
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0381AL242_2-D2
# Molecule2: number of CA atoms  176 ( 1314),  selected  176 , name T0381_D2.pdb
# PARAMETERS: T0381AL242_2-D2.T0381_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      90           -
LGA    -       -      S      91           -
LGA    -       -      L      92           -
LGA    -       -      P      93           -
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      A      96           -
LGA    -       -      Q      97           -
LGA    -       -      P      98           -
LGA    -       -      H      99           -
LGA    -       -      L     100           -
LGA    -       -      E     101           -
LGA    -       -      K     102           -
LGA    -       -      L     103           -
LGA    -       -      S     104           -
LGA    -       -      H     105           -
LGA    -       -      K     106           -
LGA    -       -      V     107           -
LGA    -       -      H     108           -
LGA    -       -      E     109           -
LGA    -       -      S     110           -
LGA    -       -      S     111           -
LGA    -       -      S     112           -
LGA    -       -      V     113           -
LGA    -       -      S     114           -
LGA    -       -      I     115           -
LGA    -       -      L     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      A     119           -
LGA    -       -      D     120           -
LGA    -       -      I     121           -
LGA    -       -      V     122           -
LGA    -       -      Y     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      R     126           -
LGA    -       -      V     127           -
LGA    -       -      P     128           -
LGA    -       -      V     129           -
LGA    -       -      S     130           -
LGA    -       -      R     131           -
LGA    -       -      I     132           -
LGA    -       -      M     133           -
LGA    -       -      T     134           -
LGA    -       -      V     135           -
LGA    -       -      G     136           -
LGA    -       -      I     137           -
LGA    -       -      T     138           -
LGA    -       -      I     139           -
LGA    -       -      G     140           -
LGA    -       -      T     141           -
LGA    -       -      R     142           -
LGA    -       -      L     143           -
LGA    -       -      P     144           -
LGA    -       -      A     145           -
LGA    -       -      Y     146           -
LGA    -       -      A     147           -
LGA    -       -      T     148           -
LGA    -       -      S     149           -
LGA    -       -      M     150           -
LGA    -       -      G     151           -
LGA    -       -      R     152           -
LGA    -       -      V     153           -
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      A     156           -
LGA    -       -      G     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      D     160           -
LGA    -       -      D     161           -
LGA    -       -      E     162           -
LGA    -       -      L     163           -
LGA    -       -      D     164           -
LGA    -       -      A     165           -
LGA    -       -      Y     166           -
LGA    -       -      L     167           -
LGA    -       -      E     168           -
LGA    -       -      K     169           -
LGA    -       -      L     170           -
LGA    -       -      D     171           -
LGA    -       -      I     172           -
LGA    -       -      Q     173           -
LGA    -       -      R     174           -
LGA    -       -      L     175           -
LGA    -       -      T     176           -
LGA    -       -      E     177           -
LGA    -       -      R     178           -
LGA    -       -      T     179           -
LGA    -       -      I     180           -
LGA    -       -      T     181           -
LGA    -       -      A     182           -
LGA    -       -      R     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      L     186           -
LGA    -       -      K     187           -
LGA    -       -      A     188           -
LGA    -       -      A     189           -
LGA    -       -      I     190           -
LGA    -       -      L     191           -
LGA    -       -      A     192           -
LGA    -       -      V     193           -
LGA    -       -      R     194           -
LGA    -       -      A     195           -
LGA    -       -      D     196           -
LGA    -       -      G     197           -
LGA    -       -      I     198           -
LGA    -       -      C     199           -
LGA    -       -      V     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Q     203           -
LGA    -       -      E     204           -
LGA    -       -      L     205           -
LGA    -       -      E     206           -
