
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0386TS125_3u-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS125_3u-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    -       -      P     220           -
LGA    -       -      E     221           -
LGA    P     220      K     222          3.563
LGA    E     221      I     223          1.968
LGA    K     222      R     224          2.049
LGA    I     223      L     225          3.651
LGA    R     224      L     226          2.086
LGA    -       -      K     227           -
LGA    L     225      E     228          0.692
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    L     226      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    K     227      G     262          2.321
LGA    -       -      L     263           -
LGA    E     228      E     264          2.031
LGA    F     229      G     265          1.718
LGA    M     230      F     266          2.460
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          4.673
LGA    M     233      N     278          4.293
LGA    K     234      I     279          3.468
LGA    N     235      D     280          1.992
LGA    T     236      H     281          1.760
LGA    G     237      L     282          2.131
LGA    R     238      P     283          2.167
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)   19   81    5.0     17    2.72     5.88     13.661     0.602

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.974496 * X  +   0.094532 * Y  +   0.203524 * Z  +  23.104782
  Y_new =   0.174469 * X  +   0.251237 * Y  +  -0.952072 * Z  +  48.776073
  Z_new =  -0.141134 * X  +   0.963298 * Y  +   0.228336 * Z  +  31.472588 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.338056   -1.803536  [ DEG:    76.6650   -103.3350 ]
  Theta =   0.141607    2.999985  [ DEG:     8.1135    171.8865 ]
  Phi   =   0.177159   -2.964434  [ DEG:    10.1504   -169.8496 ]
 
# 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: T0386TS125_3u-D2                              
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS125_3u-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   81   5.0   17   2.72    5.88  13.661
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS125_3u-D2
PFRMAT   TS
TARGET   T0386
MODEL    3  UNREFINED
PARENT   2f6sa   
ATOM     1   N   PRO   220       3.240  58.270  77.927    1.00  0.50
ATOM     1   CA  PRO   220       3.069  59.662  77.515    1.00  0.50
ATOM     1   C   PRO   220       3.815  59.938  76.220    1.00  0.50
ATOM     1   O   PRO   220       4.892  59.366  75.986    1.00  0.50
ATOM     1   N   GLU   221       3.239  60.814  75.392    1.00  0.50
ATOM     1   CA  GLU   221       3.895  61.322  74.179    1.00  0.50
ATOM     1   C   GLU   221       4.875  62.461  74.471    1.00  0.50
ATOM     1   O   GLU   221       5.672  62.839  73.620    1.00  0.50
ATOM     1   N   LYS   222       4.817  62.980  75.688    1.00  0.50
ATOM     1   CA  LYS   222       5.628  64.104  76.092    1.00  0.50
ATOM     1   C   LYS   222       7.041  63.677  76.496    1.00  0.50
ATOM     1   O   LYS   222       7.468  63.864  77.642    1.00  0.50
ATOM     1   N   ILE   223       7.774  63.134  75.536    1.00  0.50
ATOM     1   CA  ILE   223       9.000  62.393  75.836    1.00  0.50
ATOM     1   C   ILE   223      10.189  63.271  76.201    1.00  0.50
ATOM     1   O   ILE   223      11.257  62.761  76.564    1.00  0.50
ATOM     1   N   ARG   224      10.010  64.583  76.090    1.00  0.50
ATOM     1   CA  ARG   224      11.129  65.507  76.174    1.00  0.50
ATOM     1   C   ARG   224      11.016  66.524  77.299    1.00  0.50
ATOM     1   O   ARG   224      11.990  67.214  77.597    1.00  0.50
ATOM     1   N   LEU   225       9.836  66.629  77.911    1.00  0.50
