
#######################################################
#                                                     #
#                        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 (   39),  selected    5 , name T0298TS671_3-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_3-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    P     129      A      40          2.516
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    V     316      Q      45          2.374
LGA    -       -      R      46           -
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    R     317      V      56          2.220
LGA    K     318      G      57          0.549
LGA    G     319      D      58          3.565
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    2.45     0.00      2.783     0.196

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.156788 * X  +   0.922680 * Y  +  -0.352248 * Z  + -33.597012
  Y_new =  -0.698290 * X  +  -0.148658 * Y  +  -0.700209 * Z  +  22.399683
  Z_new =  -0.698434 * X  +   0.355755 * Y  +   0.620990 * Z  + -42.943871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.520242   -2.621350  [ DEG:    29.8077   -150.1923 ]
  Theta =   0.773206    2.368386  [ DEG:    44.3015    135.6985 ]
  Phi   =  -1.349928    1.791664  [ DEG:   -77.3452    102.6548 ]
 
# 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: T0298TS671_3-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_3-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   2.45    0.00   2.783
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_3-D1
PFRMAT TS
TARGET T0298
MODEL  3  REFINED
PARENT 1PQP_A 1MB4_B 1T4B_B
ATOM      1  N   PRO   129     -10.133  57.639 -20.801  1.00  0.00
ATOM      2  CA  PRO   129     -10.632  56.459 -20.287  1.00  0.00
ATOM      3  C   PRO   129     -10.613  56.375 -18.767  1.00  0.00
ATOM      4  O   PRO   129     -11.521  55.767 -18.212  1.00  0.00
ATOM      5  CB  PRO   129      -9.763  55.356 -20.949  1.00  0.00
ATOM      6  CG  PRO   129      -9.479  55.988 -22.253  1.00  0.00
ATOM      7  CD  PRO   129      -9.155  57.363 -21.739  1.00  0.00
ATOM   1402  N   VAL   316     -17.916  53.841 -11.243  1.00  0.00
ATOM   1403  CA  VAL   316     -18.110  52.549 -11.887  1.00  0.00
ATOM   1404  C   VAL   316     -18.862  52.628 -13.258  1.00  0.00
ATOM   1405  O   VAL   316     -18.578  51.752 -14.082  1.00  0.00
ATOM   1406  CB  VAL   316     -18.850  51.588 -10.936  1.00  0.00
ATOM   1407  CG1 VAL   316     -18.875  50.150 -11.538  1.00  0.00
ATOM   1408  CG2 VAL   316     -18.141  51.571  -9.583  1.00  0.00
ATOM   1409  N   ARG   317     -19.950  53.426 -13.420  1.00  0.00
ATOM   1410  CA  ARG   317     -20.758  53.467 -14.646  1.00  0.00
ATOM   1411  C   ARG   317     -20.194  54.387 -15.770  1.00  0.00
ATOM   1412  O   ARG   317     -19.709  53.817 -16.735  1.00  0.00
ATOM   1413  CB  ARG   317     -22.166  53.939 -14.310  1.00  0.00
ATOM   1414  CG  ARG   317     -23.058  53.051 -13.538  1.00  0.00
ATOM   1415  CD  ARG   317     -23.849  52.137 -14.387  1.00  0.00
ATOM   1416  NE  ARG   317     -25.303  52.353 -14.295  1.00  0.00
ATOM   1417  CZ  ARG   317     -25.997  52.873 -15.306  1.00  0.00
ATOM   1418  NH1 ARG   317     -25.494  53.143 -16.499  1.00  0.00
ATOM   1419  NH2 ARG   317     -27.244  53.275 -15.030  1.00  0.00
ATOM   1420  N   LYS   318     -19.895  55.679 -15.520  1.00  0.00
ATOM   1421  CA  LYS   318     -19.359  56.623 -16.470  1.00  0.00
ATOM   1422  C   LYS   318     -17.827  56.494 -16.628  1.00  0.00
ATOM   1423  O   LYS   318     -17.315  56.371 -17.736  1.00  0.00
ATOM   1424  CB  LYS   318     -19.618  58.059 -15.962  1.00  0.00
ATOM   1425  CG  LYS   318     -21.064  58.482 -16.128  1.00  0.00
ATOM   1426  CD  LYS   318     -21.385  58.915 -17.545  1.00  0.00
ATOM   1427  CE  LYS   318     -22.521  59.941 -17.566  1.00  0.00
ATOM   1428  NZ  LYS   318     -23.341  59.629 -18.785  1.00  0.00
ATOM   1429  N   GLY   319     -17.090  56.501 -15.521  1.00  0.00
ATOM   1430  CA  GLY   319     -15.676  56.338 -15.466  1.00  0.00
ATOM   1431  C   GLY   319     -15.319  54.836 -15.472  1.00  0.00
ATOM   1432  O   GLY   319     -14.182  54.443 -15.230  1.00  0.00
ATOM   1433  OXT GLY   319     -16.220  54.034 -15.827  1.00  0.00
TER
END
