
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0386AL316_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL316_1-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    N     219      P     220          3.178
LGA    P     220      E     221          3.475
LGA    E     221      K     222          2.242
LGA    N     235      I     223          1.372
LGA    T     236      R     224          1.854
LGA    G     237      L     225          2.359
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    R     238      E     228          2.622
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    N     239      E     264          3.412
LGA    V     240      G     265          3.635
LGA    N     241      F     266          3.053
LGA    D     242      A     267           -
LGA    R     243      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    P     244      N     278          3.172
LGA    V     245      I     279          3.023
LGA    M     246      D     280          3.113
LGA    V     247      H     281          2.530
LGA    A     248      L     282          2.401
LGA    K     249      P     283          4.135
LGA    E     250      P     284          2.436
LGA    G     251      E     285          4.184
LGA    E     252      Q     286          3.491
LGA    T     253      L     287          3.155
LGA    Y     254      K     288          1.241
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   81    5.0     21    2.96     0.00     15.754     0.686

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.872179 * X  +   0.444435 * Y  +   0.204405 * Z  +   0.955500
  Y_new =  -0.137419 * X  +   0.623613 * Y  +  -0.769560 * Z  +  23.371756
  Z_new =  -0.469490 * X  +   0.643105 * Y  +   0.604976 * Z  +  43.254776 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.815938   -2.325654  [ DEG:    46.7498   -133.2502 ]
  Theta =   0.488713    2.652880  [ DEG:    28.0012    151.9988 ]
  Phi   =  -0.156273    2.985319  [ DEG:    -8.9538    171.0462 ]
 
# 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: T0386AL316_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL316_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   81   5.0   21   2.96    0.00  15.754
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL316_1-D2
REMARK Aligment from pdb entry: 2f6s_A
ATOM    621  N   ASN   219      -1.310  57.908  78.900  1.00  0.00              
ATOM    622  CA  ASN   219      -1.089  57.656  77.469  1.00  0.00              
ATOM    623  C   ASN   219       0.007  58.545  76.877  1.00  0.00              
ATOM    624  O   ASN   219       0.478  58.309  75.770  1.00  0.00              
ATOM    625  N   PRO   220       0.416  59.548  77.638  1.00  0.00              
ATOM    626  CA  PRO   220       1.394  60.513  77.191  1.00  0.00              
ATOM    627  C   PRO   220       2.825  59.996  77.349  1.00  0.00              
ATOM    628  O   PRO   220       3.640  60.567  78.083  1.00  0.00              
ATOM    629  N   GLU   221       3.134  58.929  76.627  1.00  0.00              
ATOM    630  CA  GLU   221       4.333  58.137  76.907  1.00  0.00              
ATOM    631  C   GLU   221       5.633  58.784  76.446  1.00  0.00              
ATOM    632  O   GLU   221       6.721  58.257  76.706  1.00  0.00              
ATOM    633  N   ASN   235       5.517  59.911  75.752  1.00  0.00              
ATOM    634  CA  ASN   235       6.655  60.489  75.057  1.00  0.00              
ATOM    635  C   ASN   235       7.016  61.896  75.510  1.00  0.00              
ATOM    636  O   ASN   235       8.078  62.399  75.147  1.00  0.00              
ATOM    637  N   THR   236       6.136  62.531  76.285  1.00  0.00              
ATOM    638  CA  THR   236       6.423  63.852  76.823  1.00  0.00              
ATOM    639  C   THR   236       7.665  63.834  77.743  1.00  0.00              
ATOM    640  O   THR   236       7.642  63.195  78.815  1.00  0.00              
ATOM    641  N   GLY   237       8.763  64.524  77.337  1.00  0.00              
ATOM    642  CA  GLY   237       9.943  64.346  78.202  1.00  0.00              
ATOM    643  C   GLY   237       9.815  65.082  79.555  1.00  0.00              
ATOM    644  O   GLY   237      10.457  64.657  80.524  1.00  0.00              
ATOM    645  N   ARG   238       8.977  66.125  79.640  1.00  0.00              
ATOM    646  CA  ARG   238       8.695  66.753  80.947  1.00  0.00              
ATOM    647  C   ARG   238       8.069  65.728  81.915  1.00  0.00              
ATOM    648  O   ARG   238       8.544  65.545  83.047  1.00  0.00              
ATOM    649  N   ASN   239       7.018  65.054  81.446  1.00  0.00              
ATOM    650  CA  ASN   239       6.347  63.990  82.189  1.00  0.00              
ATOM    651  C   ASN   239       7.335  62.894  82.613  1.00  0.00              
ATOM    652  O   ASN   239       7.300  62.419  83.744  1.00  0.00              
