
#######################################################
#                                                     #
#                        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 (   89),  selected   18 , name T0386TS261_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS261_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    K     222      P     244           #
LGA    I     223      V     245          3.587
LGA    R     224      M     246          1.737
LGA    L     225      -       -           -
LGA    L     226      V     247          3.710
LGA    K     227      A     248          2.335
LGA    E     228      K     249          3.574
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    -       -      E     264           -
LGA    -       -      G     265           -
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    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    F     229      P     284          2.294
LGA    M     230      E     285          2.815
LGA    H     231      Q     286          1.162
LGA    T     232      L     287          2.897
LGA    M     233      K     288          3.784
LGA    K     234      I     289          2.101
LGA    N     235      L     290          2.634
LGA    T     236      K     291          3.940
LGA    G     237      P     292          3.964
LGA    R     238      G     293          4.293
LGA    N     239      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     15    3.12     0.00     12.564     0.466

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.365372 * X  +   0.871859 * Y  +   0.326136 * Z  + -37.389038
  Y_new =   0.791453 * X  +   0.106534 * Y  +   0.601874 * Z  +  70.584526
  Z_new =   0.490005 * X  +   0.478029 * Y  +  -0.728960 * Z  +  75.653976 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.561173   -0.580420  [ DEG:   146.7444    -33.2556 ]
  Theta =  -0.512095   -2.629497  [ DEG:   -29.3409   -150.6591 ]
  Phi   =   2.003294   -1.138299  [ DEG:   114.7803    -65.2197 ]
 
# 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: T0386TS261_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS261_1-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   15   3.12    0.00  12.564
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS261_1-D2
PFRMAT TS
TARGET T0386
MODEL  1
PARENT 2f6s_A
ATOM    724  N   LYS   222      18.567  61.218  75.045  1.00  6.52
ATOM    725  CA  LYS   222      17.878  61.528  76.276  1.00  6.52
ATOM    726  C   LYS   222      16.588  60.723  76.391  1.00  6.52
ATOM    727  O   LYS   222      16.293  60.205  77.463  1.00  6.52
ATOM    728  CB  LYS   222      17.659  63.066  76.503  1.00  6.52
ATOM    729  N   ILE   223      15.837  60.587  75.296  1.00  6.44
ATOM    730  CA  ILE   223      14.596  59.802  75.332  1.00  6.44
ATOM    731  C   ILE   223      14.887  58.370  75.752  1.00  6.44
ATOM    732  O   ILE   223      14.200  57.828  76.606  1.00  6.44
ATOM    733  CB  ILE   223      13.880  59.786  73.985  1.00  6.44
ATOM    734  N   ARG   224      15.919  57.765  75.168  1.00  6.76
ATOM    735  CA  ARG   224      16.272  56.374  75.451  1.00  6.76
ATOM    736  C   ARG   224      16.757  56.218  76.884  1.00  6.76
ATOM    737  O   ARG   224      16.390  55.263  77.573  1.00  6.76
ATOM    738  CB  ARG   224      17.374  55.884  74.470  1.00  6.76
ATOM    739  N   LEU   225      17.580  57.161  77.329  1.00  4.98
ATOM    740  CA  LEU   225      18.192  57.096  78.642  1.00  4.98
ATOM    741  C   LEU   225      17.128  57.171  79.725  1.00  4.98
ATOM    742  O   LEU   225      17.114  56.353  80.651  1.00  4.98
ATOM    743  CB  LEU   225      19.195  58.233  78.806  1.00  4.98
ATOM    744  N   LEU   226      16.233  58.152  79.601  1.00  5.03
ATOM    745  CA  LEU   226      15.131  58.311  80.550  1.00  5.03
ATOM    746  C   LEU   226      14.152  57.150  80.542  1.00  5.03
ATOM    747  O   LEU   226      13.734  56.704  81.606  1.00  5.03
ATOM    748  CB  LEU   226      14.386  59.628  80.316  1.00  5.03
ATOM    749  N   LYS   227      13.799  56.644  79.359  1.00  5.51
ATOM    750  CA  LYS   227      12.776  55.591  79.271  1.00  5.51
