
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0372AL333_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL333_1-D2.T0372_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    -       -      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    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
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    R     118      V     178          4.298
LGA    A     119      N     179          2.252
LGA    Y     120      N     180          2.507
LGA    A     121      C     181          1.250
LGA    I     124      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    Y     125      R     191          2.175
LGA    L     126      R     192          0.220
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    K     134      L     204          1.784
LGA    G     135      G     205          0.848
LGA    K     136      L     206          1.355
LGA    K     137      T     207          1.468
LGA    F     138      G     208          1.650
LGA    Q     139      G     209          0.971
LGA    A     140      I     210          2.608
LGA    K     141      -       -           -
LGA    R     142      L     211          2.657
LGA    P     225      H     212          4.730
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    I     226      E     236           #
LGA    N     227      K     237           #
LGA    H     228      A     238          3.889
LGA    E     229      D     239          4.523
LGA    T     230      T     240          3.629
LGA    F     231      S     241          4.695
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    G     232      Y     246          3.411
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    V     233      D     269           #
LGA    H     234      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    V     235      G     274           #
LGA    E     236      L     275           #
LGA    A     247      R     276           #
LGA    M     248      -       -           -
LGA    N     250      K     277          4.868
LGA    Y     251      A     278           -
LGA    E     252      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)   33  172    5.0     21    3.01     9.52      8.031     0.676

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.139182 * X  +   0.482197 * Y  +   0.864936 * Z  +   8.950992
  Y_new =  -0.454312 * X  +   0.807186 * Y  +  -0.376896 * Z  +  29.474882
  Z_new =  -0.879903 * X  +  -0.340494 * Y  +   0.331413 * Z  +  85.889488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.798912    2.342681  [ DEG:   -45.7743    134.2257 ]
  Theta =   1.075658    2.065935  [ DEG:    61.6306    118.3694 ]
  Phi   =  -1.273518    1.868075  [ DEG:   -72.9672    107.0328 ]
 
# 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: T0372AL333_1-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  172   5.0   21   3.01    9.52   8.031
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_1-D2
REMARK Aligment from pdb entry: 1nu0_A
ATOM    293  N   ARG   118      36.589  21.653  21.516  1.00  0.00              
ATOM    294  CA  ARG   118      37.583  21.265  20.498  1.00  0.00              
ATOM    295  C   ARG   118      38.556  22.409  20.251  1.00  0.00              
ATOM    296  O   ARG   118      38.156  23.575  20.210  1.00  0.00              
ATOM    297  N   ALA   119      39.810  22.046  20.072  1.00  0.00              
ATOM    298  CA  ALA   119      40.843  23.037  19.693  1.00  0.00              
ATOM    299  C   ALA   119      40.501  23.608  18.307  1.00  0.00              
ATOM    300  O   ALA   119      39.998  22.888  17.413  1.00  0.00              
ATOM    301  N   TYR   120      40.812  24.883  18.099  1.00  0.00              
ATOM    302  CA  TYR   120      40.592  25.497  16.801  1.00  0.00              
ATOM    303  C   TYR   120      41.752  26.467  16.585  1.00  0.00              
ATOM    304  O   TYR   120      42.445  26.847  17.532  1.00  0.00              
ATOM    305  N   ALA   121      41.935  26.878  15.317  1.00  0.00              
ATOM    306  CA  ALA   121      42.981  27.861  14.997  1.00  0.00              
ATOM    307  C   ALA   121      42.578  29.285  15.329  1.00  0.00              
ATOM    308  O   ALA   121      41.523  29.760  14.878  1.00  0.00              
ATOM    309  N   ILE   124      43.405  29.965  16.100  1.00  0.00              
ATOM    310  CA  ILE   124      43.176  31.383  16.454  1.00  0.00              
ATOM    311  C   ILE   124      43.744  32.110  15.221  1.00  0.00              
