
#######################################################
#                                                     #
#                        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    6 (   30),  selected    6 , name T0372TS103_1_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_1_1-D1.T0372_D1.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    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    F     112      C      27          0.976
LGA    I     113      D      28          1.063
LGA    F     114      L      29          0.715
LGA    T     115      S      30          1.261
LGA    E     116      F      31          3.072
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    D     117      L      34          1.506
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  126    5.0      6    1.63     0.00      4.532     0.347

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.490328 * X  +   0.738257 * Y  +   0.463201 * Z  +  20.709377
  Y_new =  -0.680155 * X  +   0.008179 * Y  +  -0.733023 * Z  +  97.531586
  Z_new =  -0.544947 * X  +  -0.674470 * Y  +   0.498119 * Z  +  -1.533443 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.934674    2.206918  [ DEG:   -53.5529    126.4471 ]
  Theta =   0.576326    2.565267  [ DEG:    33.0210    146.9790 ]
  Phi   =  -2.195416    0.946177  [ DEG:  -125.7881     54.2119 ]
 
# 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: T0372TS103_1_1-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_1_1-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  126   5.0    6   1.63    0.00   4.532
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_1_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1h1y_A
ATOM    398  N   PHE   112      33.899  48.763  13.998  1.00  1.00
ATOM    399  CA  PHE   112      35.102  48.130  14.536  1.00  1.00
ATOM    400  C   PHE   112      36.191  47.943  13.469  1.00  1.00
ATOM    401  O   PHE   112      37.359  48.249  13.710  1.00  1.00
ATOM    402  CB  PHE   112      34.744  46.791  15.198  1.00  1.00
ATOM    403  N   ILE   113      35.829  47.438  12.281  1.00  1.00
ATOM    404  CA  ILE   113      36.843  47.255  11.231  1.00  1.00
ATOM    405  C   ILE   113      37.544  48.567  10.843  1.00  1.00
ATOM    406  O   ILE   113      38.729  48.572  10.505  1.00  1.00
ATOM    407  CB  ILE   113      36.041  46.684  10.068  1.00  1.00
ATOM    408  N   PHE   114      36.807  49.676  10.885  1.00  1.00
ATOM    409  CA  PHE   114      37.373  50.976  10.526  1.00  1.00
ATOM    410  C   PHE   114      38.367  51.486  11.557  1.00  1.00
ATOM    411  O   PHE   114      39.312  52.197  11.218  1.00  1.00
ATOM    412  CB  PHE   114      36.257  52.019  10.312  1.00  1.00
ATOM    413  N   THR   115      38.146  51.132  12.822  1.00  1.00
ATOM    414  CA  THR   115      39.035  51.542  13.899  1.00  1.00
ATOM    415  C   THR   115      40.284  50.650  13.897  1.00  1.00
ATOM    416  O   THR   115      41.381  51.098  14.215  1.00  1.00
ATOM    417  CB  THR   115      38.336  51.403  15.286  1.00  1.00
ATOM    418  N   GLU   116      40.099  49.394  13.519  1.00  1.00
ATOM    419  CA  GLU   116      41.193  48.423  13.523  1.00  1.00
ATOM    420  C   GLU   116      41.993  48.280  12.228  1.00  1.00
ATOM    421  O   GLU   116      42.949  47.506  12.175  1.00  1.00
ATOM    422  CB  GLU   116      40.628  47.057  13.930  1.00  1.00
ATOM    423  N   ASP   117      41.614  49.029  11.199  1.00  1.00
ATOM    424  CA  ASP   117      42.289  48.962   9.900  1.00  1.00
ATOM    425  C   ASP   117      43.735  49.453   9.920  1.00  1.00
ATOM    426  O   ASP   117      44.127  50.203  10.808  1.00  1.00
ATOM    427  CB  ASP   117      41.493  49.765   8.872  1.00  1.00
TER
END
