
#######################################################
#                                                     #
#                        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_2-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_2-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    -       -      H     377           -
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    -       -      R     380           -
LGA    -       -      V     381           -
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    F     348      G     384          0.941
LGA    P     349      V     385          0.284
LGA    E     350      W     386          0.728
LGA    I     351      S     387          0.744
LGA    V     352      F     388          2.277
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    D     353      F     392          1.935
LGA    F     354      M     393          0.719
LGA    Y     355      Y     394          2.478
LGA    L     356      T     395          2.970
LGA    -       -      K     396           -
LGA    P     357      F     397          2.797
LGA    P     358      V     398          3.541
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    2.06     9.09      7.869     0.509

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.214235 * X  +  -0.681955 * Y  +   0.699315 * Z  +  46.698387
  Y_new =   0.346721 * X  +   0.722408 * Y  +   0.598257 * Z  +  21.003262
  Z_new =  -0.913175 * X  +   0.114299 * Y  +   0.391213 * Z  + 115.386665 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.284255   -2.857338  [ DEG:    16.2866   -163.7134 ]
  Theta =   1.151006    1.990586  [ DEG:    65.9478    114.0522 ]
  Phi   =   1.017327   -2.124266  [ DEG:    58.2885   -121.7115 ]
 
# 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_2-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_2-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   2.06    9.09   7.869
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_2-D3
REMARK Aligment from pdb entry: 1xov_A
ATOM    213  N   PHE   348      56.623  59.925  54.080  1.00  0.00              
ATOM    214  CA  PHE   348      57.732  60.837  54.262  1.00  0.00              
ATOM    215  C   PHE   348      57.892  61.186  55.738  1.00  0.00              
ATOM    216  O   PHE   348      58.996  61.200  56.277  1.00  0.00              
ATOM    217  N   PRO   349      56.776  61.423  56.424  1.00  0.00              
ATOM    218  CA  PRO   349      56.851  61.773  57.840  1.00  0.00              
ATOM    219  C   PRO   349      57.397  60.603  58.656  1.00  0.00              
ATOM    220  O   PRO   349      58.260  60.801  59.501  1.00  0.00              
ATOM    221  N   GLU   350      56.932  59.392  58.384  1.00  0.00              
ATOM    222  CA  GLU   350      57.449  58.218  59.114  1.00  0.00              
ATOM    223  C   GLU   350      58.896  57.919  58.757  1.00  0.00              
ATOM    224  O   GLU   350      59.707  57.515  59.609  1.00  0.00              
ATOM    225  N   ILE   351      59.245  58.118  57.492  1.00  0.00              
ATOM    226  CA  ILE   351      60.654  57.954  57.105  1.00  0.00              
ATOM    227  C   ILE   351      61.596  58.940  57.745  1.00  0.00              
ATOM    228  O   ILE   351      62.742  58.595  58.123  1.00  0.00              
ATOM    229  N   VAL   352      61.142  60.181  57.898  1.00  0.00              
ATOM    230  CA  VAL   352      61.950  61.184  58.536  1.00  0.00              
ATOM    231  C   VAL   352      62.075  60.975  60.037  1.00  0.00              
ATOM    232  O   VAL   352      63.153  61.149  60.633  1.00  0.00              
ATOM    233  N   ASP   353      60.964  60.621  60.670  1.00  0.00              
ATOM    234  CA  ASP   353      60.944  60.617  62.136  1.00  0.00              
ATOM    235  C   ASP   353      61.161  59.252  62.765  1.00  0.00              
ATOM    236  O   ASP   353      61.503  59.170  63.951  1.00  0.00              
ATOM    237  N   PHE   354      60.941  58.190  62.014  1.00  0.00              
ATOM    238  CA  PHE   354      61.035  56.835  62.537  1.00  0.00              
ATOM    239  C   PHE   354      59.873  56.463  63.438  1.00  0.00              
ATOM    240  O   PHE   354      59.951  55.474  64.160  1.00  0.00              
ATOM    241  N   TYR   355      58.778  57.231  63.390  1.00  0.00              
ATOM    242  CA  TYR   355      57.633  57.006  64.265  1.00  0.00              
ATOM    243  C   TYR   355      56.350  56.932  63.463  1.00  0.00              
ATOM    244  O   TYR   355      56.118  57.754  62.592  1.00  0.00              
ATOM    245  N   LEU   356      55.530  55.935  63.760  1.00  0.00              
ATOM    246  CA  LEU   356      54.282  55.729  63.047  1.00  0.00              
ATOM    247  C   LEU   356      53.334  56.891  63.332  1.00  0.00              
ATOM    248  O   LEU   356      53.212  57.314  64.468  1.00  0.00              
ATOM    249  N   PRO   357      52.686  57.419  62.295  1.00  0.00              
ATOM    250  CA  PRO   357      51.816  58.572  62.488  1.00  0.00              
ATOM    251  C   PRO   357      50.516  58.129  63.140  1.00  0.00              
ATOM    252  O   PRO   357      50.060  57.009  62.953  1.00  0.00              
ATOM    253  N   PRO   358      49.926  59.024  63.918  1.00  0.00              
ATOM    254  CA  PRO   358      48.661  58.759  64.565  1.00  0.00              
ATOM    255  C   PRO   358      47.446  58.794  63.634  1.00  0.00              
ATOM    256  O   PRO   358      46.524  58.012  63.812  1.00  0.00              
END
