
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0347AL242_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL242_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     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    P     135      S     177          2.290
LGA    F     136      F     178          1.898
LGA    R     137      D     179          1.936
LGA    S     138      D     180          1.067
LGA    L     139      A     181          0.565
LGA    A     140      L     182          0.558
LGA    G     141      A     183          0.222
LGA    A     142      E     184          0.521
LGA    L     143      A     185          0.708
LGA    R     144      M     186          1.210
LGA    M     145      K     187          1.030
LGA    A     146      L     188          0.240
LGA    G     147      A     189          0.318
LGA    G     148      K     190          0.723
LGA    Y     149      S     191          1.216
LGA    -       -      R     192           -
LGA    A     150      E     193          2.943
LGA    K     151      A     194          2.877
LGA    V     152      R     195          2.603
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    I     153      V     203          4.091
LGA    I     154      E     204          1.960
LGA    P     155      -       -           -
LGA    F     156      -       -           -
LGA    S     157      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   71    5.0     20    1.79     5.00     25.877     1.058

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.259912 * X  +   0.675424 * Y  +   0.690108 * Z  +  21.369968
  Y_new =   0.963002 * X  +   0.234015 * Y  +   0.133655 * Z  +  46.245384
  Z_new =  -0.071222 * X  +   0.699314 * Y  +  -0.711258 * Z  +  38.179150 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.364662   -0.776931  [ DEG:   135.4851    -44.5149 ]
  Theta =   0.071282    3.070310  [ DEG:     4.0842    175.9158 ]
  Phi   =   1.834413   -1.307180  [ DEG:   105.1041    -74.8959 ]
 
# 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: T0347AL242_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL242_4-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   71   5.0   20   1.79    5.00  25.877
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL242_4-D2
REMARK Aligment from pdb entry: 3crd
ATOM    309  N   PRO   135      11.137  64.793  -6.153  1.00  0.00              
ATOM    310  CA  PRO   135      11.881  66.055  -6.234  1.00  0.00              
ATOM    311  C   PRO   135      13.385  65.864  -6.058  1.00  0.00              
ATOM    312  O   PRO   135      14.111  66.828  -5.818  1.00  0.00              
ATOM    313  N   PHE   136      13.831  64.620  -6.157  1.00  0.00              
ATOM    314  CA  PHE   136      15.252  64.263  -5.992  1.00  0.00              
ATOM    315  C   PHE   136      16.205  65.461  -6.067  1.00  0.00              
ATOM    316  O   PHE   136      16.950  65.718  -5.121  1.00  0.00              
ATOM    317  N   ARG   137      16.217  66.197  -7.196  1.00  0.00              
ATOM    318  CA  ARG   137      17.098  67.345  -7.388  1.00  0.00              
ATOM    319  C   ARG   137      17.408  68.096  -6.096  1.00  0.00              
ATOM    320  O   ARG   137      18.480  68.683  -5.956  1.00  0.00              
ATOM    321  N   SER   138      16.473  68.075  -5.156  1.00  0.00              
ATOM    322  CA  SER   138      16.667  68.755  -3.881  1.00  0.00              
ATOM    323  C   SER   138      16.422  67.817  -2.704  1.00  0.00              
ATOM    324  O   SER   138      16.993  67.998  -1.629  1.00  0.00              
ATOM    325  N   LEU   139      15.576  66.812  -2.903  1.00  0.00              
ATOM    326  CA  LEU   139      15.273  65.864  -1.839  1.00  0.00              
ATOM    327  C   LEU   139      16.310  64.750  -1.794  1.00  0.00              
ATOM    328  O   LEU   139      16.701  64.304  -0.720  1.00  0.00              
ATOM    329  N   ALA   140      16.749  64.308  -2.971  1.00  0.00              
ATOM    330  CA  ALA   140      17.740  63.243  -3.070  1.00  0.00              
ATOM    331  C   ALA   140      19.100  63.732  -2.590  1.00  0.00              
ATOM    332  O   ALA   140      19.785  63.042  -1.836  1.00  0.00              
ATOM    333  N   GLY   141      19.481  64.927  -3.018  1.00  0.00              
ATOM    334  CA  GLY   141      20.749  65.497  -2.612  1.00  0.00              
ATOM    335  C   GLY   141      20.785  65.636  -1.104  1.00  0.00              
ATOM    336  O   GLY   141      21.665  65.092  -0.442  1.00  0.00              
ATOM    337  N   ALA   142      19.811  66.358  -0.566  1.00  0.00              
ATOM    338  CA  ALA   142      19.724  66.558   0.870  1.00  0.00              
ATOM    339  C   ALA   142      19.598  65.222   1.595  1.00  0.00              
ATOM    340  O   ALA   142      19.892  65.120   2.786  1.00  0.00              