ATOM    653  N   VAL   240       8.221  62.522  81.696  1.00  0.00              
ATOM    654  CA  VAL   240       9.182  61.464  81.933  1.00  0.00              
ATOM    655  C   VAL   240      10.218  61.873  82.980  1.00  0.00              
ATOM    656  O   VAL   240      10.558  61.086  83.862  1.00  0.00              
ATOM    657  N   ASN   241      10.693  63.111  82.898  1.00  0.00              
ATOM    658  CA  ASN   241      11.660  63.632  83.859  1.00  0.00              
ATOM    659  C   ASN   241      11.044  63.750  85.260  1.00  0.00              
ATOM    660  O   ASN   241      11.666  63.341  86.239  1.00  0.00              
ATOM    661  N   ASP   242       9.827  64.285  85.347  1.00  0.00              
ATOM    662  CA  ASP   242       9.084  64.296  86.608  1.00  0.00              
ATOM    663  C   ASP   242       8.963  62.896  87.203  1.00  0.00              
ATOM    664  O   ASP   242       9.132  62.709  88.410  1.00  0.00              
ATOM    665  N   ARG   243       8.691  61.920  86.343  1.00  0.00              
ATOM    666  CA  ARG   243       8.613  60.536  86.734  1.00  0.00              
ATOM    667  C   ARG   243       9.913  60.012  87.312  1.00  0.00              
ATOM    668  O   ARG   243       9.922  59.391  88.390  1.00  0.00              
ATOM    669  N   PRO   244      11.017  60.256  86.614  1.00  0.00              
ATOM    670  CA  PRO   244      12.300  59.718  87.046  1.00  0.00              
ATOM    671  C   PRO   244      12.799  60.422  88.296  1.00  0.00              
ATOM    672  O   PRO   244      13.409  59.796  89.143  1.00  0.00              
ATOM    673  N   VAL   245      12.521  61.719  88.421  1.00  0.00              
ATOM    674  CA  VAL   245      12.860  62.462  89.624  1.00  0.00              
ATOM    675  C   VAL   245      12.162  61.819  90.830  1.00  0.00              
ATOM    676  O   VAL   245      12.750  61.694  91.895  1.00  0.00              
ATOM    677  N   MET   246      10.916  61.396  90.662  1.00  0.00              
ATOM    678  CA  MET   246      10.179  60.789  91.754  1.00  0.00              
ATOM    679  C   MET   246      10.754  59.413  92.073  1.00  0.00              
ATOM    680  O   MET   246      10.891  59.047  93.248  1.00  0.00              
ATOM    681  N   VAL   247      11.112  58.665  91.026  1.00  0.00              
ATOM    682  CA  VAL   247      11.735  57.371  91.199  1.00  0.00              
ATOM    683  C   VAL   247      12.975  57.499  92.097  1.00  0.00              
ATOM    684  O   VAL   247      13.165  56.704  93.018  1.00  0.00              
ATOM    685  N   ALA   248      13.809  58.505  91.828  1.00  0.00              
ATOM    686  CA  ALA   248      15.010  58.755  92.635  1.00  0.00              
ATOM    687  C   ALA   248      14.665  59.253  94.035  1.00  0.00              
ATOM    688  O   ALA   248      15.380  58.971  95.004  1.00  0.00              
ATOM    689  N   LYS   249      13.551  59.973  94.131  1.00  0.00              
ATOM    690  CA  LYS   249      13.054  60.410  95.410  1.00  0.00              
ATOM    691  C   LYS   249      12.660  59.237  96.306  1.00  0.00              
ATOM    692  O   LYS   249      12.783  59.336  97.532  1.00  0.00              
ATOM    693  N   GLU   250      12.192  58.137  95.694  1.00  0.00              
ATOM    694  CA  GLU   250      11.768  56.949  96.426  1.00  0.00              
ATOM    695  C   GLU   250      12.957  56.357  97.187  1.00  0.00              
ATOM    696  O   GLU   250      12.778  55.704  98.205  1.00  0.00              
ATOM    697  N   GLY   251      14.160  56.575  96.650  1.00  0.00              
ATOM    698  CA  GLY   251      15.392  56.076  97.220  1.00  0.00              
ATOM    699  C   GLY   251      16.024  57.070  98.203  1.00  0.00              
ATOM    700  O   GLY   251      17.129  56.831  98.694  1.00  0.00              
ATOM    701  N   GLU   252      15.335  58.186  98.480  1.00  0.00              
ATOM    702  CA  GLU   252      15.815  59.186  99.439  1.00  0.00              
ATOM    703  C   GLU   252      16.559  60.395  98.877  1.00  0.00              
ATOM    704  O   GLU   252      17.178  61.152  99.631  1.00  0.00              
ATOM    705  N   THR   253      16.515  60.589  97.561  1.00  0.00              
ATOM    706  CA  THR   253      17.119  61.777  96.951  1.00  0.00              
ATOM    707  C   THR   253      16.127  62.940  96.957  1.00  0.00              
ATOM    708  O   THR   253      15.069  62.858  96.329  1.00  0.00              
ATOM    709  N   TYR   254      16.473  64.020  97.666  1.00  0.00              
ATOM    710  CA  TYR   254      15.543  65.129  97.911  1.00  0.00              
ATOM    711  C   TYR   254      15.964  66.420  97.234  1.00  0.00              
ATOM    712  O   TYR   254      15.842  66.563  96.012  1.00  0.00              
END
