
#######################################################
#                                                     #
#                        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   10 (   10),  selected   10 , name T0342TS464_4_2-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS464_4_2-D1.T0342_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    -       -      E      14           -
LGA    -       -      E      15           -
LGA    -       -      S      16           -
LGA    -       -      F      17           -
LGA    -       -      L      18           -
LGA    -       -      Y      19           -
LGA    -       -      F      20           -
LGA    -       -      A      21           -
LGA    -       -      Y      22           -
LGA    E      78      G      23          1.762
LGA    V      79      S      24          1.260
LGA    W      80      N      25          0.855
LGA    G      81      L      26          1.162
LGA    V      82      L      27          2.541
LGA    V      83      -       -           -
LGA    W      84      T      28          1.996
LGA    K      85      E      29          3.209
LGA    M      86      R      30          4.257
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    -       -      A      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      C      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      Q      47           -
LGA    -       -      D      48           -
LGA    -       -      F      49           -
LGA    -       -      K      50           -
LGA    -       -      L      51           -
LGA    -       -      D      52           -
LGA    -       -      F      53           -
LGA    -       -      G      54           -
LGA    -       -      N      55           -
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    P     135      K      59          1.642
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    -       -      T      70           -
LGA    -       -      I      71           -
LGA    -       -      F      72           -
LGA    -       -      Q      73           -
LGA    -       -      S      74           -
LGA    -       -      P      75           -
LGA    -       -      G      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      V      79           -
LGA    -       -      W      80           -
LGA    -       -      G      81           -
LGA    -       -      V      82           -
LGA    -       -      V      83           -
LGA    -       -      W      84           -
LGA    -       -      K      85           -
LGA    -       -      M      86           -
LGA    -       -      N      87           -
LGA    -       -      K      88           -
LGA    -       -      S      89           -
LGA    -       -      N      90           -
LGA    -       -      L      91           -
LGA    -       -      N      92           -
LGA    -       -      S      93           -
LGA    -       -      L      94           -
LGA    -       -      D      95           -
LGA    -       -      E      96           -
LGA    -       -      Q      97           -
LGA    -       -      E      98           -
LGA    -       -      G      99           -
LGA    -       -      V     100           -
LGA    -       -      K     101           -
LGA    -       -      S     102           -
LGA    -       -      G     103           -
LGA    -       -      M     104           -
LGA    -       -      Y     105           -
LGA    -       -      V     106           -
LGA    -       -      V     107           -
LGA    -       -      I     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      K     111           -
LGA    -       -      V     112           -
LGA    -       -      A     113           -
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      C     122           -
LGA    -       -      R     123           -
LGA    -       -      S     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      M     127           -
LGA    -       -      T     128           -
LGA    -       -      N     129           -
LGA    -       -      Y     130           -
LGA    -       -      E     131           -
LGA    -       -      S     132           -
LGA    -       -      A     133           -
LGA    -       -      P     134           -
LGA    -       -      P     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  122    5.0      9    2.32     0.00      5.957     0.372

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.771769 * X  +  -0.523841 * Y  +  -0.360504 * Z  +  80.045212
  Y_new =  -0.501858 * X  +  -0.153589 * Y  +  -0.851204 * Z  + 147.193588
  Z_new =   0.390526 * X  +   0.837855 * Y  +  -0.381429 * Z  + -93.131508 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.998003   -1.143589  [ DEG:   114.4771    -65.5229 ]
  Theta =  -0.401203   -2.740389  [ DEG:   -22.9873   -157.0127 ]
  Phi   =  -0.576565    2.565028  [ DEG:   -33.0347    146.9653 ]
 
# 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: T0342TS464_4_2-D1                             
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS464_4_2-D1.T0342_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  122   5.0    9   2.32    0.00   5.957
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0342
PARENT N/A
ATOM      6  CA  GLU    78       3.706  88.024  10.322  1.00  0.00
ATOM      7  CA  VAL    79       0.184  86.791   9.643  1.00  0.00
ATOM      8  CA  TRP    80       1.121  85.080   6.375  1.00  0.00
ATOM      9  CA  GLY    81       3.968  83.257   8.142  1.00  0.00
ATOM     10  CA  VAL    82       1.527  81.854  10.708  1.00  0.00
ATOM     11  CA  VAL    83      -1.035  80.815   8.086  1.00  0.00
ATOM     12  CA  TRP    84       1.608  78.918   6.081  1.00  0.00
ATOM     13  CA  LYS    85       2.932  77.279   9.236  1.00  0.00
ATOM     14  CA  MET    86      -0.536  75.940  10.070  1.00  0.00
ATOM     15  CA  PRO   135      -9.901 102.142  13.777  1.00  0.00
TER
END
