
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0381AL242_3-D2
# Molecule2: number of CA atoms  176 ( 1314),  selected  176 , name T0381_D2.pdb
# PARAMETERS: T0381AL242_3-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      L      90           -
LGA    S      91      S      91           -
LGA    L      92      L      92           -
LGA    P      93      P      93           -
LGA    E      94      E      94           -
LGA    V      95      V      95           -
LGA    A      96      A      96           -
LGA    Q      97      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    P      98      T     148           #
LGA    H      99      S     149          0.504
LGA    L     100      M     150          4.833
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    E     101      V     200          2.082
LGA    K     102      L     201          1.418
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    L     103      S     211          1.243
LGA    S     104      M     212          4.164
LGA    H     105      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    K     106      S     230           #
LGA    V     107      T     231          1.781
LGA    H     108      P     232          3.753
LGA    E     109      A     233          1.040
LGA    S     110      A     234          4.264
LGA    S     111      -       -           -
LGA    S     112      R     235          5.180
LGA    V     113      Y     236          3.612
LGA    S     114      S     237          1.313
LGA    I     115      L     238          2.464
LGA    L     116      E     239          1.642
LGA    D     117      D     240          3.775
LGA    G     118      L     241          3.793
LGA    -       -      H     242           -
LGA    -       -      S     243           -
LGA    -       -      D     244           -
LGA    -       -      L     245           -
LGA    -       -      I     246           -
LGA    A     119      P     247          1.561
LGA    D     120      S     248          3.068
LGA    I     121      L     249          3.967
LGA    -       -      R     250           -
LGA    -       -      V     251           -
LGA    V     122      T     252          1.770
LGA    -       -      A     253           -
LGA    -       -      T     254           -
LGA    Y     123      D     255          0.806
LGA    V     124      I     256          2.486
LGA    -       -      E     257           -
LGA    -       -      Q     258           -
LGA    A     125      D     259          1.403
LGA    R     126      L     260          3.062
LGA    V     127      A     261          4.484
LGA    -       -      T     262           -
LGA    -       -      V     263           -
LGA    P     128      N     264          0.899
LGA    -       -      R     265           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  176    5.0     27    2.95     7.41      9.415     0.887

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.522305 * X  +  -0.621733 * Y  +  -0.583648 * Z  +   0.322847
  Y_new =   0.521029 * X  +  -0.309145 * Y  +   0.795586 * Z  + -13.260808
  Z_new =  -0.675074 * X  +  -0.719637 * Y  +   0.162473 * Z  +  53.602654 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.348748    1.792845  [ DEG:   -77.2776    102.7224 ]
  Theta =   0.741065    2.400527  [ DEG:    42.4599    137.5401 ]
  Phi   =   0.784175   -2.357417  [ DEG:    44.9299   -135.0701 ]
 
# 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_3-D2                               
REMARK     2: T0381_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL242_3-D2.T0381_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  176   5.0   27   2.95    7.41   9.415
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL242_3-D2
REMARK Aligment from pdb entry: 1mzb_A
ATOM    337  N   LEU    90       1.040  36.601  23.221  1.00  0.00              
ATOM    338  CA  LEU    90      -0.191  36.144  23.858  1.00  0.00              
ATOM    339  C   LEU    90      -0.687  34.825  23.235  1.00  0.00              
ATOM    340  O   LEU    90      -1.691  34.283  23.710  1.00  0.00              
