
#######################################################
#                                                     #
#                        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 T0372AL044_4-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_4-D2.T0372_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    R     118      S     128          2.211
LGA    A     119      D     129          3.310
LGA    Y     120      L     130          2.166
LGA    A     121      A     131          5.031
LGA    D     122      T     132           #
LGA    Y     123      -       -           -
LGA    I     124      L     133          2.737
LGA    Y     125      K     134          3.401
LGA    L     126      G     135          2.906
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    R     127      F     138          0.949
LGA    S     128      Q     139          0.740
LGA    D     129      A     140          1.201
LGA    L     130      K     141          2.251
LGA    A     131      R     142          2.321
LGA    T     132      N     143          1.420
LGA    L     133      H     144          0.418
LGA    K     134      I     145          1.846
LGA    -       -      N     146           -
LGA    G     135      R     147          1.342
LGA    -       -      F     148           -
LGA    K     136      R     149          3.050
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  172    5.0     17    2.47     5.88      7.842     0.662

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.698479 * X  +  -0.010722 * Y  +  -0.715550 * Z  +  75.009796
  Y_new =  -0.244911 * X  +  -0.935929 * Y  +   0.253093 * Z  +  85.214729
  Z_new =  -0.672417 * X  +   0.352026 * Y  +   0.651101 * Z  +  44.561527 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.495646   -2.645946  [ DEG:    28.3984   -151.6016 ]
  Theta =   0.737470    2.404123  [ DEG:    42.2539    137.7461 ]
  Phi   =  -2.804353    0.337240  [ DEG:  -160.6776     19.3224 ]
 
# 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: T0372AL044_4-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_4-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  172   5.0   17   2.47    5.88   7.842
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_4-D2
REMARK Aligment from pdb entry: 1lq9_A
ATOM    157  N   ARG   118      27.134  53.917  30.134  1.00  0.00              
ATOM    158  CA  ARG   118      25.709  53.657  30.181  1.00  0.00              
ATOM    159  C   ARG   118      25.373  52.262  29.720  1.00  0.00              
ATOM    160  O   ARG   118      24.542  51.554  30.330  1.00  0.00              
ATOM    161  N   ALA   119      26.001  51.799  28.617  1.00  0.00              
ATOM    162  CA  ALA   119      25.690  50.465  28.119  1.00  0.00              
ATOM    163  C   ALA   119      26.070  49.422  29.143  1.00  0.00              
ATOM    164  O   ALA   119      25.381  48.423  29.341  1.00  0.00              
ATOM    165  N   TYR   120      27.233  49.604  29.776  1.00  0.00              
ATOM    166  CA  TYR   120      27.680  48.675  30.824  1.00  0.00              
ATOM    167  C   TYR   120      26.638  48.630  31.947  1.00  0.00              
ATOM    168  O   TYR   120      26.262  47.570  32.432  1.00  0.00              
ATOM    169  N   ALA   121      26.193  49.808  32.413  1.00  0.00              
ATOM    170  CA  ALA   121      25.273  49.874  33.539  1.00  0.00              
ATOM    171  C   ALA   121      23.920  49.245  33.196  1.00  0.00              
ATOM    172  O   ALA   121      23.330  48.519  34.009  1.00  0.00              
ATOM    173  N   ASP   122      23.386  49.562  32.012  1.00  0.00              
ATOM    174  CA  ASP   122      22.069  49.090  31.612  1.00  0.00              
ATOM    175  C   ASP   122      22.065  47.636  31.237  1.00  0.00              
ATOM    176  O   ASP   122      21.143  46.920  31.614  1.00  0.00              
ATOM    177  N   TYR   123      23.062  47.275  30.415  1.00  0.00              
ATOM    178  CA  TYR   123      22.984  45.960  29.802  1.00  0.00              
ATOM    179  C   TYR   123      23.793  44.912  30.518  1.00  0.00              
ATOM    180  O   TYR   123      23.762  43.695  30.209  1.00  0.00              
