
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0356AL044_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_1-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      F     348           -
LGA    -       -      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    -       -      V     352           -
LGA    -       -      D     353           -
LGA    -       -      F     354           -
LGA    -       -      Y     355           -
LGA    -       -      L     356           -
LGA    -       -      P     357           -
LGA    -       -      P     358           -
LGA    -       -      E     359           -
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    -       -      A     366           -
LGA    -       -      V     367           -
LGA    -       -      V     368           -
LGA    -       -      T     369           -
LGA    -       -      I     370           -
LGA    -       -      K     371           -
LGA    -       -      K     372           -
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    F     348      H     377          0.626
LGA    P     349      A     378          0.343
LGA    E     350      K     379          0.111
LGA    I     351      R     380          0.086
LGA    V     352      V     381          0.374
LGA    D     353      M     382          0.820
LGA    F     354      M     383          0.924
LGA    Y     355      G     384          0.536
LGA    L     356      V     385          0.650
LGA    P     357      W     386          1.855
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    P     358      V     398          3.267
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    -       -      A     455           -
LGA    -       -      T     456           -
LGA    -       -      N     457           -
LGA    -       -      K     458           -
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11  120    5.0     11    1.24     9.09      8.925     0.819

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.572209 * X  +  -0.124643 * Y  +   0.810580 * Z  +  21.099533
  Y_new =  -0.663378 * X  +  -0.510781 * Y  +  -0.546839 * Z  + 124.949005
  Z_new =   0.482188 * X  +  -0.850628 * Y  +   0.209588 * Z  +  45.560116 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.329217    1.812376  [ DEG:   -76.1585    103.8415 ]
  Theta =  -0.503151   -2.638442  [ DEG:   -28.8284   -151.1716 ]
  Phi   =  -2.282542    0.859051  [ DEG:  -130.7800     49.2200 ]
 
# 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: T0356AL044_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11  120   5.0   11   1.24    9.09   8.925
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_1-D3
REMARK Aligment from pdb entry: 1jwq_A
ATOM    209  N   PHE   348      48.476  63.050  47.370  1.00  0.00              
ATOM    210  CA  PHE   348      49.241  64.105  48.024  1.00  0.00              
ATOM    211  C   PHE   348      49.278  63.839  49.529  1.00  0.00              
ATOM    212  O   PHE   348      50.321  63.978  50.176  1.00  0.00              
ATOM    213  N   PRO   349      48.137  63.435  50.078  1.00  0.00              
ATOM    214  CA  PRO   349      48.055  63.129  51.499  1.00  0.00              
ATOM    215  C   PRO   349      49.018  61.991  51.834  1.00  0.00              
ATOM    216  O   PRO   349      49.722  62.049  52.836  1.00  0.00              
ATOM    217  N   GLU   350      49.051  60.960  50.993  1.00  0.00              
ATOM    218  CA  GLU   350      49.943  59.826  51.227  1.00  0.00              
ATOM    219  C   GLU   350      51.404  60.281  51.214  1.00  0.00              
ATOM    220  O   GLU   350      52.202  59.852  52.043  1.00  0.00              
ATOM    221  N   ILE   351      51.749  61.151  50.271  1.00  0.00              
ATOM    222  CA  ILE   351      53.112  61.645  50.198  1.00  0.00              
ATOM    223  C   ILE   351      53.537  62.267  51.518  1.00  0.00              
ATOM    224  O   ILE   351      54.651  62.050  51.995  1.00  0.00              
ATOM    225  N   VAL   352      52.637  63.037  52.118  1.00  0.00              
ATOM    226  CA  VAL   352      52.912  63.699  53.390  1.00  0.00              
ATOM    227  C   VAL   352      52.952  62.695  54.535  1.00  0.00              
ATOM    228  O   VAL   352      53.864  62.712  55.364  1.00  0.00              
ATOM    229  N   ASP   353      51.956  61.822  54.569  1.00  0.00              
ATOM    230  CA  ASP   353      51.861  60.807  55.607  1.00  0.00              
ATOM    231  C   ASP   353      53.064  59.872  55.587  1.00  0.00              
ATOM    232  O   ASP   353      53.640  59.566  56.631  1.00  0.00              
ATOM    233  N   PHE   354      53.440  59.419  54.397  1.00  0.00              
ATOM    234  CA  PHE   354      54.575  58.516  54.261  1.00  0.00              
ATOM    235  C   PHE   354      55.876  59.197  54.655  1.00  0.00              
ATOM    236  O   PHE   354      56.677  58.624  55.385  1.00  0.00              
ATOM    237  N   TYR   355      56.086  60.420  54.178  1.00  0.00              
ATOM    238  CA  TYR   355      57.314  61.139  54.497  1.00  0.00              
ATOM    239  C   TYR   355      57.452  61.413  55.987  1.00  0.00              
ATOM    240  O   TYR   355      58.533  61.255  56.557  1.00  0.00              
ATOM    241  N   LEU   356      56.357  61.828  56.616  1.00  0.00              
ATOM    242  CA  LEU   356      56.371  62.137  58.039  1.00  0.00              
ATOM    243  C   LEU   356      56.263  60.888  58.905  1.00  0.00              
ATOM    244  O   LEU   356      56.329  60.967  60.130  1.00  0.00              
ATOM    245  N   PRO   357      56.099  59.742  58.252  1.00  0.00              
ATOM    246  CA  PRO   357      56.011  58.459  58.939  1.00  0.00              
ATOM    247  C   PRO   357      54.982  58.478  60.066  1.00  0.00              
ATOM    248  O   PRO   357      55.280  58.136  61.210  1.00  0.00              
ATOM    249  N   PRO   358      53.760  58.885  59.731  1.00  0.00              
ATOM    250  CA  PRO   358      52.680  58.936  60.710  1.00  0.00              
ATOM    251  C   PRO   358      51.504  58.061  60.282  1.00  0.00              
ATOM    252  O   PRO   358      50.347  58.389  60.543  1.00  0.00              
END
