
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0386AL380_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_4-D2.T0386_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    N     219      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    P     220      K     222           #
LGA    E     221      I     223          1.361
LGA    K     222      -       -           -
LGA    I     223      R     224          3.470
LGA    R     224      L     225          2.932
LGA    L     225      -       -           -
LGA    L     226      L     226           #
LGA    -       -      K     227           -
LGA    -       -      E     228           -
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    K     227      E     264          2.114
LGA    E     228      G     265          4.920
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      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    F     229      N     278          2.259
LGA    M     230      I     279          1.164
LGA    H     231      D     280          0.978
LGA    T     232      H     281          0.860
LGA    M     233      L     282          0.325
LGA    K     234      P     283          0.763
LGA    N     235      P     284          2.690
LGA    T     236      E     285          4.486
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
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)   18   81    5.0     13    2.59     0.00     12.379     0.483

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.522660 * X  +  -0.332771 * Y  +  -0.784914 * Z  +  33.941269
  Y_new =  -0.689626 * X  +  -0.706325 * Y  +  -0.159756 * Z  + 110.884598
  Z_new =  -0.501242 * X  +   0.624795 * Y  +  -0.598655 * Z  +  98.035561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.334832   -0.806761  [ DEG:   133.7760    -46.2240 ]
  Theta =   0.525033    2.616559  [ DEG:    30.0822    149.9178 ]
  Phi   =  -0.922265    2.219327  [ DEG:   -52.8419    127.1581 ]
 
# 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: T0386AL380_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   81   5.0   13   2.59    0.00  12.379
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_4-D2
REMARK Aligment from pdb entry: 1eh9A
ATOM    517  N   ASN   219       8.963  68.223  74.241  1.00  0.00              
ATOM    518  CA  ASN   219       7.821  67.627  73.642  1.00  0.00              
ATOM    519  C   ASN   219       7.063  66.822  74.677  1.00  0.00              
ATOM    520  O   ASN   219       7.619  66.303  75.653  1.00  0.00              
ATOM    521  N   PRO   220       5.784  66.719  74.439  1.00  0.00              
ATOM    522  CA  PRO   220       4.876  66.031  75.314  1.00  0.00              
ATOM    523  C   PRO   220       5.317  64.637  75.662  1.00  0.00              
ATOM    524  O   PRO   220       5.159  64.221  76.799  1.00  0.00              
ATOM    525  N   GLU   221       5.845  63.880  74.704  1.00  0.00              
ATOM    526  CA  GLU   221       6.245  62.534  75.096  1.00  0.00              
ATOM    527  C   GLU   221       7.259  62.646  76.209  1.00  0.00              
ATOM    528  O   GLU   221       7.121  62.017  77.262  1.00  0.00              
ATOM    529  N   LYS   222       8.249  63.512  75.942  1.00  0.00              
ATOM    530  CA  LYS   222       9.321  63.849  76.852  1.00  0.00              
ATOM    531  C   LYS   222       8.719  64.172  78.220  1.00  0.00              
ATOM    532  O   LYS   222       8.718  63.351  79.175  1.00  0.00              
ATOM    533  N   ILE   223       8.125  65.356  78.314  1.00  0.00              
ATOM    534  CA  ILE   223       7.470  65.735  79.557  1.00  0.00              
ATOM    535  C   ILE   223       6.757  64.548  80.267  1.00  0.00              
ATOM    536  O   ILE   223       6.534  64.503  81.462  1.00  0.00              
ATOM    537  N   ARG   224       6.356  63.538  79.542  1.00  0.00              
ATOM    538  CA  ARG   224       5.692  62.449  80.214  1.00  0.00              
