
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0289AL380_3-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL380_3-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          4.415
LGA    M     225      M     225          3.683
LGA    E     226      E     226          3.642
LGA    K     227      K     227          4.301
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    -       -      Y     230           -
LGA    V     238      P     231          3.978
LGA    -       -      R     232           -
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    A     239      A     239           #
LGA    N     245      A     240          3.822
LGA    L     246      V     241          3.017
LGA    Q     247      I     242          3.858
LGA    D     248      H     243          3.010
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    -       -      L     246           -
LGA    Q     249      Q     247          2.084
LGA    -       -      D     248           -
LGA    -       -      Q     249           -
LGA    D     250      D     250          3.188
LGA    W     251      W     251          4.411
LGA    -       -      K     252           -
LGA    -       -      P     253           -
LGA    C     275      L     254          3.764
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    -       -      L     271           -
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    T     276      P     279          2.937
LGA    V     277      V     280          2.511
LGA    Y     278      F     281          1.889
LGA    P     279      V     282          4.123
LGA    K     291      N     283          4.456
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    E     292      Y     287           #
LGA    A     293      Y     288          2.383
LGA    -       -      E     289           -
LGA    F     294      K     290          4.345
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22   74    5.0     20    3.58    40.00     16.343     0.543

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.528055 * X  +  -0.771469 * Y  +   0.354954 * Z  +  12.132805
  Y_new =   0.566185 * X  +   0.008310 * Y  +  -0.824236 * Z  +  54.110527
  Z_new =   0.632923 * X  +   0.636212 * Y  +   0.441183 * Z  + -40.085533 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.964478   -2.177114  [ DEG:    55.2605   -124.7395 ]
  Theta =  -0.685323   -2.456270  [ DEG:   -39.2661   -140.7339 ]
  Phi   =   0.820230   -2.321363  [ DEG:    46.9957   -133.0043 ]
 
# 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: T0289AL380_3-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL380_3-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22   74   5.0   20   3.58   40.00  16.343
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL380_3-D2
REMARK Aligment from pdb entry: 2bcoB
ATOM    773  N   ILE   224      30.880  26.694  19.255  1.00  0.00              
ATOM    774  CA  ILE   224      29.572  26.592  19.894  1.00  0.00              
ATOM    775  C   ILE   224      28.890  27.922  20.184  1.00  0.00              
ATOM    776  O   ILE   224      29.523  28.883  20.621  1.00  0.00              
ATOM    777  N   MET   225      27.587  27.956  19.923  1.00  0.00              
ATOM    778  CA  MET   225      26.772  29.138  20.149  1.00  0.00              
ATOM    779  C   MET   225      25.618  28.754  21.068  1.00  0.00              
ATOM    780  O   MET   225      24.449  28.846  20.691  1.00  0.00              
ATOM    781  N   GLU   226      25.958  28.310  22.272  1.00  0.00              
ATOM    782  CA  GLU   226      24.962  27.906  23.255  1.00  0.00              
ATOM    783  C   GLU   226      23.991  29.050  23.532  1.00  0.00              
ATOM    784  O   GLU   226      24.272  29.935  24.341  1.00  0.00              
ATOM    785  N   LYS   227      22.849  29.025  22.852  1.00  0.00              
ATOM    786  CA  LYS   227      21.834  30.059  23.016  1.00  0.00              
ATOM    787  C   LYS   227      20.694  29.582  23.910  1.00  0.00              
ATOM    788  O   LYS   227      20.503  30.091  25.017  1.00  0.00              
ATOM    789  N   VAL   238      22.049  41.227  34.235  1.00  0.00              
ATOM    790  CA  VAL   238      22.791  41.630  35.422  1.00  0.00              
ATOM    791  C   VAL   238      23.673  42.840  35.134  1.00  0.00              
ATOM    792  O   VAL   238      23.525  43.892  35.751  1.00  0.00              
ATOM    793  N   ALA   239      24.589  42.686  34.186  1.00  0.00              
ATOM    794  CA  ALA   239      25.504  43.761  33.822  1.00  0.00              
ATOM    795  C   ALA   239      24.806  44.915  33.112  1.00  0.00              
ATOM    796  O   ALA   239      23.590  44.893  32.920  1.00  0.00              
ATOM    797  N   ASN   245      25.587  45.919  32.728  1.00  0.00              
ATOM    798  CA  ASN   245      25.058  47.098  32.045  1.00  0.00              
ATOM    799  C   ASN   245      25.214  46.980  30.534  1.00  0.00              
