
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS102_3.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    H      83      D      58          1.172
LGA    H      84      A      59          1.563
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    H      85      G      62          0.803
LGA    H      86      L      63          2.034
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    H      87      Y      66          1.912
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
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    1.57     0.00      7.117     0.300

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.186315 * X  +   0.911843 * Y  +   0.365827 * Z  + -25.946581
  Y_new =  -0.517519 * X  +  -0.225421 * Y  +   0.825445 * Z  + -37.319817
  Z_new =   0.835141 * X  +  -0.343115 * Y  +   0.429897 * Z  +  -8.473977 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.673602    2.467991  [ DEG:   -38.5945    141.4055 ]
  Theta =  -0.988389   -2.153203  [ DEG:   -56.6305   -123.3695 ]
  Phi   =  -1.225227    1.916366  [ DEG:   -70.2003    109.7997 ]
 
# 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_3                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS102_3.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   1.57    0.00   7.117
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS102_3
PFRMAT TS
TARGET T0358
MODEL 3
PARENT 1zko_A
ATOM      1  N   HIS    83       8.051   6.927   6.125  1.00  1.00
ATOM      2  CA  HIS    83       7.680   5.488   6.224  1.00  1.00
ATOM      3  C   HIS    83       6.264   5.337   6.740  1.00  1.00
ATOM      4  O   HIS    83       5.831   6.077   7.624  1.00  1.00
ATOM      5  CB  HIS    83       8.659   4.741   7.126  1.00  1.00
ATOM      6  N   HIS    84       5.558   4.367   6.178  1.00  1.00
ATOM      7  CA  HIS    84       4.145   4.171   6.453  1.00  1.00
ATOM      8  C   HIS    84       3.917   2.870   7.199  1.00  1.00
ATOM      9  O   HIS    84       4.698   1.927   7.056  1.00  1.00
ATOM     10  CB  HIS    84       3.359   4.227   5.147  1.00  1.00
ATOM     11  N   HIS    85       2.868   2.841   8.019  1.00  1.00
ATOM     12  CA  HIS    85       2.549   1.679   8.844  1.00  1.00
ATOM     13  C   HIS    85       2.402   0.419   7.995  1.00  1.00
ATOM     14  O   HIS    85       1.610   0.376   7.053  1.00  1.00
ATOM     15  CB  HIS    85       1.270   1.955   9.642  1.00  1.00
ATOM     16  N   HIS    86       3.184  -0.602   8.327  1.00  1.00
ATOM     17  CA  HIS    86       3.148  -1.859   7.595  1.00  1.00
ATOM     18  C   HIS    86       1.842  -2.591   7.859  1.00  1.00
ATOM     19  O   HIS    86       1.419  -2.709   9.004  1.00  1.00
ATOM     20  CB  HIS    86       4.323  -2.732   8.028  1.00  1.00
ATOM     21  N   HIS    87       1.210  -3.063   6.789  1.00  1.00
ATOM     22  CA  HIS    87       0.064  -3.952   6.905  1.00  1.00
ATOM     23  C   HIS    87       0.542  -5.330   7.337  1.00  1.00
ATOM     24  O   HIS    87       1.693  -5.697   7.105  1.00  1.00
ATOM     25  CB  HIS    87      -0.650  -4.113   5.573  1.00  1.00
TER
END