ATOM    181  N   ILE   124      24.568  45.296  31.532  1.00  0.00              
ATOM    182  CA  ILE   124      25.320  44.367  32.327  1.00  0.00              
ATOM    183  C   ILE   124      24.940  44.472  33.800  1.00  0.00              
ATOM    184  O   ILE   124      24.295  43.573  34.332  1.00  0.00              
ATOM    185  N   TYR   125      25.266  45.596  34.428  1.00  0.00              
ATOM    186  CA  TYR   125      25.062  45.782  35.859  1.00  0.00              
ATOM    187  C   TYR   125      23.621  45.621  36.292  1.00  0.00              
ATOM    188  O   TYR   125      23.351  45.077  37.396  1.00  0.00              
ATOM    189  N   LEU   126      22.687  46.099  35.480  1.00  0.00              
ATOM    190  CA  LEU   126      21.260  46.062  35.844  1.00  0.00              
ATOM    191  C   LEU   126      20.572  44.753  35.480  1.00  0.00              
ATOM    192  O   LEU   126      19.412  44.510  35.887  1.00  0.00              
ATOM    193  N   ARG   127      21.241  43.879  34.747  1.00  0.00              
ATOM    194  CA  ARG   127      20.674  42.581  34.381  1.00  0.00              
ATOM    195  C   ARG   127      20.998  41.639  35.517  1.00  0.00              
ATOM    196  O   ARG   127      22.178  41.500  35.878  1.00  0.00              
ATOM    197  N   SER   128      20.026  40.965  36.137  1.00  0.00              
ATOM    198  CA  SER   128      20.294  40.021  37.212  1.00  0.00              
ATOM    199  C   SER   128      21.221  38.890  36.787  1.00  0.00              
ATOM    200  O   SER   128      21.856  38.248  37.632  1.00  0.00              
ATOM    201  N   ASP   129      21.354  38.596  35.496  1.00  0.00              
ATOM    202  CA  ASP   129      22.317  37.592  35.034  1.00  0.00              
ATOM    203  C   ASP   129      23.725  37.980  35.420  1.00  0.00              
ATOM    204  O   ASP   129      24.572  37.105  35.565  1.00  0.00              
ATOM    205  N   LEU   130      24.066  39.266  35.642  1.00  0.00              
ATOM    206  CA  LEU   130      25.416  39.629  36.083  1.00  0.00              
ATOM    207  C   LEU   130      25.597  39.131  37.511  1.00  0.00              
ATOM    208  O   LEU   130      26.721  38.739  37.866  1.00  0.00              
ATOM    209  N   ALA   131      24.545  39.084  38.318  1.00  0.00              
ATOM    210  CA  ALA   131      24.679  38.576  39.698  1.00  0.00              
ATOM    211  C   ALA   131      24.802  37.069  39.658  1.00  0.00              
ATOM    212  O   ALA   131      25.584  36.456  40.394  1.00  0.00              
ATOM    213  N   THR   132      24.119  36.415  38.682  1.00  0.00              
ATOM    214  CA  THR   132      24.283  34.956  38.540  1.00  0.00              
ATOM    215  C   THR   132      25.691  34.622  38.071  1.00  0.00              
ATOM    216  O   THR   132      26.291  33.652  38.527  1.00  0.00              
ATOM    217  N   LEU   133      26.248  35.446  37.163  1.00  0.00              
ATOM    218  CA  LEU   133      27.602  35.232  36.685  1.00  0.00              
ATOM    219  C   LEU   133      28.582  35.467  37.829  1.00  0.00              
ATOM    220  O   LEU   133      29.540  34.675  38.031  1.00  0.00              
ATOM    221  N   LYS   134      28.378  36.506  38.642  1.00  0.00              
ATOM    222  CA  LYS   134      29.223  36.748  39.796  1.00  0.00              
ATOM    223  C   LYS   134      29.154  35.543  40.732  1.00  0.00              
ATOM    224  O   LYS   134      30.211  35.071  41.171  1.00  0.00              
ATOM    225  N   GLY   135      27.962  34.991  40.982  1.00  0.00              
ATOM    226  CA  GLY   135      27.905  33.811  41.820  1.00  0.00              
ATOM    227  C   GLY   135      28.705  32.659  41.225  1.00  0.00              
ATOM    228  O   GLY   135      29.415  31.939  41.941  1.00  0.00              
ATOM    229  N   LYS   136      32.384  33.132  41.656  1.00  0.00              
ATOM    230  CA  LYS   136      32.761  33.093  43.064  1.00  0.00              
ATOM    231  C   LYS   136      32.794  31.669  43.590  1.00  0.00              
ATOM    232  O   LYS   136      33.319  31.431  44.691  1.00  0.00              
END
