
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0299AL243_2-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_2-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      F      82           -
LGA    -       -      E      83           -
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    -       -      W      93           -
LGA    -       -      S      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      R      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      F     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
LGA    -       -      K     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    -       -      G     138           -
LGA    -       -      K     139           -
LGA    -       -      F     140           -
LGA    -       -      S     141           -
LGA    L      79      E     142          1.274
LGA    E      80      E     143          1.380
LGA    D      81      S     144          0.633
LGA    F      82      Y     145          0.780
LGA    E      83      S     146          0.332
LGA    A      84      K     147          1.173
LGA    E      85      T     148          1.529
LGA    -       -      A     149           -
LGA    -       -      Y     150           -
LGA    L      86      H     151          0.494
LGA    E      87      K     152          1.131
LGA    N      88      Y     153          2.666
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    -       -      F     159           -
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    -       -      I     163           -
LGA    -       -      T     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10   89    5.0     10    1.30    10.00     10.896     0.713

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.205478 * X  +  -0.117591 * Y  +  -0.971572 * Z  +  39.527946
  Y_new =   0.880913 * X  +  -0.454708 * Y  +  -0.131270 * Z  +  10.021465
  Z_new =  -0.426345 * X  +  -0.882843 * Y  +   0.197020 * Z  +  27.320915 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.351229    1.790364  [ DEG:   -77.4197    102.5803 ]
  Theta =   0.440449    2.701144  [ DEG:    25.2359    154.7641 ]
  Phi   =   1.799954   -1.341639  [ DEG:   103.1298    -76.8702 ]
 
# 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: T0299AL243_2-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_2-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10   89   5.0   10   1.30   10.00  10.896
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_2-D2
REMARK Aligment from pdb entry: 1k1wA
ATOM    181  N   LEU    79      19.951  52.276 -16.027  1.00  0.00              
ATOM    182  CA  LEU    79      21.059  53.215 -16.180  1.00  0.00              
ATOM    183  C   LEU    79      22.042  52.899 -15.059  1.00  0.00              
ATOM    184  O   LEU    79      21.656  52.794 -13.901  1.00  0.00              
ATOM    185  N   GLU    80      23.327  52.751 -15.395  1.00  0.00              
ATOM    186  CA  GLU    80      24.414  52.437 -14.466  1.00  0.00              
ATOM    187  C   GLU    80      24.565  53.492 -13.390  1.00  0.00              
ATOM    188  O   GLU    80      25.552  54.220 -13.362  1.00  0.00              
ATOM    189  N   ASP    81      23.598  53.572 -12.494  1.00  0.00              
ATOM    190  CA  ASP    81      23.648  54.583 -11.451  1.00  0.00              
ATOM    191  C   ASP    81      22.566  54.263 -10.456  1.00  0.00              
ATOM    192  O   ASP    81      22.512  54.838  -9.375  1.00  0.00              
ATOM    193  N   PHE    82      21.693  53.341 -10.836  1.00  0.00              
ATOM    194  CA  PHE    82      20.628  52.921  -9.944  1.00  0.00              
ATOM    195  C   PHE    82      21.284  52.004  -8.906  1.00  0.00              
ATOM    196  O   PHE    82      20.706  51.690  -7.863  1.00  0.00              
ATOM    197  N   GLU    83      22.510  51.589  -9.198  1.00  0.00              
ATOM    198  CA  GLU    83      23.223  50.709  -8.295  1.00  0.00              
ATOM    199  C   GLU    83      23.337  51.368  -6.926  1.00  0.00              
ATOM    200  O   GLU    83      22.941  50.787  -5.926  1.00  0.00              
ATOM    201  N   ALA    84      23.863  52.590  -6.894  1.00  0.00              
ATOM    202  CA  ALA    84      24.015  53.337  -5.648  1.00  0.00              
ATOM    203  C   ALA    84      22.683  53.432  -4.892  1.00  0.00              
ATOM    204  O   ALA    84      22.622  53.140  -3.700  1.00  0.00              
ATOM    205  N   GLU    85      21.621  53.834  -5.587  1.00  0.00              
ATOM    206  CA  GLU    85      20.309  53.986  -4.957  1.00  0.00              
ATOM    207  C   GLU    85      19.797  52.669  -4.391  1.00  0.00              
ATOM    208  O   GLU    85      19.455  52.570  -3.208  1.00  0.00              
ATOM    209  N   LEU    86      19.744  51.657  -5.248  1.00  0.00              
ATOM    210  CA  LEU    86      19.282  50.342  -4.850  1.00  0.00              
ATOM    211  C   LEU    86      20.036  49.834  -3.618  1.00  0.00              
ATOM    212  O   LEU    86      19.446  49.241  -2.721  1.00  0.00              
ATOM    213  N   GLU    87      21.337  50.083  -3.570  1.00  0.00              
ATOM    214  CA  GLU    87      22.160  49.651  -2.452  1.00  0.00              
ATOM    215  C   GLU    87      21.812  50.363  -1.158  1.00  0.00              
ATOM    216  O   GLU    87      21.761  49.738  -0.092  1.00  0.00              
ATOM    217  N   ASN    88      21.583  51.673  -1.254  1.00  0.00              
ATOM    218  CA  ASN    88      21.244  52.475  -0.095  1.00  0.00              
ATOM    219  C   ASN    88      19.859  52.091   0.355  1.00  0.00              
ATOM    220  O   ASN    88      19.526  52.225   1.527  1.00  0.00              
END
