
#######################################################
#                                                     #
#                        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 T0386AL243_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL243_2-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    N     219      K     222          3.695
LGA    P     220      I     223          1.981
LGA    K     222      R     224          2.770
LGA    I     223      L     225          4.090
LGA    R     224      L     226          2.148
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    L     225      M     230          4.856
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    L     226      A     261           #
LGA    K     227      G     262          2.380
LGA    -       -      L     263           -
LGA    E     228      E     264          2.674
LGA    F     229      G     265          2.097
LGA    M     230      F     266          2.050
LGA    H     231      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    T     232      G     277          4.747
LGA    M     233      N     278          3.976
LGA    K     234      I     279          3.168
LGA    N     235      D     280          1.290
LGA    T     236      H     281          0.968
LGA    G     237      L     282          1.897
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
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     16    3.02     6.25     12.430     0.512

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.991832 * X  +   0.091569 * Y  +   0.088794 * Z  +  23.296452
  Y_new =   0.059558 * X  +   0.283126 * Y  +  -0.957232 * Z  +  45.020523
  Z_new =  -0.112793 * X  +   0.954701 * Y  +   0.275360 * Z  +  32.301968 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.289992   -1.851600  [ DEG:    73.9111   -106.0889 ]
  Theta =   0.113033    3.028560  [ DEG:     6.4763    173.5237 ]
  Phi   =   0.059976   -3.081617  [ DEG:     3.4364   -176.5636 ]
 
# 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_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL243_2-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   16   3.02    6.25  12.430
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL243_2-D2
REMARK Aligment from pdb entry: 2f6sA
ATOM    621  N   ASN   219       3.161  58.758  77.563  1.00  0.00              
ATOM    622  CA  ASN   219       3.159  60.140  77.088  1.00  0.00              
ATOM    623  C   ASN   219       3.972  60.272  75.810  1.00  0.00              
ATOM    624  O   ASN   219       4.985  59.576  75.640  1.00  0.00              
ATOM    625  N   PRO   220       3.524  61.168  74.925  1.00  0.00              
ATOM    626  CA  PRO   220       4.270  61.545  73.717  1.00  0.00              
ATOM    627  C   PRO   220       5.361  62.581  73.996  1.00  0.00              
ATOM    628  O   PRO   220       6.222  62.830  73.160  1.00  0.00              
ATOM    629  N   LYS   222       5.323  63.158  75.187  1.00  0.00              
ATOM    630  CA  LYS   222       6.241  64.204  75.574  1.00  0.00              
ATOM    631  C   LYS   222       7.584  63.643  76.046  1.00  0.00              
ATOM    632  O   LYS   222       7.993  63.834  77.198  1.00  0.00              
ATOM    633  N   ILE   223       8.282  62.979  75.137  1.00  0.00              
ATOM    634  CA  ILE   223       9.407  62.122  75.512  1.00  0.00              
ATOM    635  C   ILE   223      10.675  62.880  75.883  1.00  0.00              
ATOM    636  O   ILE   223      11.667  62.273  76.306  1.00  0.00              
ATOM    637  N   ARG   224      10.647  64.197  75.710  1.00  0.00              
ATOM    638  CA  ARG   224      11.859  64.995  75.796  1.00  0.00              
ATOM    639  C   ARG   224      11.824  66.069  76.873  1.00  0.00              
ATOM    640  O   ARG   224      12.860  66.660  77.177  1.00  0.00              
ATOM    641  N   LEU   225      10.645  66.331  77.437  1.00  0.00              
ATOM    642  CA  LEU   225      10.525  67.292  78.521  1.00  0.00              