ATOM    751  C   LYS   227      13.175  54.335  80.033  1.00  5.51
ATOM    752  O   LYS   227      12.323  53.598  80.496  1.00  5.51
ATOM    753  CB  LYS   227      12.434  55.254  77.827  1.00  5.51
ATOM    754  N   GLU   228      14.476  54.123  80.187  1.00  5.26
ATOM    755  CA  GLU   228      15.012  52.923  80.831  1.00  5.26
ATOM    756  C   GLU   228      15.086  52.986  82.355  1.00  5.26
ATOM    757  O   GLU   228      15.421  51.996  82.981  1.00  5.26
ATOM    758  CB  GLU   228      16.408  52.619  80.287  1.00  5.26
ATOM    759  N   PHE   229      12.754  59.394  96.238  1.00  2.98
ATOM    760  CA  PHE   229      12.742  60.770  95.786  1.00  2.98
ATOM    761  C   PHE   229      13.995  61.519  96.238  1.00  2.98
ATOM    762  O   PHE   229      14.591  62.264  95.461  1.00  2.98
ATOM    763  CB  PHE   229      11.466  61.464  96.270  1.00  2.98
ATOM    764  N   MET   230      14.408  61.297  97.481  1.00  3.96
ATOM    765  CA  MET   230      15.611  61.925  98.019  1.00  3.96
ATOM    766  C   MET   230      16.870  61.420  97.300  1.00  3.96
ATOM    767  O   MET   230      17.725  62.222  96.926  1.00  3.96
ATOM    768  CB  MET   230      15.716  61.761  99.579  1.00  3.96
ATOM    769  N   HIS   231      16.970  60.108  97.095  1.00  5.48
ATOM    770  CA  HIS   231      18.045  59.540  96.280  1.00  5.48
ATOM    771  C   HIS   231      18.102  60.179  94.896  1.00  5.48
ATOM    772  O   HIS   231      19.182  60.494  94.393  1.00  5.48
ATOM    773  CB  HIS   231      17.888  58.038  96.128  1.00  5.48
ATOM    774  N   THR   232      16.930  60.386  94.303  1.00  3.05
ATOM    775  CA  THR   232      16.809  61.043  93.027  1.00  3.05
ATOM    776  C   THR   232      17.343  62.462  93.040  1.00  3.05
ATOM    777  O   THR   232      18.133  62.850  92.160  1.00  3.05
ATOM    778  CB  THR   232      15.331  61.016  92.601  1.00  3.05
ATOM    779  N   MET   233      16.927  63.246  94.029  1.00  5.81
ATOM    780  CA  MET   233      17.318  64.649  94.075  1.00  5.81
ATOM    781  C   MET   233      18.789  64.799  94.423  1.00  5.81
ATOM    782  O   MET   233      19.444  65.691  93.919  1.00  5.81
ATOM    783  CB  MET   233      16.422  65.459  95.025  1.00  5.81
ATOM    784  N   LYS   234      19.313  63.911  95.268  1.00  5.54
ATOM    785  CA  LYS   234      20.731  63.901  95.585  1.00  5.54
ATOM    786  C   LYS   234      21.537  63.699  94.295  1.00  5.54
ATOM    787  O   LYS   234      22.564  64.334  94.097  1.00  5.54
ATOM    788  CB  LYS   234      21.068  62.810  96.637  1.00  5.54
ATOM    789  N   ASN   235      21.067  62.830  93.410  1.00  4.31
ATOM    790  CA  ASN   235      21.774  62.569  92.170  1.00  4.31
ATOM    791  C   ASN   235      21.677  63.780  91.247  1.00  4.31
ATOM    792  O   ASN   235      22.662  64.154  90.597  1.00  4.31
ATOM    793  CB  ASN   235      21.202  61.351  91.483  1.00  4.31
ATOM    794  N   THR   236      20.495  64.401  91.211  1.00  1.91
ATOM    795  CA  THR   236      20.297  65.602  90.429  1.00  1.91
ATOM    796  C   THR   236      21.344  66.659  90.813  1.00  1.91
ATOM    797  O   THR   236      21.952  67.281  89.942  1.00  1.91
ATOM    798  CB  THR   236      18.876  66.139  90.633  1.00  1.91
ATOM    799  N   GLY   237      21.552  66.853  92.117  1.00  1.75
ATOM    800  CA  GLY   237      22.550  67.809  92.611  1.00  1.75
ATOM    801  C   GLY   237      23.975  67.346  92.327  1.00  1.75
ATOM    802  O   GLY   237      24.876  68.163  92.102  1.00  1.75
ATOM    803  N   ARG   238      24.161  66.029  92.315  1.00  7.65
ATOM    804  CA  ARG   238      25.432  65.459  91.952  1.00  7.65
ATOM    805  C   ARG   238      25.810  65.767  90.504  1.00  7.65
ATOM    806  O   ARG   238      26.999  65.898  90.197  1.00  7.65
ATOM    807  CB  ARG   238      25.447  63.949  92.203  1.00  7.65
ATOM    808  N   ASN   239      29.230  66.714  95.668  1.00  5.57
ATOM    809  CA  ASN   239      29.712  65.368  96.000  1.00  5.57
ATOM    810  C   ASN   239      29.583  65.037  97.475  1.00  5.57
ATOM    811  O   ASN   239      28.480  64.784  97.972  1.00  5.57
ATOM    812  CB  ASN   239      31.176  65.236  95.546  1.00  5.57
TER
END
