
#######################################################
#                                                     #
#                        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    5 (   25),  selected    5 , name T0358TS102_1
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS102_1.T0358.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    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    H      83      R      65          1.055
LGA    H      84      Y      66          0.714
LGA    H      85      I      67          0.934
LGA    H      86      R      68          0.609
LGA    H      87      T      69          1.129
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   66    5.0      5    0.91     0.00      7.456     0.495

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.173460 * X  +  -0.932429 * Y  +   0.316999 * Z  + 184.095642
  Y_new =   0.963069 * X  +  -0.227904 * Y  +  -0.143379 * Z  + -153.063889
  Z_new =   0.205936 * X  +   0.280421 * Y  +   0.937526 * Z  + -133.941681 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.290638   -2.850955  [ DEG:    16.6523   -163.3477 ]
  Theta =  -0.207420   -2.934172  [ DEG:   -11.8843   -168.1157 ]
  Phi   =   1.748997   -1.392596  [ DEG:   100.2101    -79.7899 ]
 
# 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: T0358TS102_1                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS102_1.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   66   5.0    5   0.91    0.00   7.456
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS102_1
PFRMAT TS
TARGET T0358
MODEL 1
PARENT 1vlv_A
ATOM      1  N   HIS    83       2.902  -5.990  10.759  1.00  1.00
ATOM      2  CA  HIS    83       3.401  -4.784  10.037  1.00  1.00
ATOM      3  C   HIS    83       2.338  -4.258   9.084  1.00  1.00
ATOM      4  O   HIS    83       2.712  -3.657   8.061  1.00  1.00
ATOM      5  CB  HIS    83       4.648  -5.092   9.152  1.00  1.00
ATOM      6  N   HIS    84       1.044  -4.439   9.409  1.00  1.00
ATOM      7  CA  HIS    84      -0.103  -4.423   8.423  1.00  1.00
ATOM      8  C   HIS    84      -0.143  -5.698   7.551  1.00  1.00
ATOM      9  O   HIS    84      -1.191  -6.343   7.487  1.00  1.00
ATOM     10  CB  HIS    84      -0.149  -3.199   7.508  1.00  1.00
ATOM     11  N   HIS    85       0.948  -5.995   6.833  1.00  1.00
ATOM     12  CA  HIS    85       1.233  -7.373   6.367  1.00  1.00
ATOM     13  C   HIS    85       2.506  -7.778   7.052  1.00  1.00
ATOM     14  O   HIS    85       3.577  -7.255   6.755  1.00  1.00
ATOM     15  CB  HIS    85       1.362  -7.518   4.842  1.00  1.00
ATOM     16  N   HIS    86       2.367  -8.688   8.005  1.00  1.00
ATOM     17  CA  HIS    86       3.499  -9.242   8.722  1.00  1.00
ATOM     18  C   HIS    86       4.436 -10.091   7.805  1.00  1.00
ATOM     19  O   HIS    86       3.975 -11.006   7.110  1.00  1.00
ATOM     20  CB  HIS    86       2.949 -10.070   9.893  1.00  1.00
ATOM     21  N   HIS    87       5.739  -9.788   7.823  1.00  1.00
ATOM     22  CA  HIS    87       6.730 -10.531   7.056  1.00  1.00
ATOM     23  C   HIS    87       7.049 -11.863   7.753  1.00  1.00
ATOM     24  O   HIS    87       7.400 -11.852   8.947  1.00  1.00
ATOM     25  CB  HIS    87       8.035  -9.729   6.893  1.00  1.00
TER
END