ATOM    643  C   LEU   225      11.350  66.863  79.755  1.00  0.00              
ATOM    644  O   LEU   225      11.045  65.829  80.386  1.00  0.00              
ATOM    645  N   LEU   226      12.406  67.640  80.112  1.00  0.00              
ATOM    646  CA  LEU   226      13.217  67.091  81.213  1.00  0.00              
ATOM    647  C   LEU   226      12.513  67.184  82.585  1.00  0.00              
ATOM    648  O   LEU   226      12.826  66.376  83.469  1.00  0.00              
ATOM    649  N   LYS   227      11.555  68.106  82.752  1.00  0.00              
ATOM    650  CA  LYS   227      10.740  68.124  83.985  1.00  0.00              
ATOM    651  C   LYS   227       9.971  66.797  84.143  1.00  0.00              
ATOM    652  O   LYS   227      10.037  66.141  85.195  1.00  0.00              
ATOM    653  N   GLU   228       9.265  66.405  83.082  1.00  0.00              
ATOM    654  CA  GLU   228       8.540  65.138  83.020  1.00  0.00              
ATOM    655  C   GLU   228       9.465  63.948  83.313  1.00  0.00              
ATOM    656  O   GLU   228       9.103  63.038  84.054  1.00  0.00              
ATOM    657  N   PHE   229      10.662  63.985  82.739  1.00  0.00              
ATOM    658  CA  PHE   229      11.622  62.910  82.882  1.00  0.00              
ATOM    659  C   PHE   229      12.149  62.817  84.314  1.00  0.00              
ATOM    660  O   PHE   229      12.268  61.723  84.865  1.00  0.00              
ATOM    661  N   MET   230      12.435  63.963  84.921  1.00  0.00              
ATOM    662  CA  MET   230      12.912  64.009  86.300  1.00  0.00              
ATOM    663  C   MET   230      11.830  63.532  87.279  1.00  0.00              
ATOM    664  O   MET   230      12.120  62.734  88.170  1.00  0.00              
ATOM    665  N   HIS   231      10.596  64.001  87.100  1.00  0.00              
ATOM    666  CA  HIS   231       9.463  63.488  87.871  1.00  0.00              
ATOM    667  C   HIS   231       9.348  61.970  87.763  1.00  0.00              
ATOM    668  O   HIS   231       9.106  61.285  88.759  1.00  0.00              
ATOM    669  N   THR   232       9.544  61.458  86.552  1.00  0.00              
ATOM    670  CA  THR   232       9.539  60.040  86.296  1.00  0.00              
ATOM    671  C   THR   232      10.613  59.297  87.066  1.00  0.00              
ATOM    672  O   THR   232      10.332  58.276  87.720  1.00  0.00              
ATOM    673  N   MET   233      11.843  59.795  87.004  1.00  0.00              
ATOM    674  CA  MET   233      12.955  59.101  87.639  1.00  0.00              
ATOM    675  C   MET   233      12.871  59.199  89.153  1.00  0.00              
ATOM    676  O   MET   233      13.228  58.261  89.842  1.00  0.00              
ATOM    677  N   LYS   234      12.378  60.324  89.669  1.00  0.00              
ATOM    678  CA  LYS   234      12.157  60.479  91.097  1.00  0.00              
ATOM    679  C   LYS   234      11.182  59.397  91.579  1.00  0.00              
ATOM    680  O   LYS   234      11.368  58.821  92.641  1.00  0.00              
ATOM    681  N   ASN   235      10.152  59.108  90.794  1.00  0.00              
ATOM    682  CA  ASN   235       9.176  58.108  91.180  1.00  0.00              
ATOM    683  C   ASN   235       9.797  56.716  91.117  1.00  0.00              
ATOM    684  O   ASN   235       9.563  55.884  92.002  1.00  0.00              
ATOM    685  N   THR   236      10.608  56.478  90.082  1.00  0.00              
ATOM    686  CA  THR   236      11.313  55.222  89.948  1.00  0.00              
ATOM    687  C   THR   236      12.122  54.935  91.222  1.00  0.00              
ATOM    688  O   THR   236      12.091  53.820  91.744  1.00  0.00              
ATOM    689  N   GLY   237      12.840  55.944  91.718  1.00  0.00              
ATOM    690  CA  GLY   237      13.628  55.806  92.950  1.00  0.00              
ATOM    691  C   GLY   237      12.742  55.668  94.183  1.00  0.00              
ATOM    692  O   GLY   237      13.102  54.988  95.152  1.00  0.00              
END
