ATOM   1016  N   ILE   154      32.146  59.766   9.969  1.00  0.00
ATOM   1017  CA  ILE   154      32.786  60.325   8.737  1.00  0.00
ATOM   1018  C   ILE   154      32.662  61.896   8.871  1.00  0.00
ATOM   1019  O   ILE   154      32.983  62.318  10.001  1.00  0.00
ATOM   1020  CB  ILE   154      32.353  59.673   7.452  1.00  0.00
ATOM   1021  CG1 ILE   154      32.357  58.184   7.452  1.00  0.00
ATOM   1022  CG2 ILE   154      33.056  60.252   6.239  1.00  0.00
ATOM   1023  CD1 ILE   154      31.434  57.558   6.423  1.00  0.00
ATOM   1024  N   PRO   155      32.550  62.875   7.887  1.00  0.00
ATOM   1025  CA  PRO   155      32.545  64.239   8.250  1.00  0.00
ATOM   1026  C   PRO   155      31.860  64.650   9.562  1.00  0.00
ATOM   1027  O   PRO   155      32.167  65.779   9.996  1.00  0.00
ATOM   1028  CB  PRO   155      32.337  65.222   7.036  1.00  0.00
ATOM   1029  CG  PRO   155      32.274  64.208   5.833  1.00  0.00
ATOM   1030  CD  PRO   155      32.345  62.781   6.395  1.00  0.00
ATOM   1031  N   PHE   156      30.873  63.966  10.199  1.00  0.00
ATOM   1032  CA  PHE   156      30.447  64.509  11.519  1.00  0.00
ATOM   1033  C   PHE   156      31.696  64.756  12.466  1.00  0.00
ATOM   1034  O   PHE   156      31.801  65.872  12.991  1.00  0.00
ATOM   1035  CB  PHE   156      29.440  63.656  12.345  1.00  0.00
ATOM   1036  CG  PHE   156      28.030  63.706  11.850  1.00  0.00
ATOM   1037  CD1 PHE   156      27.215  64.724  12.363  1.00  0.00
ATOM   1038  CD2 PHE   156      27.503  62.753  10.975  1.00  0.00
ATOM   1039  CE1 PHE   156      25.871  64.784  11.998  1.00  0.00
ATOM   1040  CE2 PHE   156      26.158  62.823  10.618  1.00  0.00
ATOM   1041  CZ  PHE   156      25.346  63.834  11.126  1.00  0.00
ATOM   1042  N   SER   157      32.521  63.738  12.825  1.00  0.00
ATOM   1043  CA  SER   157      33.637  63.840  13.737  1.00  0.00
ATOM   1044  C   SER   157      34.957  63.690  12.943  1.00  0.00
ATOM   1045  O   SER   157      35.813  64.581  12.988  1.00  0.00
ATOM   1046  CB  SER   157      33.453  62.753  14.824  1.00  0.00
ATOM   1047  OG  SER   157      32.774  63.229  16.021  1.00  0.00
ATOM   1048  OXT SER   157      35.147  62.643  12.304  1.00  0.00
TER
END