ATOM    341  N   SER    91       0.030  34.285  22.239  1.00  0.00              
ATOM    342  CA  SER    91      -0.405  33.033  21.589  1.00  0.00              
ATOM    343  C   SER    91      -0.426  31.898  22.634  1.00  0.00              
ATOM    344  O   SER    91       0.518  31.746  23.421  1.00  0.00              
ATOM    345  N   LEU    92      -1.504  31.132  22.637  1.00  0.00              
ATOM    346  CA  LEU    92      -1.651  30.010  23.588  1.00  0.00              
ATOM    347  C   LEU    92      -1.555  28.712  22.821  1.00  0.00              
ATOM    348  O   LEU    92      -2.273  28.509  21.813  1.00  0.00              
ATOM    349  N   PRO    93      -0.698  27.829  23.323  1.00  0.00              
ATOM    350  CA  PRO    93      -0.434  26.530  22.718  1.00  0.00              
ATOM    351  C   PRO    93      -0.762  25.435  23.736  1.00  0.00              
ATOM    352  O   PRO    93      -0.155  25.370  24.800  1.00  0.00              
ATOM    353  N   GLU    94      -1.741  24.592  23.425  1.00  0.00              
ATOM    354  CA  GLU    94      -2.064  23.491  24.332  1.00  0.00              
ATOM    355  C   GLU    94      -1.066  22.336  24.168  1.00  0.00              
ATOM    356  O   GLU    94      -0.522  22.098  23.079  1.00  0.00              
ATOM    357  N   VAL    95      -0.821  21.619  25.259  1.00  0.00              
ATOM    358  CA  VAL    95       0.046  20.445  25.211  1.00  0.00              
ATOM    359  C   VAL    95      -0.394  19.513  26.314  1.00  0.00              
ATOM    360  O   VAL    95      -1.127  19.905  27.220  1.00  0.00              
ATOM    361  N   ALA    96       0.027  18.265  26.219  1.00  0.00              
ATOM    362  CA  ALA    96      -0.298  17.267  27.222  1.00  0.00              
ATOM    363  C   ALA    96       0.896  16.325  27.211  1.00  0.00              
ATOM    364  O   ALA    96       1.161  15.649  26.206  1.00  0.00              
ATOM    365  N   GLN    97       1.643  16.313  28.299  1.00  0.00              
ATOM    366  CA  GLN    97       2.812  15.460  28.367  1.00  0.00              
ATOM    367  C   GLN    97       2.554  14.337  29.371  1.00  0.00              
ATOM    368  O   GLN    97       2.476  14.596  30.566  1.00  0.00              
ATOM    369  N   PRO    98       2.465  13.096  28.893  1.00  0.00              
ATOM    370  CA  PRO    98       2.188  11.979  29.795  1.00  0.00              
ATOM    371  C   PRO    98       3.265  11.830  30.885  1.00  0.00              
ATOM    372  O   PRO    98       2.959  11.419  31.992  1.00  0.00              
ATOM    373  N   HIS    99       4.507  12.169  30.588  1.00  0.00              
ATOM    374  CA  HIS    99       5.566  12.028  31.592  1.00  0.00              
ATOM    375  C   HIS    99       5.294  12.944  32.791  1.00  0.00              
ATOM    376  O   HIS    99       5.351  12.518  33.929  1.00  0.00              
ATOM    377  N   LEU   100       4.963  14.200  32.518  1.00  0.00              
ATOM    378  CA  LEU   100       4.671  15.153  33.596  1.00  0.00              
ATOM    379  C   LEU   100       3.417  14.746  34.337  1.00  0.00              
ATOM    380  O   LEU   100       3.376  14.834  35.543  1.00  0.00              
ATOM    381  N   GLU   101       2.381  14.320  33.619  1.00  0.00              
ATOM    382  CA  GLU   101       1.149  13.900  34.287  1.00  0.00              
ATOM    383  C   GLU   101       1.402  12.743  35.262  1.00  0.00              
ATOM    384  O   GLU   101       0.844  12.708  36.363  1.00  0.00              
ATOM    385  N   LYS   102       2.220  11.774  34.858  1.00  0.00              
ATOM    386  CA  LYS   102       2.462  10.656  35.752  1.00  0.00              
ATOM    387  C   LYS   102       3.381  11.090  36.896  1.00  0.00              
ATOM    388  O   LYS   102       3.201  10.647  38.031  1.00  0.00              
ATOM    389  N   LEU   103       4.327  11.983  36.612  1.00  0.00              
ATOM    390  CA  LEU   103       5.231  12.462  37.669  1.00  0.00              
ATOM    391  C   LEU   103       4.443  13.252  38.734  1.00  0.00              