ATOM    312  O   ILE   124      44.909  31.944  14.907  1.00  0.00              
ATOM    313  N   TYR   125      42.984  32.913  14.492  1.00  0.00              
ATOM    314  CA  TYR   125      43.681  33.433  13.320  1.00  0.00              
ATOM    315  C   TYR   125      44.741  34.479  13.580  1.00  0.00              
ATOM    316  O   TYR   125      44.757  35.147  14.615  1.00  0.00              
ATOM    317  N   LEU   126      45.677  34.549  12.639  1.00  0.00              
ATOM    318  CA  LEU   126      46.801  35.469  12.704  1.00  0.00              
ATOM    319  C   LEU   126      46.316  36.915  12.718  1.00  0.00              
ATOM    320  O   LEU   126      45.256  37.225  12.155  1.00  0.00              
ATOM    321  N   LYS   134      49.030  48.455  19.099  1.00  0.00              
ATOM    322  CA  LYS   134      49.276  49.887  19.024  1.00  0.00              
ATOM    323  C   LYS   134      48.025  50.672  19.375  1.00  0.00              
ATOM    324  O   LYS   134      47.330  51.177  18.497  1.00  0.00              
ATOM    325  N   GLY   135      47.761  50.791  20.673  1.00  0.00              
ATOM    326  CA  GLY   135      46.573  51.471  21.153  1.00  0.00              
ATOM    327  C   GLY   135      45.808  50.352  21.829  1.00  0.00              
ATOM    328  O   GLY   135      44.694  50.509  22.331  1.00  0.00              
ATOM    329  N   LYS   136      46.473  49.202  21.808  1.00  0.00              
ATOM    330  CA  LYS   136      46.050  47.919  22.368  1.00  0.00              
ATOM    331  C   LYS   136      45.629  47.962  23.847  1.00  0.00              
ATOM    332  O   LYS   136      46.217  48.679  24.669  1.00  0.00              
ATOM    333  N   LYS   137      44.627  47.164  24.192  1.00  0.00              
ATOM    334  CA  LYS   137      44.205  47.056  25.577  1.00  0.00              
ATOM    335  C   LYS   137      43.772  45.617  25.850  1.00  0.00              
ATOM    336  O   LYS   137      43.035  45.002  25.067  1.00  0.00              
ATOM    337  N   PHE   138      44.249  45.074  26.963  1.00  0.00              
ATOM    338  CA  PHE   138      43.915  43.703  27.331  1.00  0.00              
ATOM    339  C   PHE   138      43.493  43.571  28.803  1.00  0.00              
ATOM    340  O   PHE   138      43.946  44.328  29.657  1.00  0.00              
ATOM    341  N   GLN   139      42.617  42.615  29.092  1.00  0.00              
ATOM    342  CA  GLN   139      42.178  42.381  30.471  1.00  0.00              
ATOM    343  C   GLN   139      43.409  42.000  31.303  1.00  0.00              
ATOM    344  O   GLN   139      44.471  41.691  30.741  1.00  0.00              
ATOM    345  N   ALA   140      43.281  42.047  32.627  1.00  0.00              
ATOM    346  CA  ALA   140      44.394  41.639  33.462  1.00  0.00              
ATOM    347  C   ALA   140      44.562  40.147  33.204  1.00  0.00              
ATOM    348  O   ALA   140      43.587  39.434  32.845  1.00  0.00              
ATOM    349  N   LYS   141      45.805  39.698  33.371  1.00  0.00              
ATOM    350  CA  LYS   141      46.216  38.346  33.097  1.00  0.00              
ATOM    351  C   LYS   141      45.331  37.238  33.653  1.00  0.00              
ATOM    352  O   LYS   141      45.078  36.249  32.939  1.00  0.00              
ATOM    353  N   ARG   142      44.885  37.396  34.900  1.00  0.00              
ATOM    354  CA  ARG   142      44.045  36.383  35.555  1.00  0.00              
ATOM    355  C   ARG   142      42.751  36.157  34.794  1.00  0.00              
ATOM    356  O   ARG   142      42.291  35.020  34.648  1.00  0.00              
ATOM    357  N   PRO   225      42.142  37.229  34.296  1.00  0.00              
ATOM    358  CA  PRO   225      40.920  37.041  33.540  1.00  0.00              
ATOM    359  C   PRO   225      41.203  36.589  32.099  1.00  0.00              
ATOM    360  O   PRO   225      40.411  35.838  31.515  1.00  0.00              
ATOM    361  N   ILE   226      42.321  37.032  31.520  1.00  0.00              
ATOM    362  CA  ILE   226      42.690  36.615  30.168  1.00  0.00              
ATOM    363  C   ILE   226      42.867  35.092  30.195  1.00  0.00              
ATOM    364  O   ILE   226      42.441  34.368  29.276  1.00  0.00              
ATOM    365  N   ASN   227      43.456  34.578  31.288  1.00  0.00              
ATOM    366  CA  ASN   227      43.663  33.109  31.413  1.00  0.00              
ATOM    367  C   ASN   227      42.360  32.298  31.533  1.00  0.00              
ATOM    368  O   ASN   227      42.377  31.050  31.440  1.00  0.00              
