
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0378AL243_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL243_5-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    T      79      I       7          0.691
LGA    T      80      K       8          0.994
LGA    P      81      F       9          0.615
LGA    Q      82      L      10          0.891
LGA    P      83      R      11          1.242
LGA    L      84      S      12          0.952
LGA    M      85      L      13          1.871
LGA    A      86      R      14          2.055
LGA    V      87      E      15          1.203
LGA    F      88      R      16          2.570
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    D      89      R      19          4.247
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11   89    5.0     11    1.88     0.00     11.551     0.555

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.618723 * X  +   0.680911 * Y  +  -0.391844 * Z  +  30.148716
  Y_new =  -0.661995 * X  +   0.720456 * Y  +   0.206651 * Z  + -11.865347
  Z_new =   0.423018 * X  +   0.131539 * Y  +   0.896523 * Z  + -55.345146 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.145682   -2.995911  [ DEG:     8.3470   -171.6530 ]
  Theta =  -0.436773   -2.704819  [ DEG:   -25.0253   -154.9747 ]
  Phi   =  -0.819173    2.322420  [ DEG:   -46.9352    133.0648 ]
 
# 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: T0378AL243_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL243_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   89   5.0   11   1.88    0.00  11.551
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL243_5-D1
REMARK Aligment from pdb entry: 1zjrA
ATOM      1  N   THR    79       7.241  33.330  51.614  1.00  0.00              
ATOM      2  CA  THR    79       7.797  33.014  50.303  1.00  0.00              
ATOM      3  C   THR    79       9.321  32.994  50.350  1.00  0.00              
ATOM      4  O   THR    79       9.957  32.084  49.819  1.00  0.00              
ATOM      5  N   THR    80       9.900  34.002  50.994  1.00  0.00              
ATOM      6  CA  THR    80      11.348  34.103  51.105  1.00  0.00              
ATOM      7  C   THR    80      11.917  32.891  51.840  1.00  0.00              
ATOM      8  O   THR    80      13.068  32.509  51.624  1.00  0.00              
ATOM      9  N   PRO    81      11.105  32.292  52.706  1.00  0.00              
ATOM     10  CA  PRO    81      11.523  31.117  53.464  1.00  0.00              
ATOM     11  C   PRO    81      11.698  29.947  52.505  1.00  0.00              
ATOM     12  O   PRO    81      12.595  29.119  52.670  1.00  0.00              
ATOM     13  N   GLN    82      10.828  29.889  51.501  1.00  0.00              
ATOM     14  CA  GLN    82      10.861  28.827  50.506  1.00  0.00              
ATOM     15  C   GLN    82      12.148  28.854  49.690  1.00  0.00              
ATOM     16  O   GLN    82      12.767  27.816  49.460  1.00  0.00              
ATOM     17  N   PRO    83      12.549  30.045  49.255  1.00  0.00              
ATOM     18  CA  PRO    83      13.764  30.188  48.461  1.00  0.00              
ATOM     19  C   PRO    83      14.980  29.780  49.289  1.00  0.00              
ATOM     20  O   PRO    83      15.880  29.104  48.792  1.00  0.00              
ATOM     21  N   LEU    84      14.998  30.186  50.555  1.00  0.00              
ATOM     22  CA  LEU    84      16.100  29.843  51.451  1.00  0.00              
ATOM     23  C   LEU    84      16.112  28.342  51.698  1.00  0.00              
ATOM     24  O   LEU    84      17.174  27.727  51.816  1.00  0.00              
ATOM     25  N   MET    85      14.920  27.759  51.777  1.00  0.00              
ATOM     26  CA  MET    85      14.774  26.328  51.994  1.00  0.00              
ATOM     27  C   MET    85      15.386  25.625  50.788  1.00  0.00              
ATOM     28  O   MET    85      16.145  24.664  50.920  1.00  0.00              
ATOM     29  N   ALA    86      15.050  26.129  49.607  1.00  0.00              
ATOM     30  CA  ALA    86      15.548  25.565  48.364  1.00  0.00              
ATOM     31  C   ALA    86      17.051  25.790  48.245  1.00  0.00              
ATOM     32  O   ALA    86      17.780  24.931  47.751  1.00  0.00              
ATOM     33  N   VAL    87      17.508  26.947  48.713  1.00  0.00              
ATOM     34  CA  VAL    87      18.923  27.289  48.663  1.00  0.00              
ATOM     35  C   VAL    87      19.690  26.279  49.516  1.00  0.00              
ATOM     36  O   VAL    87      20.769  25.826  49.149  1.00  0.00              
ATOM     37  N   PHE    88      19.115  25.929  50.660  1.00  0.00              
ATOM     38  CA  PHE    88      19.742  24.976  51.561  1.00  0.00              
ATOM     39  C   PHE    88      19.909  23.616  50.885  1.00  0.00              
ATOM     40  O   PHE    88      20.970  23.001  50.960  1.00  0.00              
ATOM     41  N   ASP    89      18.855  23.149  50.226  1.00  0.00              
ATOM     42  CA  ASP    89      18.902  21.869  49.524  1.00  0.00              
ATOM     43  C   ASP    89      19.989  21.915  48.454  1.00  0.00              
ATOM     44  O   ASP    89      20.728  20.949  48.251  1.00  0.00              
END