ATOM    392  O   LEU   103       4.741  13.152  39.931  1.00  0.00              
ATOM    393  N   SER   104       3.474  14.069  38.302  1.00  0.00              
ATOM    394  CA  SER   104       2.619  14.811  39.239  1.00  0.00              
ATOM    395  C   SER   104       1.887  13.830  40.162  1.00  0.00              
ATOM    396  O   SER   104       1.809  14.052  41.367  1.00  0.00              
ATOM    397  N   HIS   105       1.337  12.762  39.588  1.00  0.00              
ATOM    398  CA  HIS   105       0.631  11.746  40.394  1.00  0.00              
ATOM    399  C   HIS   105       1.575  11.069  41.388  1.00  0.00              
ATOM    400  O   HIS   105       1.206  10.811  42.541  1.00  0.00              
ATOM    401  N   LYS   106       2.788  10.779  40.940  1.00  0.00              
ATOM    402  CA  LYS   106       3.773  10.109  41.785  1.00  0.00              
ATOM    403  C   LYS   106       4.160  10.976  42.985  1.00  0.00              
ATOM    404  O   LYS   106       4.228  10.483  44.110  1.00  0.00              
ATOM    405  N   VAL   107       4.396  12.259  42.721  1.00  0.00              
ATOM    406  CA  VAL   107       4.787  13.265  43.723  1.00  0.00              
ATOM    407  C   VAL   107       3.724  13.353  44.814  1.00  0.00              
ATOM    408  O   VAL   107       4.024  13.358  46.001  1.00  0.00              
ATOM    409  N   HIS   108       2.477  13.441  44.382  1.00  0.00              
ATOM    410  CA  HIS   108       1.352  13.570  45.290  1.00  0.00              
ATOM    411  C   HIS   108       1.060  12.276  46.056  1.00  0.00              
ATOM    412  O   HIS   108       0.866  12.297  47.269  1.00  0.00              
ATOM    413  N   GLU   109       1.064  11.153  45.355  1.00  0.00              
ATOM    414  CA  GLU   109       0.787   9.873  45.997  1.00  0.00              
ATOM    415  C   GLU   109       1.847   9.470  47.018  1.00  0.00              
ATOM    416  O   GLU   109       1.523   8.886  48.050  1.00  0.00              
ATOM    417  N   SER   110       3.101   9.788  46.743  1.00  0.00              
ATOM    418  CA  SER   110       4.166   9.409  47.660  1.00  0.00              
ATOM    419  C   SER   110       4.089  10.278  48.940  1.00  0.00              
ATOM    420  O   SER   110       4.752   9.988  49.940  1.00  0.00              
ATOM    421  N   SER   111       3.236  11.310  48.930  1.00  0.00              
ATOM    422  CA  SER   111       3.032  12.176  50.105  1.00  0.00              
ATOM    423  C   SER   111       1.734  11.835  50.849  1.00  0.00              
ATOM    424  O   SER   111       1.426  12.450  51.876  1.00  0.00              
ATOM    425  N   SER   112       0.975  10.878  50.312  1.00  0.00              
ATOM    426  CA  SER   112      -0.274  10.453  50.921  1.00  0.00              
ATOM    427  C   SER   112      -1.520  11.159  50.404  1.00  0.00              
ATOM    428  O   SER   112      -2.602  11.048  51.001  1.00  0.00              
ATOM    429  N   VAL   113      -1.388  11.883  49.297  1.00  0.00              
ATOM    430  CA  VAL   113      -2.515  12.619  48.733  1.00  0.00              
ATOM    431  C   VAL   113      -3.046  12.001  47.458  1.00  0.00              
ATOM    432  O   VAL   113      -2.434  11.109  46.883  1.00  0.00              
ATOM    433  N   SER   114      -4.173  12.530  47.011  1.00  0.00              
ATOM    434  CA  SER   114      -4.812  12.126  45.774  1.00  0.00              
ATOM    435  C   SER   114      -4.850  13.422  44.966  1.00  0.00              
ATOM    436  O   SER   114      -5.127  14.475  45.523  1.00  0.00              
ATOM    437  N   ILE   115      -4.574  13.351  43.669  1.00  0.00              
ATOM    438  CA  ILE   115      -4.604  14.554  42.863  1.00  0.00              
ATOM    439  C   ILE   115      -6.031  14.859  42.397  1.00  0.00              
ATOM    440  O   ILE   115      -6.663  14.080  41.665  1.00  0.00              
ATOM    441  N   LEU   116      -6.559  15.987  42.859  1.00  0.00              
