
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_5-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    -       -      G      44           -
LGA    -       -      Q      45           -
LGA    P     129      R      46          2.070
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    V     316      F      49          2.851
LGA    R     317      A      50          1.422
LGA    K     318      E      51          1.693
LGA    G     319      S      52          2.134
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
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    2.09     0.00      3.014     0.228

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.886830 * X  +   0.414587 * Y  +  -0.204083 * Z  +  -4.174616
  Y_new =   0.049836 * X  +   0.353263 * Y  +   0.934196 * Z  +  59.092819
  Z_new =   0.459400 * X  +  -0.838644 * Y  +   0.292623 * Z  +  32.881477 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.235080    1.906512  [ DEG:   -70.7649    109.2351 ]
  Theta =  -0.477320   -2.664273  [ DEG:   -27.3484   -152.6516 ]
  Phi   =   0.056136   -3.085456  [ DEG:     3.2164   -176.7836 ]
 
# 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_5-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_5-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   2.09    0.00   3.014
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_5-D1
PFRMAT TS
TARGET T0298
MODEL  5  REFINED
PARENT 1PQP_A 1MB4_B 1T4B_B
ATOM      1  N   PRO   129     -21.757  48.240  -9.575  1.00  0.00
ATOM      2  CA  PRO   129     -22.298  49.365  -8.911  1.00  0.00
ATOM      3  C   PRO   129     -23.312  50.193  -9.797  1.00  0.00
ATOM      4  O   PRO   129     -23.960  51.056  -9.200  1.00  0.00
ATOM      5  CB  PRO   129     -21.104  50.293  -8.603  1.00  0.00
ATOM      6  CG  PRO   129     -20.254  50.069  -9.851  1.00  0.00
ATOM      7  CD  PRO   129     -20.542  48.639 -10.336  1.00  0.00
ATOM   1402  N   VAL   316     -30.590  56.910  -5.979  1.00  0.00
ATOM   1403  CA  VAL   316     -29.663  57.383  -4.977  1.00  0.00
ATOM   1404  C   VAL   316     -29.430  56.323  -3.862  1.00  0.00
ATOM   1405  O   VAL   316     -28.307  56.429  -3.260  1.00  0.00
ATOM   1406  CB  VAL   316     -30.190  58.687  -4.358  1.00  0.00
ATOM   1407  CG1 VAL   316     -31.174  59.446  -5.265  1.00  0.00
ATOM   1408  CG2 VAL   316     -30.893  58.697  -2.981  1.00  0.00
ATOM   1409  N   ARG   317     -30.477  55.814  -3.175  1.00  0.00
ATOM   1410  CA  ARG   317     -30.323  54.861  -2.092  1.00  0.00
ATOM   1411  C   ARG   317     -29.554  53.529  -2.408  1.00  0.00
ATOM   1412  O   ARG   317     -28.342  53.508  -2.145  1.00  0.00
ATOM   1413  CB  ARG   317     -31.699  54.454  -1.608  1.00  0.00
ATOM   1414  CG  ARG   317     -32.531  55.496  -0.964  1.00  0.00
ATOM   1415  CD  ARG   317     -32.048  55.858   0.414  1.00  0.00
ATOM   1416  NE  ARG   317     -32.819  56.884   1.091  1.00  0.00
ATOM   1417  CZ  ARG   317     -32.824  58.200   0.770  1.00  0.00
ATOM   1418  NH1 ARG   317     -32.103  58.706  -0.271  1.00  0.00
ATOM   1419  NH2 ARG   317     -33.566  59.022   1.533  1.00  0.00
ATOM   1420  N   LYS   318     -30.067  52.639  -3.285  1.00  0.00
ATOM   1421  CA  LYS   318     -29.453  51.346  -3.553  1.00  0.00
ATOM   1422  C   LYS   318     -28.639  51.349  -4.864  1.00  0.00
ATOM   1423  O   LYS   318     -27.677  50.576  -4.940  1.00  0.00
ATOM   1424  CB  LYS   318     -30.582  50.311  -3.495  1.00  0.00
ATOM   1425  CG  LYS   318     -31.123  49.728  -2.205  1.00  0.00
ATOM   1426  CD  LYS   318     -30.020  49.104  -1.361  1.00  0.00
ATOM   1427  CE  LYS   318     -30.294  49.220   0.188  1.00  0.00
ATOM   1428  NZ  LYS   318     -31.759  48.832   0.359  1.00  0.00
ATOM   1429  N   GLY   319     -29.107  52.054  -5.893  1.00  0.00
ATOM   1430  CA  GLY   319     -28.411  52.226  -7.143  1.00  0.00
ATOM   1431  C   GLY   319     -27.345  53.326  -6.944  1.00  0.00
ATOM   1432  O   GLY   319     -26.398  53.418  -7.723  1.00  0.00
ATOM   1433  OXT GLY   319     -27.266  53.893  -5.827  1.00  0.00
TER
END