LGA    -       -      A     207           -
LGA    -       -      G     208           -
LGA    -       -      L     209           -
LGA    -       -      R     210           -
LGA    -       -      S     211           -
LGA    -       -      M     212           -
LGA    -       -      A     213           -
LGA    -       -      A     214           -
LGA    -       -      P     215           -
LGA    -       -      I     216           -
LGA    -       -      R     217           -
LGA    -       -      G     218           -
LGA    -       -      A     219           -
LGA    -       -      S     220           -
LGA    -       -      G     221           -
LGA    -       -      L     222           -
LGA    -       -      T     223           -
LGA    -       -      V     224           -
LGA    -       -      A     225           -
LGA    -       -      A     226           -
LGA    -       -      V     227           -
LGA    -       -      N     228           -
LGA    -       -      I     229           -
LGA    -       -      S     230           -
LGA    -       -      T     231           -
LGA    -       -      P     232           -
LGA    -       -      A     233           -
LGA    -       -      A     234           -
LGA    -       -      R     235           -
LGA    -       -      Y     236           -
LGA    -       -      S     237           -
LGA    -       -      L     238           -
LGA    -       -      E     239           -
LGA    -       -      D     240           -
LGA    -       -      L     241           -
LGA    -       -      H     242           -
LGA    -       -      S     243           -
LGA    -       -      D     244           -
LGA    -       -      L     245           -
LGA    L      90      I     246          0.369
LGA    S      91      P     247          0.393
LGA    L      92      S     248          0.184
LGA    P      93      L     249          0.292
LGA    E      94      R     250          0.212
LGA    V      95      V     251          0.275
LGA    A      96      T     252          0.294
LGA    Q      97      A     253          0.134
LGA    P      98      T     254          0.294
LGA    H      99      D     255          0.505
LGA    L     100      I     256          0.327
LGA    E     101      E     257          0.320
LGA    K     102      Q     258          0.378
LGA    L     103      D     259          0.331
LGA    S     104      L     260          0.170
LGA    H     105      A     261          0.386
LGA    K     106      T     262          0.474
LGA    V     107      V     263          0.472
LGA    H     108      N     264          0.879
LGA    -       -      R     265           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  176    5.0     19    0.39    15.79     10.795     3.906

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.498919 * X  +  -0.541413 * Y  +  -0.676721 * Z  +  21.515236
  Y_new =  -0.271680 * X  +  -0.643781 * Y  +   0.715358 * Z  +  32.082790
  Z_new =  -0.822964 * X  +   0.540757 * Y  +   0.174104 * Z  +  60.048992 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.259314   -1.882279  [ DEG:    72.1534   -107.8466 ]
  Theta =   0.966609    2.174984  [ DEG:    55.3826    124.6174 ]
  Phi   =  -2.642954    0.498639  [ DEG:  -151.4301     28.5699 ]
 
# 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: T0381AL242_2-D2                               
REMARK     2: T0381_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL242_2-D2.T0381_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  176   5.0   19   0.39   15.79  10.795
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL242_2-D2
REMARK Aligment from pdb entry: 1r7j_A
ATOM    285  N   LEU    90      -1.606  21.703  37.817  1.00  0.00              
ATOM    286  CA  LEU    90      -1.573  21.363  36.400  1.00  0.00              
ATOM    287  C   LEU    90      -1.842  22.571  35.518  1.00  0.00              
ATOM    288  O   LEU    90      -1.278  22.682  34.430  1.00  0.00              
ATOM    289  N   SER    91      -2.700  23.472  35.980  1.00  0.00              
ATOM    290  CA  SER    91      -3.010  24.671  35.210  1.00  0.00              
ATOM    291  C   SER    91      -1.771  25.564  35.200  1.00  0.00              
ATOM    292  O   SER    91      -1.451  26.188  34.186  1.00  0.00              
ATOM    293  N   LEU    92      -1.067  25.614  36.327  1.00  0.00              
ATOM    294  CA  LEU    92       0.146  26.419  36.418  1.00  0.00              
ATOM    295  C   LEU    92       1.179  25.884  35.438  1.00  0.00              
ATOM    296  O   LEU    92       1.874  26.657  34.771  1.00  0.00              
ATOM    297  N   PRO    93       1.285  24.563  35.357  1.00  0.00              
ATOM    298  CA  PRO    93       2.244  23.938  34.455  1.00  0.00              
ATOM    299  C   PRO    93       1.917  24.295  33.012  1.00  0.00              