ATOM    341  N   LEU   143      19.161  64.193   0.873  1.00  0.00              
ATOM    342  CA  LEU   143      19.003  62.875   1.463  1.00  0.00              
ATOM    343  C   LEU   143      20.331  62.153   1.548  1.00  0.00              
ATOM    344  O   LEU   143      20.836  61.881   2.637  1.00  0.00              
ATOM    345  N   ARG   144      20.900  61.857   0.393  1.00  0.00              
ATOM    346  CA  ARG   144      22.178  61.182   0.349  1.00  0.00              
ATOM    347  C   ARG   144      23.180  61.987   1.139  1.00  0.00              
ATOM    348  O   ARG   144      24.189  61.458   1.604  1.00  0.00              
ATOM    349  N   MET   145      22.871  63.265   1.344  1.00  0.00              
ATOM    350  CA  MET   145      23.731  64.098   2.141  1.00  0.00              
ATOM    351  C   MET   145      23.635  63.609   3.576  1.00  0.00              
ATOM    352  O   MET   145      24.633  63.499   4.290  1.00  0.00              
ATOM    353  N   ALA   146      22.402  63.298   3.974  1.00  0.00              
ATOM    354  CA  ALA   146      22.127  62.796   5.305  1.00  0.00              
ATOM    355  C   ALA   146      22.579  61.347   5.432  1.00  0.00              
ATOM    356  O   ALA   146      22.654  60.810   6.532  1.00  0.00              
ATOM    357  N   GLY   147      22.910  60.720   4.308  1.00  0.00              
ATOM    358  CA  GLY   147      23.381  59.352   4.331  1.00  0.00              
ATOM    359  C   GLY   147      24.834  59.389   4.729  1.00  0.00              
ATOM    360  O   GLY   147      25.342  58.524   5.443  1.00  0.00              
ATOM    361  N   GLY   148      25.475  60.437   4.263  1.00  0.00              
ATOM    362  CA  GLY   148      26.867  60.686   4.548  1.00  0.00              
ATOM    363  C   GLY   148      27.009  61.320   5.930  1.00  0.00              
ATOM    364  O   GLY   148      27.995  61.096   6.633  1.00  0.00              
ATOM    365  N   TYR   149      26.012  62.123   6.302  1.00  0.00              
ATOM    366  CA  TYR   149      26.007  62.811   7.590  1.00  0.00              
ATOM    367  C   TYR   149      25.302  62.001   8.682  1.00  0.00              
ATOM    368  O   TYR   149      25.875  61.753   9.743  1.00  0.00              
ATOM    369  N   ALA   150      24.048  61.616   8.433  1.00  0.00              
ATOM    370  CA  ALA   150      23.272  60.862   9.419  1.00  0.00              
ATOM    371  C   ALA   150      23.946  59.542   9.780  1.00  0.00              
ATOM    372  O   ALA   150      23.879  59.096  10.926  1.00  0.00              
ATOM    373  N   LYS   151      24.594  58.919   8.803  1.00  0.00              
ATOM    374  CA  LYS   151      25.274  57.649   9.031  1.00  0.00              
ATOM    375  C   LYS   151      26.381  57.800  10.071  1.00  0.00              
ATOM    376  O   LYS   151      27.405  58.433   9.814  1.00  0.00              
ATOM    377  N   VAL   152      26.168  57.212  11.245  1.00  0.00              
ATOM    378  CA  VAL   152      27.150  57.277  12.323  1.00  0.00              
ATOM    379  C   VAL   152      28.529  56.864  11.821  1.00  0.00              
ATOM    380  O   VAL   152      28.732  55.724  11.402  1.00  0.00              
ATOM    381  N   ILE   153      29.474  57.797  11.861  1.00  0.00              
ATOM    382  CA  ILE   153      30.832  57.529  11.405  1.00  0.00              
ATOM    383  C   ILE   153      31.763  57.256  12.582  1.00  0.00              
ATOM    384  O   ILE   153      31.556  57.767  13.684  1.00  0.00              
ATOM    385  N   ILE   154      32.792  56.450  12.338  1.00  0.00              
ATOM    386  CA  ILE   154      33.760  56.111  13.374  1.00  0.00              
ATOM    387  C   ILE   154      34.832  57.190  13.485  1.00  0.00              
ATOM    388  O   ILE   154      35.157  57.650  14.579  1.00  0.00              
ATOM    389  N   PRO   155      35.394  57.605  12.340  1.00  0.00              
ATOM    390  CA  PRO   155      36.436  58.637  12.292  1.00  0.00              
ATOM    391  C   PRO   155      36.002  59.929  12.976  1.00  0.00              
ATOM    392  O   PRO   155      34.900  60.016  13.520  1.00  0.00              
ATOM    393  N   PHE   156      36.874  60.929  12.945  1.00  0.00              
ATOM    394  CA  PHE   156      36.582  62.217  13.560  1.00  0.00              
ATOM    395  C   PHE   156      37.729  63.199  13.346  1.00  0.00              
ATOM    396  O   PHE   156      38.569  63.390  14.225  1.00  0.00              
ATOM    397  N   SER   157      37.756  63.819  12.170  1.00  0.00              
ATOM    398  CA  SER   157      38.804  64.774  11.861  1.00  0.00              
ATOM    399  C   SER   157      39.739  64.279  10.776  1.00  0.00              
ATOM    400  O   SER   157      39.272  63.545   9.880  1.00  0.00              
END
