
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0386AL243_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL243_1-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           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      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    N     219      A     261          0.791
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    P     220      G     265          1.909
LGA    E     221      F     266          3.283
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    -       -      N     278           -
LGA    K     222      I     279          1.580
LGA    I     223      D     280          0.772
LGA    R     224      H     281          2.336
LGA    L     225      L     282          2.783
LGA    L     226      P     283          2.607
LGA    K     227      -       -           -
LGA    E     228      P     284          1.775
LGA    F     229      E     285          1.930
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)   11   81    5.0     10    2.12    10.00      9.946     0.450

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.086929 * X  +  -0.153869 * Y  +  -0.984260 * Z  +  18.988539
  Y_new =  -0.979330 * X  +  -0.194331 * Y  +  -0.056114 * Z  +  65.996826
  Z_new =  -0.182638 * X  +   0.968793 * Y  +  -0.167582 * Z  +  36.661514 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.742081   -1.399511  [ DEG:    99.8139    -80.1861 ]
  Theta =   0.183669    2.957924  [ DEG:    10.5234    169.4766 ]
  Phi   =  -1.482265    1.659328  [ DEG:   -84.9275     95.0725 ]
 
# 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: T0386AL243_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL243_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   81   5.0   10   2.12   10.00   9.946
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL243_1-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    657  N   ASN   219      14.525  67.373  87.661  1.00  0.00              
ATOM    658  CA  ASN   219      14.656  66.113  86.938  1.00  0.00              
ATOM    659  C   ASN   219      13.291  65.784  86.374  1.00  0.00              
ATOM    660  O   ASN   219      12.286  66.080  87.000  1.00  0.00              
ATOM    661  N   PRO   220      13.220  65.175  85.196  1.00  0.00              
ATOM    662  CA  PRO   220      11.914  64.713  84.750  1.00  0.00              
ATOM    663  C   PRO   220      11.652  63.253  85.073  1.00  0.00              
ATOM    664  O   PRO   220      10.648  62.697  84.650  1.00  0.00              
ATOM    665  N   GLU   221      12.530  62.657  85.867  1.00  0.00              
ATOM    666  CA  GLU   221      12.350  61.272  86.295  1.00  0.00              
ATOM    667  C   GLU   221      11.517  61.293  87.592  1.00  0.00              
ATOM    668  O   GLU   221      12.020  60.971  88.662  1.00  0.00              
ATOM    669  N   LYS   222      10.243  61.669  87.476  1.00  0.00              
ATOM    670  CA  LYS   222       9.457  62.168  88.611  1.00  0.00              
ATOM    671  C   LYS   222       9.011  61.062  89.580  1.00  0.00              
ATOM    672  O   LYS   222       8.579  61.361  90.710  1.00  0.00              
ATOM    673  N   ILE   223       9.120  59.808  89.141  1.00  0.00              
ATOM    674  CA  ILE   223       8.627  58.670  89.909  1.00  0.00              
ATOM    675  C   ILE   223       9.737  57.692  90.271  1.00  0.00              
ATOM    676  O   ILE   223       9.475  56.581  90.704  1.00  0.00              
ATOM    677  N   ARG   224      10.973  58.116  90.087  1.00  0.00              
ATOM    678  CA  ARG   224      12.119  57.288  90.393  1.00  0.00              
ATOM    679  C   ARG   224      12.274  57.091  91.912  1.00  0.00              
ATOM    680  O   ARG   224      12.295  58.057  92.675  1.00  0.00              
ATOM    681  N   LEU   225      12.341  55.836  92.350  1.00  0.00              
ATOM    682  CA  LEU   225      12.441  55.522  93.776  1.00  0.00              
ATOM    683  C   LEU   225      13.625  56.221  94.479  1.00  0.00              
ATOM    684  O   LEU   225      13.473  56.716  95.591  1.00  0.00              
ATOM    685  N   LEU   226      14.780  56.286  93.826  1.00  0.00              
ATOM    686  CA  LEU   226      15.960  56.875  94.436  1.00  0.00              
ATOM    687  C   LEU   226      15.827  58.395  94.607  1.00  0.00              
ATOM    688  O   LEU   226      16.183  58.953  95.659  1.00  0.00              
ATOM    689  N   LYS   227      15.303  59.065  93.581  1.00  0.00              
ATOM    690  CA  LYS   227      15.035  60.496  93.641  1.00  0.00              
ATOM    691  C   LYS   227      13.992  60.789  94.710  1.00  0.00              
ATOM    692  O   LYS   227      14.166  61.718  95.501  1.00  0.00              
ATOM    693  N   GLU   228      12.913  60.010  94.751  1.00  0.00              
ATOM    694  CA  GLU   228      11.887  60.226  95.775  1.00  0.00              
ATOM    695  C   GLU   228      12.478  60.027  97.199  1.00  0.00              
ATOM    696  O   GLU   228      12.453  60.934  98.025  1.00  0.00              
ATOM    697  N   PHE   229      13.054  58.869  97.466  1.00  0.00              
ATOM    698  CA  PHE   229      13.487  58.561  98.823  1.00  0.00              
ATOM    699  C   PHE   229      14.739  59.297  99.335  1.00  0.00              
ATOM    700  O   PHE   229      14.755  59.701 100.487  1.00  0.00              
END