ATOM     1   CA  LEU   225       9.650  67.524  79.042    1.00  0.50
ATOM     1   C   LEU   225      10.562  67.138  80.228    1.00  0.50
ATOM     1   O   LEU   225      10.395  66.051  80.820    1.00  0.50
ATOM     1   N   LEU   226      11.538  68.012  80.587    1.00  0.50
ATOM     1   CA  LEU   226      12.445  67.511  81.635    1.00  0.50
ATOM     1   C   LEU   226      11.785  67.468  83.032    1.00  0.50
ATOM     1   O   LEU   226      12.217  66.663  83.868    1.00  0.50
ATOM     1   N   LYS   227      10.738  68.270  83.271    1.00  0.50
ATOM     1   CA  LYS   227       9.972  68.145  84.528    1.00  0.50
ATOM     1   C   LYS   227       9.359  66.735  84.650    1.00  0.50
ATOM     1   O   LYS   227       9.535  66.047  85.668    1.00  0.50
ATOM     1   N   GLU   228       8.662  66.311  83.594    1.00  0.50
ATOM     1   CA  GLU   228       8.080  64.976  83.497    1.00  0.50
ATOM     1   C   GLU   228       9.140  63.885  83.707    1.00  0.50
ATOM     1   O   GLU   228       8.907  62.910  84.416    1.00  0.50
ATOM     1   N   PHE   229      10.303  64.079  83.098    1.00  0.50
ATOM     1   CA  PHE   229      11.381  63.112  83.161    1.00  0.50
ATOM     1   C   PHE   229      11.967  63.019  84.570    1.00  0.50
ATOM     1   O   PHE   229      12.225  61.923  85.066    1.00  0.50
ATOM     1   N   MET   230      12.146  64.164  85.219    1.00  0.50
ATOM     1   CA  MET   230      12.666  64.205  86.583    1.00  0.50
ATOM     1   C   MET   230      11.679  63.568  87.573    1.00  0.50
ATOM     1   O   MET   230      12.087  62.772  88.417    1.00  0.50
ATOM     1   N   HIS   231      10.395  63.904  87.455    1.00  0.50
ATOM     1   CA  HIS   231       9.355  63.236  88.237    1.00  0.50
ATOM     1   C   HIS   231       9.403  61.721  88.063    1.00  0.50
ATOM     1   O   HIS   231       9.274  60.972  89.034    1.00  0.50
ATOM     1   N   THR   232       9.610  61.285  86.824    1.00  0.50
ATOM     1   CA  THR   232       9.751  59.888  86.504    1.00  0.50
ATOM     1   C   THR   232      10.928  59.237  87.205    1.00  0.50
ATOM     1   O   THR   232      10.785  58.165  87.820    1.00  0.50
ATOM     1   N   MET   233      12.093  59.871  87.127    1.00  0.50
ATOM     1   CA  MET   233      13.297  59.280  87.694    1.00  0.50
ATOM     1   C   MET   233      13.258  59.304  89.213    1.00  0.50
ATOM     1   O   MET   233      13.740  58.384  89.847    1.00  0.50
ATOM     1   N   LYS   234      12.663  60.345  89.795    1.00  0.50
ATOM     1   CA  LYS   234      12.479  60.414  91.235    1.00  0.50
ATOM     1   C   LYS   234      11.647  59.211  91.698    1.00  0.50
ATOM     1   O   LYS   234      11.933  58.614  92.726    1.00  0.50
ATOM     1   N   ASN   235      10.627  58.842  90.933    1.00  0.50
ATOM     1   CA  ASN   235       9.781  57.724  91.303    1.00  0.50
ATOM     1   C   ASN   235      10.550  56.414  91.157    1.00  0.50
ATOM     1   O   ASN   235      10.440  55.524  92.010    1.00  0.50
ATOM     1   N   THR   236      11.343  56.311  90.088    1.00  0.50
ATOM     1   CA  THR   236      12.177  55.149  89.874    1.00  0.50
ATOM     1   C   THR   236      13.059  54.900  91.107    1.00  0.50
ATOM     1   O   THR   236      13.169  53.767  91.579    1.00  0.50
ATOM     1   N   GLY   237      13.679  55.961  91.626    1.00  0.50
ATOM     1   CA  GLY   237      14.521  55.861  92.825    1.00  0.50
ATOM     1   C   GLY   237      13.701  55.573  94.078    1.00  0.50
ATOM     1   O   GLY   237      14.168  54.897  95.002    1.00  0.50
ATOM     1   N   ARG   238      12.468  56.071  94.085    1.00  0.50
ATOM     1   CA  ARG   238      11.553  55.779  95.159    1.00  0.50
ATOM     1   C   ARG   238      11.211  54.293  95.237    1.00  0.50
ATOM     1   O   ARG   238      10.968  53.779  96.334    1.00  0.50
TER
END