ATOM    300  O   PRO    93       2.810  24.612  32.224  1.00  0.00              
ATOM    301  N   GLU    94       0.637  24.241  32.668  1.00  0.00              
ATOM    302  CA  GLU    94       0.198  24.570  31.318  1.00  0.00              
ATOM    303  C   GLU    94       0.583  26.002  30.965  1.00  0.00              
ATOM    304  O   GLU    94       1.141  26.258  29.892  1.00  0.00              
ATOM    305  N   VAL    95       0.287  26.940  31.861  1.00  0.00              
ATOM    306  CA  VAL    95       0.611  28.344  31.615  1.00  0.00              
ATOM    307  C   VAL    95       2.113  28.564  31.556  1.00  0.00              
ATOM    308  O   VAL    95       2.597  29.385  30.777  1.00  0.00              
ATOM    309  N   ALA    96       2.855  27.840  32.384  1.00  0.00              
ATOM    310  CA  ALA    96       4.303  27.979  32.390  1.00  0.00              
ATOM    311  C   ALA    96       4.869  27.479  31.065  1.00  0.00              
ATOM    312  O   ALA    96       5.706  28.144  30.453  1.00  0.00              
ATOM    313  N   GLN    97       4.415  26.310  30.619  1.00  0.00              
ATOM    314  CA  GLN    97       4.890  25.750  29.355  1.00  0.00              
ATOM    315  C   GLN    97       4.618  26.714  28.207  1.00  0.00              
ATOM    316  O   GLN    97       5.452  26.871  27.314  1.00  0.00              
ATOM    317  N   PRO    98       3.452  27.355  28.221  1.00  0.00              
ATOM    318  CA  PRO    98       3.120  28.280  27.149  1.00  0.00              
ATOM    319  C   PRO    98       4.009  29.514  27.191  1.00  0.00              
ATOM    320  O   PRO    98       4.441  30.003  26.147  1.00  0.00              
ATOM    321  N   HIS    99       4.293  30.015  28.391  1.00  0.00              
ATOM    322  CA  HIS    99       5.148  31.191  28.523  1.00  0.00              
ATOM    323  C   HIS    99       6.564  30.837  28.081  1.00  0.00              
ATOM    324  O   HIS    99       7.272  31.678  27.524  1.00  0.00              
ATOM    325  N   LEU   100       6.980  29.597  28.320  1.00  0.00              
ATOM    326  CA  LEU   100       8.305  29.165  27.904  1.00  0.00              
ATOM    327  C   LEU   100       8.373  29.176  26.376  1.00  0.00              
ATOM    328  O   LEU   100       9.402  29.517  25.805  1.00  0.00              
ATOM    329  N   GLU   101       7.275  28.812  25.720  1.00  0.00              
ATOM    330  CA  GLU   101       7.242  28.813  24.259  1.00  0.00              
ATOM    331  C   GLU   101       7.361  30.254  23.764  1.00  0.00              
ATOM    332  O   GLU   101       8.014  30.521  22.753  1.00  0.00              
ATOM    333  N   LYS   102       6.734  31.184  24.478  1.00  0.00              
ATOM    334  CA  LYS   102       6.777  32.595  24.098  1.00  0.00              
ATOM    335  C   LYS   102       8.216  33.088  24.199  1.00  0.00              
ATOM    336  O   LYS   102       8.739  33.723  23.282  1.00  0.00              
ATOM    337  N   LEU   103       8.853  32.782  25.321  1.00  0.00              
ATOM    338  CA  LEU   103      10.233  33.177  25.560  1.00  0.00              
ATOM    339  C   LEU   103      11.151  32.571  24.501  1.00  0.00              
ATOM    340  O   LEU   103      11.982  33.270  23.917  1.00  0.00              
ATOM    341  N   SER   104      10.995  31.277  24.239  1.00  0.00              
ATOM    342  CA  SER   104      11.842  30.635  23.248  1.00  0.00              
ATOM    343  C   SER   104      11.650  31.204  21.847  1.00  0.00              
ATOM    344  O   SER   104      12.609  31.294  21.085  1.00  0.00              
ATOM    345  N   HIS   105      10.427  31.601  21.508  1.00  0.00              
ATOM    346  CA  HIS   105      10.166  32.162  20.183  1.00  0.00              
ATOM    347  C   HIS   105      10.924  33.474  19.978  1.00  0.00              
ATOM    348  O   HIS   105      11.359  33.780  18.867  1.00  0.00              
ATOM    349  N   LYS   106      11.078  34.246  21.048  1.00  0.00              
ATOM    350  CA  LYS   106      11.790  35.520  20.971  1.00  0.00              
ATOM    351  C   LYS   106      13.290  35.279  20.827  1.00  0.00              
ATOM    352  O   LYS   106      13.980  36.016  20.122  1.00  0.00              
ATOM    353  N   VAL   107      13.790  34.243  21.490  1.00  0.00              
ATOM    354  CA  VAL   107      15.212  33.919  21.451  1.00  0.00              
ATOM    355  C   VAL   107      15.571  32.966  20.322  1.00  0.00              
ATOM    356  O   VAL   107      16.746  32.706  20.073  1.00  0.00              
ATOM    357  N   HIS   108      14.556  32.450  19.640  1.00  0.00              
ATOM    358  CA  HIS   108      14.770  31.507  18.550  1.00  0.00              
ATOM    359  C   HIS   108      13.449  31.176  17.871  1.00  0.00              
ATOM    360  O   HIS   108      13.021  30.006  17.953  1.00  0.00              
END