ATOM    539  C   ARG   224       6.738  61.533  80.801  1.00  0.00              
ATOM    540  O   ARG   224       6.575  60.935  81.886  1.00  0.00              
ATOM    541  N   LEU   225       7.811  61.421  80.034  1.00  0.00              
ATOM    542  CA  LEU   225       8.900  60.591  80.426  1.00  0.00              
ATOM    543  C   LEU   225       9.461  61.114  81.716  1.00  0.00              
ATOM    544  O   LEU   225       9.525  60.399  82.709  1.00  0.00              
ATOM    545  N   LEU   226       9.860  62.394  81.684  1.00  0.00              
ATOM    546  CA  LEU   226      10.417  63.050  82.867  1.00  0.00              
ATOM    547  C   LEU   226       9.644  62.657  84.090  1.00  0.00              
ATOM    548  O   LEU   226      10.127  61.969  85.011  1.00  0.00              
ATOM    549  N   LYS   227       8.420  63.121  84.084  1.00  0.00              
ATOM    550  CA  LYS   227       7.588  62.806  85.185  1.00  0.00              
ATOM    551  C   LYS   227       7.857  61.392  85.665  1.00  0.00              
ATOM    552  O   LYS   227       8.085  61.172  86.848  1.00  0.00              
ATOM    553  N   GLU   228       7.882  60.434  84.749  1.00  0.00              
ATOM    554  CA  GLU   228       8.154  59.059  85.154  1.00  0.00              
ATOM    555  C   GLU   228       9.373  58.963  86.070  1.00  0.00              
ATOM    556  O   GLU   228       9.264  58.597  87.267  1.00  0.00              
ATOM    557  N   PHE   229      10.527  59.289  85.440  1.00  0.00              
ATOM    558  CA  PHE   229      11.872  59.324  86.015  1.00  0.00              
ATOM    559  C   PHE   229      11.901  59.729  87.469  1.00  0.00              
ATOM    560  O   PHE   229      12.329  58.992  88.371  1.00  0.00              
ATOM    561  N   MET   230      11.415  60.926  87.685  1.00  0.00              
ATOM    562  CA  MET   230      11.404  61.471  88.996  1.00  0.00              
ATOM    563  C   MET   230      10.470  60.867  89.959  1.00  0.00              
ATOM    564  O   MET   230      10.630  61.145  91.112  1.00  0.00              
ATOM    565  N   HIS   231       9.471  60.108  89.528  1.00  0.00              
ATOM    566  CA  HIS   231       8.565  59.606  90.524  1.00  0.00              
ATOM    567  C   HIS   231       8.790  58.185  90.682  1.00  0.00              
ATOM    568  O   HIS   231       8.257  57.564  91.592  1.00  0.00              
ATOM    569  N   THR   232       9.593  57.688  89.780  1.00  0.00              
ATOM    570  CA  THR   232       9.877  56.283  89.821  1.00  0.00              
ATOM    571  C   THR   232      11.237  55.997  90.408  1.00  0.00              
ATOM    572  O   THR   232      11.741  54.856  90.407  1.00  0.00              
ATOM    573  N   MET   233      11.792  57.102  90.940  1.00  0.00              
ATOM    574  CA  MET   233      13.069  57.141  91.631  1.00  0.00              
ATOM    575  C   MET   233      12.876  56.674  93.072  1.00  0.00              
ATOM    576  O   MET   233      11.753  56.729  93.602  1.00  0.00              
ATOM    577  N   LYS   234      13.982  56.219  93.707  1.00  0.00              
ATOM    578  CA  LYS   234      13.996  55.743  95.115  1.00  0.00              
ATOM    579  C   LYS   234      13.952  56.925  96.053  1.00  0.00              
ATOM    580  O   LYS   234      13.655  56.797  97.230  1.00  0.00              
ATOM    581  N   ASN   235      14.235  58.073  95.437  1.00  0.00              
ATOM    582  CA  ASN   235      14.242  59.380  96.004  1.00  0.00              
ATOM    583  C   ASN   235      12.917  59.807  96.554  1.00  0.00              
ATOM    584  O   ASN   235      12.087  58.987  96.942  1.00  0.00              
ATOM    585  N   THR   236      12.775  61.096  96.712  1.00  0.00              
ATOM    586  CA  THR   236      11.598  61.607  97.333  1.00  0.00              
ATOM    587  C   THR   236      11.061  62.686  96.506  1.00  0.00              
ATOM    588  O   THR   236      11.344  63.857  96.684  1.00  0.00              
END