ATOM    442  CA  LEU   116      -7.912  16.440  42.524  1.00  0.00              
ATOM    443  C   LEU   116      -7.992  17.226  41.208  1.00  0.00              
ATOM    444  O   LEU   116      -8.913  17.051  40.387  1.00  0.00              
ATOM    445  N   ASP   117      -7.013  18.093  40.991  1.00  0.00              
ATOM    446  CA  ASP   117      -7.019  18.931  39.802  1.00  0.00              
ATOM    447  C   ASP   117      -5.626  19.539  39.758  1.00  0.00              
ATOM    448  O   ASP   117      -4.834  19.353  40.680  1.00  0.00              
ATOM    449  N   GLY   118      -5.316  20.251  38.685  1.00  0.00              
ATOM    450  CA  GLY   118      -4.031  20.904  38.588  1.00  0.00              
ATOM    451  C   GLY   118      -4.040  21.904  37.464  1.00  0.00              
ATOM    452  O   GLY   118      -4.892  21.859  36.538  1.00  0.00              
ATOM    453  N   ALA   119      -3.078  22.809  37.550  1.00  0.00              
ATOM    454  CA  ALA   119      -2.900  23.821  36.518  1.00  0.00              
ATOM    455  C   ALA   119      -1.427  23.987  36.214  1.00  0.00              
ATOM    456  O   ALA   119      -0.621  24.231  37.120  1.00  0.00              
ATOM    457  N   ASP   120      -1.061  23.854  34.951  1.00  0.00              
ATOM    458  CA  ASP   120       0.341  24.037  34.566  1.00  0.00              
ATOM    459  C   ASP   120       0.396  24.999  33.379  1.00  0.00              
ATOM    460  O   ASP   120      -0.242  24.757  32.351  1.00  0.00              
ATOM    461  N   ILE   121       1.092  26.118  33.544  1.00  0.00              
ATOM    462  CA  ILE   121       1.227  27.055  32.412  1.00  0.00              
ATOM    463  C   ILE   121       2.707  27.302  32.224  1.00  0.00              
ATOM    464  O   ILE   121       3.427  27.582  33.196  1.00  0.00              
ATOM    465  N   VAL   122       3.187  27.184  30.983  1.00  0.00              
ATOM    466  CA  VAL   122       4.596  27.424  30.727  1.00  0.00              
ATOM    467  C   VAL   122       4.658  28.706  29.899  1.00  0.00              
ATOM    468  O   VAL   122       4.061  28.762  28.843  1.00  0.00              
ATOM    469  N   TYR   123       5.326  29.735  30.412  1.00  0.00              
ATOM    470  CA  TYR   123       5.412  30.992  29.680  1.00  0.00              
ATOM    471  C   TYR   123       6.665  30.887  28.861  1.00  0.00              
ATOM    472  O   TYR   123       7.721  30.591  29.395  1.00  0.00              
ATOM    473  N   VAL   124       6.536  31.142  27.565  1.00  0.00              
ATOM    474  CA  VAL   124       7.681  30.955  26.680  1.00  0.00              
ATOM    475  C   VAL   124       7.961  32.089  25.706  1.00  0.00              
ATOM    476  O   VAL   124       7.156  33.001  25.518  1.00  0.00              
ATOM    477  N   ALA   125       9.123  31.996  25.071  1.00  0.00              
ATOM    478  CA  ALA   125       9.518  32.999  24.077  1.00  0.00              
ATOM    479  C   ALA   125      10.305  32.223  23.015  1.00  0.00              
ATOM    480  O   ALA   125      11.044  31.324  23.360  1.00  0.00              
ATOM    481  N   ARG   126      10.115  32.537  21.733  1.00  0.00              
ATOM    482  CA  ARG   126      10.840  31.829  20.673  1.00  0.00              
ATOM    483  C   ARG   126      12.335  32.053  20.863  1.00  0.00              
ATOM    484  O   ARG   126      12.776  33.193  21.044  1.00  0.00              
ATOM    485  N   VAL   127      13.109  30.965  20.834  1.00  0.00              
ATOM    486  CA  VAL   127      14.561  31.040  21.009  1.00  0.00              
ATOM    487  C   VAL   127      15.134  31.910  19.907  1.00  0.00              
ATOM    488  O   VAL   127      16.210  32.492  20.051  1.00  0.00              
ATOM    489  N   PRO   128      14.389  31.993  18.808  1.00  0.00              
ATOM    490  CA  PRO   128      14.784  32.794  17.660  1.00  0.00              
ATOM    491  C   PRO   128      14.444  34.268  17.911  1.00  0.00              
ATOM    492  O   PRO   128      15.381  35.027  18.271  1.00  0.00              
END