ATOM    800  O   ASN   245      25.725  45.981  30.032  1.00  0.00              
ATOM    801  N   LEU   246      24.772  48.008  29.813  1.00  0.00              
ATOM    802  CA  LEU   246      24.869  48.021  28.358  1.00  0.00              
ATOM    803  C   LEU   246      26.219  48.560  27.885  1.00  0.00              
ATOM    804  O   LEU   246      26.401  48.845  26.698  1.00  0.00              
ATOM    805  N   GLN   247      27.164  48.695  28.810  1.00  0.00              
ATOM    806  CA  GLN   247      28.494  49.205  28.479  1.00  0.00              
ATOM    807  C   GLN   247      29.524  48.078  28.413  1.00  0.00              
ATOM    808  O   GLN   247      30.676  48.305  28.049  1.00  0.00              
ATOM    809  N   ASP   248      29.099  46.866  28.760  1.00  0.00              
ATOM    810  CA  ASP   248      29.978  45.697  28.757  1.00  0.00              
ATOM    811  C   ASP   248      30.570  45.356  27.393  1.00  0.00              
ATOM    812  O   ASP   248      30.050  45.769  26.355  1.00  0.00              
ATOM    813  N   GLN   249      31.658  44.589  27.409  1.00  0.00              
ATOM    814  CA  GLN   249      32.347  44.186  26.186  1.00  0.00              
ATOM    815  C   GLN   249      32.028  42.756  25.758  1.00  0.00              
ATOM    816  O   GLN   249      31.686  41.909  26.587  1.00  0.00              
ATOM    817  N   ASP   250      32.145  42.498  24.457  1.00  0.00              
ATOM    818  CA  ASP   250      31.871  41.179  23.896  1.00  0.00              
ATOM    819  C   ASP   250      32.912  40.165  24.350  1.00  0.00              
ATOM    820  O   ASP   250      33.984  40.534  24.828  1.00  0.00              
ATOM    821  N   TRP   251      32.585  38.885  24.193  1.00  0.00              
ATOM    822  CA  TRP   251      33.479  37.801  24.596  1.00  0.00              
ATOM    823  C   TRP   251      33.826  37.908  26.074  1.00  0.00              
ATOM    824  O   TRP   251      32.989  38.298  26.888  1.00  0.00              
ATOM    825  N   CYS   275      32.920  34.453  26.402  1.00  0.00              
ATOM    826  CA  CYS   275      31.918  34.339  27.453  1.00  0.00              
ATOM    827  C   CYS   275      30.529  34.603  26.886  1.00  0.00              
ATOM    828  O   CYS   275      29.763  33.675  26.631  1.00  0.00              
ATOM    829  N   THR   276      30.212  35.880  26.698  1.00  0.00              
ATOM    830  CA  THR   276      28.925  36.297  26.157  1.00  0.00              
ATOM    831  C   THR   276      29.201  37.200  24.958  1.00  0.00              
ATOM    832  O   THR   276      30.230  37.877  24.915  1.00  0.00              
ATOM    833  N   VAL   277      28.296  37.205  23.984  1.00  0.00              
ATOM    834  CA  VAL   277      28.479  38.031  22.798  1.00  0.00              
ATOM    835  C   VAL   277      27.174  38.674  22.339  1.00  0.00              
ATOM    836  O   VAL   277      26.103  38.081  22.452  1.00  0.00              
ATOM    837  N   TYR   278      27.278  39.897  21.832  1.00  0.00              
ATOM    838  CA  TYR   278      26.127  40.634  21.317  1.00  0.00              
ATOM    839  C   TYR   278      24.943  40.835  22.257  1.00  0.00              
ATOM    840  O   TYR   278      23.794  40.758  21.818  1.00  0.00              
ATOM    841  N   PRO   279      25.187  41.096  23.551  1.00  0.00              
ATOM    842  CA  PRO   279      24.044  41.294  24.448  1.00  0.00              
ATOM    843  C   PRO   279      23.301  42.605  24.169  1.00  0.00              
ATOM    844  O   PRO   279      23.924  43.645  23.948  1.00  0.00              
ATOM    845  N   LYS   291      21.970  42.551  24.177  1.00  0.00              
ATOM    846  CA  LYS   291      21.145  43.733  23.915  1.00  0.00              
ATOM    847  C   LYS   291      19.712  43.496  24.388  1.00  0.00              
ATOM    848  O   LYS   291      18.999  42.653  23.844  1.00  0.00              
ATOM    849  N   GLU   292      19.291  44.254  25.394  1.00  0.00              
ATOM    850  CA  GLU   292      17.952  44.113  25.951  1.00  0.00              
ATOM    851  C   GLU   292      16.925  45.076  25.350  1.00  0.00              
ATOM    852  O   GLU   292      15.822  45.216  25.879  1.00  0.00              
ATOM    853  N   ALA   293      17.278  45.736  24.252  1.00  0.00              
ATOM    854  CA  ALA   293      16.359  46.678  23.615  1.00  0.00              
ATOM    855  C   ALA   293      15.793  46.159  22.296  1.00  0.00              
ATOM    856  O   ALA   293      15.244  46.925  21.506  1.00  0.00              
ATOM    857  N   PHE   294      15.934  44.860  22.059  1.00  0.00              
ATOM    858  CA  PHE   294      15.418  44.253  20.838  1.00  0.00              
ATOM    859  C   PHE   294      14.192  43.409  21.158  1.00  0.00              
ATOM    860  O   PHE   294      13.566  43.582  22.207  1.00  0.00              
END