ATOM    369  N   HIS   228      41.253  33.013  31.738  1.00  0.00              
ATOM    370  CA  HIS   228      39.915  32.400  31.816  1.00  0.00              
ATOM    371  C   HIS   228      39.108  32.593  30.556  1.00  0.00              
ATOM    372  O   HIS   228      37.962  32.241  30.528  1.00  0.00              
ATOM    373  N   GLU   229      39.724  33.105  29.502  1.00  0.00              
ATOM    374  CA  GLU   229      38.952  33.271  28.260  1.00  0.00              
ATOM    375  C   GLU   229      38.325  32.042  27.695  1.00  0.00              
ATOM    376  O   GLU   229      37.179  32.161  27.203  1.00  0.00              
ATOM    377  N   THR   230      39.008  30.885  27.754  1.00  0.00              
ATOM    378  CA  THR   230      38.409  29.674  27.220  1.00  0.00              
ATOM    379  C   THR   230      37.221  29.274  28.098  1.00  0.00              
ATOM    380  O   THR   230      36.218  28.764  27.598  1.00  0.00              
ATOM    381  N   PHE   231      37.266  29.570  29.399  1.00  0.00              
ATOM    382  CA  PHE   231      36.119  29.192  30.222  1.00  0.00              
ATOM    383  C   PHE   231      34.890  30.059  29.792  1.00  0.00              
ATOM    384  O   PHE   231      33.765  29.593  29.787  1.00  0.00              
ATOM    385  N   GLY   232      35.090  31.341  29.482  1.00  0.00              
ATOM    386  CA  GLY   232      33.980  32.177  29.034  1.00  0.00              
ATOM    387  C   GLY   232      33.424  31.596  27.716  1.00  0.00              
ATOM    388  O   GLY   232      32.232  31.518  27.534  1.00  0.00              
ATOM    389  N   VAL   233      34.307  31.190  26.807  1.00  0.00              
ATOM    390  CA  VAL   233      33.833  30.612  25.531  1.00  0.00              
ATOM    391  C   VAL   233      33.031  29.344  25.761  1.00  0.00              
ATOM    392  O   VAL   233      32.009  29.133  25.091  1.00  0.00              
ATOM    393  N   HIS   234      33.502  28.483  26.671  1.00  0.00              
ATOM    394  CA  HIS   234      32.779  27.280  26.993  1.00  0.00              
ATOM    395  C   HIS   234      31.378  27.633  27.473  1.00  0.00              
ATOM    396  O   HIS   234      30.388  27.043  27.057  1.00  0.00              
ATOM    397  N   VAL   235      31.283  28.601  28.377  1.00  0.00              
ATOM    398  CA  VAL   235      30.001  28.914  28.971  1.00  0.00              
ATOM    399  C   VAL   235      29.082  29.604  27.963  1.00  0.00              
ATOM    400  O   VAL   235      27.915  29.292  27.943  1.00  0.00              
ATOM    401  N   GLU   236      29.594  30.527  27.141  1.00  0.00              
ATOM    402  CA  GLU   236      28.757  31.166  26.132  1.00  0.00              
ATOM    403  C   GLU   236      28.268  30.075  25.144  1.00  0.00              
ATOM    404  O   GLU   236      27.067  30.081  24.754  1.00  0.00              
ATOM    405  N   ALA   247      29.138  29.144  24.778  1.00  0.00              
ATOM    406  CA  ALA   247      28.758  28.061  23.857  1.00  0.00              
ATOM    407  C   ALA   247      27.629  27.231  24.475  1.00  0.00              
ATOM    408  O   ALA   247      26.612  26.925  23.833  1.00  0.00              
ATOM    409  N   MET   248      27.816  26.856  25.737  1.00  0.00              
ATOM    410  CA  MET   248      26.844  26.042  26.428  1.00  0.00              
ATOM    411  C   MET   248      25.484  26.778  26.441  1.00  0.00              
ATOM    412  O   MET   248      24.434  26.185  26.160  1.00  0.00              
ATOM    413  N   ASN   250      24.442  29.330  24.457  1.00  0.00              
ATOM    414  CA  ASN   250      23.946  29.577  23.093  1.00  0.00              
ATOM    415  C   ASN   250      23.326  28.354  22.478  1.00  0.00              
ATOM    416  O   ASN   250      22.356  28.475  21.732  1.00  0.00              
ATOM    417  N   TYR   251      23.909  27.192  22.764  1.00  0.00              
ATOM    418  CA  TYR   251      23.413  25.941  22.215  1.00  0.00              
ATOM    419  C   TYR   251      22.152  25.511  22.920  1.00  0.00              
ATOM    420  O   TYR   251      21.570  24.465  22.581  1.00  0.00              
ATOM    421  N   GLU   252      21.721  26.294  23.907  1.00  0.00              
ATOM    422  CA  GLU   252      20.498  25.983  24.595  1.00  0.00              
ATOM    423  C   GLU   252      20.512  24.980  25.710  1.00  0.00              
ATOM    424  O   GLU   252      19.522  24.305  25.959  1.00  0.00              
END
