
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0314TS464_2_2-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS464_2_2-D1.T0314_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      I       3           -
LGA    -       -      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      C       9           -
LGA    -       -      Q      10           -
LGA    -       -      A      11           -
LGA    -       -      A      12           -
LGA    -       -      D      13           -
LGA    -       -      A      14           -
LGA    -       -      L      15           -
LGA    -       -      K      16           -
LGA    -       -      G      17           -
LGA    Q      10      F      18          2.712
LGA    A      11      V      19          3.347
LGA    -       -      G      20           -
LGA    -       -      F      21           -
LGA    -       -      N      22           -
LGA    -       -      R      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      R      27           -
LGA    -       -      Y      28           -
LGA    -       -      I      29           -
LGA    A      12      V      30          0.679
LGA    D      13      R      31          2.132
LGA    A      14      F      32          2.020
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      D      43           -
LGA    -       -      D      44           -
LGA    -       -      S      45           -
LGA    -       -      I      46           -
LGA    -       -      T      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    -       -      F      52           -
LGA    -       -      V      53           -
LGA    -       -      W      54           -
LGA    -       -      S      55           -
LGA    -       -      S      56           -
LGA    -       -      V      57           -
LGA    -       -      R      58           -
LGA    -       -      D      59           -
LGA    -       -      D      60           -
LGA    -       -      V      61           -
LGA    -       -      M      62           -
LGA    D      59      R      63           #
LGA    D      60      L      64          4.465
LGA    V      61      G      65          2.443
LGA    M      62      R      66          0.956
LGA    R      63      E      67          0.602
LGA    L      64      Q      68          0.735
LGA    G      65      L      69          1.801
LGA    R      66      Q      70          2.080
LGA    E      67      I      71          1.267
LGA    Q      68      L      72          1.712
LGA    L      69      L      73          2.754
LGA    Q      70      E      74          1.815
LGA    I      71      Q      75          2.416
LGA    L      72      -       -           -
LGA    L      73      N      76          1.940
LGA    E      74      -       -           -
LGA    Q      75      -       -           -
LGA    N      76      -       -           -
LGA    I      77      I      77          3.759
LGA    N      78      N      78          4.570
LGA    E      79      E      79          3.449
LGA    P      97      R      80          4.922
LGA    E      98      L      81          4.385
LGA    I      99      N      82          4.241
LGA    T     100      I      83          1.794
LGA    A     101      G      84          0.681
LGA    -       -      E      85           -
LGA    -       -      P      86           -
LGA    -       -      L      87           -
LGA    -       -      L      88           -
LGA    -       -      V      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      R      92           -
LGA    -       -      R      93           -
LGA    -       -      Q      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      P      97           -
LGA    -       -      E      98           -
LGA    -       -      I      99           -
LGA    -       -      T     100           -
LGA    -       -      A     101           -
LGA    -       -      Q     102           -
LGA    -       -      R     103           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31  103    5.0     26    2.77    15.38     16.926     0.905

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.607673 * X  +  -0.529191 * Y  +   0.592191 * Z  +   9.118474
  Y_new =   0.710284 * X  +  -0.028556 * Y  +   0.703336 * Z  +   6.653496
  Z_new =  -0.355289 * X  +   0.848022 * Y  +   0.393229 * Z  + -15.141495 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.136607   -2.004986  [ DEG:    65.1228   -114.8772 ]
  Theta =   0.363223    2.778369  [ DEG:    20.8112    159.1888 ]
  Phi   =   2.278495   -0.863097  [ DEG:   130.5482    -49.4518 ]
 
# 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: T0314TS464_2_2-D1                             
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS464_2_2-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31  103   5.0   26   2.77   15.38  16.926
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0314
PARENT N/A
ATOM      1  CA  GLN    10      25.707   3.782 -18.064  1.00  0.00
ATOM      2  CA  ALA    11      23.195   2.960 -15.315  1.00  0.00
ATOM      3  CA  ALA    12      23.171  -0.823 -15.830  1.00  0.00
ATOM      4  CA  ASP    13      26.898  -0.888 -16.663  1.00  0.00
ATOM      5  CA  ALA    14      27.799   1.310 -13.739  1.00  0.00
ATOM      6  CA  ASP    59       3.307   8.484 -17.835  1.00  0.00
ATOM      7  CA  ASP    60       6.531   8.785 -19.867  1.00  0.00
ATOM      8  CA  VAL    61       8.604   8.735 -16.694  1.00  0.00
ATOM      9  CA  MET    62       6.937   5.477 -15.564  1.00  0.00
ATOM     10  CA  ARG    63       7.332   3.789 -18.936  1.00  0.00
ATOM     11  CA  LEU    64      11.033   4.704 -18.902  1.00  0.00
ATOM     12  CA  GLY    65      11.409   3.676 -15.224  1.00  0.00
ATOM     13  CA  ARG    66       9.906   0.301 -16.074  1.00  0.00
ATOM     14  CA  GLU    67      12.229  -0.769 -18.877  1.00  0.00
ATOM     15  CA  GLN    68      15.196   0.323 -16.681  1.00  0.00
ATOM     16  CA  LEU    69      14.094  -1.879 -13.771  1.00  0.00
ATOM     17  CA  GLN    70      13.604  -4.854 -16.043  1.00  0.00
ATOM     18  CA  ILE    71      17.133  -4.079 -17.243  1.00  0.00
ATOM     19  CA  LEU    72      18.825  -3.853 -13.933  1.00  0.00
ATOM     20  CA  LEU    73      17.009  -6.951 -12.594  1.00  0.00
ATOM     21  CA  GLU    74      18.171  -8.928 -15.612  1.00  0.00
ATOM     22  CA  GLN    75      21.687  -8.087 -14.497  1.00  0.00
ATOM     23  CA  ASN    76      21.810  -9.095 -10.853  1.00  0.00
ATOM     24  CA  ILE    77      21.211  -5.578  -9.546  1.00  0.00
ATOM     25  CA  ASN    78      18.585  -5.331  -6.800  1.00  0.00
ATOM     26  CA  GLU    79      16.382  -2.421  -7.812  1.00  0.00
ATOM     27  CA  PRO    97      16.691   0.566  -5.201  1.00  0.00
ATOM     28  CA  GLU    98      17.285   4.174  -6.156  1.00  0.00
ATOM     29  CA  ILE    99      15.084   4.058  -9.218  1.00  0.00
ATOM     30  CA  THR   100      12.371   2.215  -7.298  1.00  0.00
ATOM     31  CA  ALA   101      12.538   4.884  -4.516  1.00  0.00
TER
END
