
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0298AL333_1-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298AL333_1-D1.T0298_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    -       -      Q       3           -
LGA    -       -      P       4           -
LGA    -       -      L       5           -
LGA    -       -      N       6           -
LGA    -       -      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    -       -      T      13           -
LGA    -       -      G      14           -
LGA    -       -      S      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    -       -      L      20           -
LGA    -       -      V      21           -
LGA    -       -      G      22           -
LGA    -       -      L      23           -
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
LGA    -       -      L      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      H      35           -
LGA    -       -      L      36           -
LGA    -       -      L      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      A      40           -
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    P     129      G      44          4.673
LGA    V     316      Q      45          3.934
LGA    R     317      R      46          1.881
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    K     318      L      54          2.406
LGA    G     319      R      55          2.658
LGA    -       -      V      56           -
LGA    -       -      G      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    -       -      S      61           -
LGA    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      A      70           -
LGA    -       -      F      71           -
LGA    -       -      F      72           -
LGA    -       -      A      73           -
LGA    -       -      A      74           -
LGA    -       -      A      75           -
LGA    -       -      A      76           -
LGA    -       -      E      77           -
LGA    -       -      V      78           -
LGA    -       -      S      79           -
LGA    -       -      R      80           -
LGA    -       -      A      81           -
LGA    -       -      H      82           -
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      S      97           -
LGA    -       -      G      98           -
LGA    -       -      A      99           -
LGA    -       -      L     100           -
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    -       -      A     105           -
LGA    -       -      P     106           -
LGA    -       -      P     107           -
LGA    -       -      V     108           -
LGA    -       -      M     109           -
LGA    -       -      V     110           -
LGA    -       -      S     111           -
LGA    -       -      V     112           -
LGA    -       -      N     113           -
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    -       -      R     116           -
LGA    -       -      L     117           -
LGA    -       -      A     118           -
LGA    -       -      S     119           -
LGA    -       -      Q     120           -
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      L     125           -
LGA    -       -      L     126           -
LGA    -       -      S     127           -
LGA    -       -      S     128           -
LGA    -       -      P     129           -
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      L     322           -
LGA    -       -      N     323           -
LGA    -       -      A     324           -
LGA    -       -      V     325           -
LGA    -       -      L     326           -
LGA    -       -      L     327           -
LGA    -       -      G     328           -
LGA    -       -      E     329           -
LGA    -       -      L     330           -
LGA    -       -      L     331           -
LGA    -       -      I     332           -
LGA    -       -      K     333           -
LGA    -       -      H     334           -
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  148    5.0      5    3.28    20.00      2.710     0.148

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.936582 * X  +  -0.346476 * Y  +  -0.052610 * Z  + -12.118284
  Y_new =   0.169529 * X  +   0.316549 * Y  +   0.933304 * Z  + -34.992458
  Z_new =  -0.306714 * X  +  -0.883035 * Y  +   0.355211 * Z  +  29.511629 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.188341    1.953251  [ DEG:   -68.0870    111.9130 ]
  Theta =   0.311739    2.829854  [ DEG:    17.8613    162.1387 ]
  Phi   =   0.179069   -2.962524  [ DEG:    10.2599   -169.7401 ]
 
# 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: T0298AL333_1-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298AL333_1-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  148   5.0    5   3.28   20.00   2.710
REMARK  ---------------------------------------------------------- 
MOLECULE T0298AL333_1-D1
REMARK Aligment from pdb entry: 1nwc_A
ATOM      1  N   PRO   129     -19.510  49.906 -19.393  1.00  0.00              
ATOM      2  CA  PRO   129     -18.954  51.155 -19.879  1.00  0.00              
ATOM      3  C   PRO   129     -18.201  51.969 -18.842  1.00  0.00              
ATOM      4  O   PRO   129     -18.214  51.650 -17.649  1.00  0.00              
ATOM    749  N   VAL   316     -18.831  52.520  -8.116  1.00  0.00              
ATOM    750  CA  VAL   316     -18.705  51.066  -8.076  1.00  0.00              
ATOM    751  C   VAL   316     -19.964  50.297  -8.475  1.00  0.00              
ATOM    752  O   VAL   316     -19.884  49.137  -8.879  1.00  0.00              
ATOM    753  N   ARG   317     -21.121  50.945  -8.379  1.00  0.00              
ATOM    754  CA  ARG   317     -22.381  50.298  -8.740  1.00  0.00              
ATOM    755  C   ARG   317     -22.728  50.520 -10.222  1.00  0.00              
ATOM    756  O   ARG   317     -22.315  49.724 -11.068  1.00  0.00              
ATOM    757  N   LYS   318     -23.468  51.576 -10.556  1.00  0.00              
ATOM    758  CA  LYS   318     -23.787  51.810 -11.970  1.00  0.00              
ATOM    759  C   LYS   318     -22.520  52.121 -12.771  1.00  0.00              
ATOM    760  O   LYS   318     -22.493  51.978 -13.994  1.00  0.00              
ATOM    761  N   GLY   319     -21.466  52.534 -12.074  1.00  0.00              
ATOM    762  CA  GLY   319     -20.223  52.842 -12.748  1.00  0.00              
ATOM    763  C   GLY   319     -19.332  51.632 -12.983  1.00  0.00              
ATOM    764  O   GLY   319     -18.355  51.730 -13.720  1.00  0.00              
END
