
#######################################################
#                                                     #
#                        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    6 (   52),  selected    6 , name T0386TS046_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS046_2-D2.T0386_D2.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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    N     219      Y     254          3.239
LGA    P     220      T     255          2.567
LGA    E     221      G     256          1.327
LGA    K     222      T     257          2.555
LGA    I     223      Y     258          2.397
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    R     224      D     294          1.874
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   81    5.0      6    2.40     0.00      6.108     0.240

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.404119 * X  +  -0.511777 * Y  +   0.758137 * Z  +  56.996475
  Y_new =  -0.464728 * X  +   0.828764 * Y  +   0.311734 * Z  +  -0.227376
  Z_new =  -0.787855 * X  +  -0.226350 * Y  +  -0.572757 * Z  +  84.553749 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.765236    0.376357  [ DEG:  -158.4364     21.5636 ]
  Theta =   0.907318    2.234274  [ DEG:    51.9855    128.0145 ]
  Phi   =  -2.286549    0.855044  [ DEG:  -131.0096     48.9904 ]
 
# 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: T0386TS046_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS046_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   81   5.0    6   2.40    0.00   6.108
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS046_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2G03_A
ATOM   1462  N   ASN   219      23.354  54.826  82.754  1.00  5.02
ATOM   1463  CA  ASN   219      22.321  55.616  83.364  1.00  5.02
ATOM   1464  C   ASN   219      22.794  56.214  84.672  1.00  5.02
ATOM   1465  O   ASN   219      22.742  57.435  84.801  1.00  5.02
ATOM   1466  CB  ASN   219      21.089  54.756  83.653  1.00  5.02
ATOM   1467  CG  ASN   219      19.953  55.553  84.263  1.00  5.02
ATOM   1468  OD1 ASN   219      19.385  56.436  83.620  1.00  5.02
ATOM   1469  ND2 ASN   219      19.618  55.244  85.511  1.00  5.02
ATOM   1470  N   PRO   220      23.264  55.481  85.656  1.00  5.69
ATOM   1471  CA  PRO   220      23.784  56.191  86.794  1.00  5.69
ATOM   1472  C   PRO   220      24.987  57.038  86.556  1.00  5.69
ATOM   1473  O   PRO   220      25.202  57.973  87.325  1.00  5.69
ATOM   1474  CB  PRO   220      24.141  55.085  87.788  1.00  5.69
ATOM   1475  CG  PRO   220      23.269  53.938  87.402  1.00  5.69
ATOM   1476  CD  PRO   220      23.149  53.992  85.904  1.00  5.69
ATOM   1477  N   GLU   221      25.794  56.739  85.529  1.00  5.62
ATOM   1478  CA  GLU   221      26.900  57.601  85.244  1.00  5.62
ATOM   1479  C   GLU   221      26.264  58.920  84.950  1.00  5.62
ATOM   1480  O   GLU   221      26.687  59.962  85.447  1.00  5.62
ATOM   1481  CB  GLU   221      27.694  57.077  84.046  1.00  5.62
ATOM   1482  CG  GLU   221      28.926  57.900  83.710  1.00  5.62
ATOM   1483  CD  GLU   221      29.718  57.319  82.556  1.00  5.62
ATOM   1484  OE1 GLU   221      29.314  56.261  82.031  1.00  5.62
ATOM   1485  OE2 GLU   221      30.745  57.922  82.177  1.00  5.62
ATOM   1486  N   LYS   222      25.171  58.873  84.165  1.00  5.81
ATOM   1487  CA  LYS   222      24.451  60.032  83.728  1.00  5.81
ATOM   1488  C   LYS   222      23.850  60.715  84.912  1.00  5.81
ATOM   1489  O   LYS   222      23.778  61.941  84.961  1.00  5.81
ATOM   1490  CB  LYS   222      23.334  59.636  82.760  1.00  5.81
ATOM   1491  CG  LYS   222      22.544  60.811  82.208  1.00  5.81
ATOM   1492  CD  LYS   222      21.506  60.353  81.197  1.00  5.81
ATOM   1493  CE  LYS   222      20.697  61.526  80.666  1.00  5.81
ATOM   1494  NZ  LYS   222      19.666  61.089  79.685  1.00  5.81
ATOM   1495  N   ILE   223      23.369  59.949  85.905  1.00  5.54
ATOM   1496  CA  ILE   223      22.848  60.632  87.049  1.00  5.54
ATOM   1497  C   ILE   223      23.843  60.491  88.164  1.00  5.54
ATOM   1498  O   ILE   223      23.882  59.489  88.875  1.00  5.54
ATOM   1499  CB  ILE   223      21.498  60.040  87.494  1.00  5.54
ATOM   1500  CG1 ILE   223      20.476  60.130  86.359  1.00  5.54
ATOM   1501  CG2 ILE   223      20.954  60.798  88.694  1.00  5.54
ATOM   1502  CD1 ILE   223      19.190  59.383  86.634  1.00  5.54
ATOM   1503  N   ARG   224      24.681  61.532  88.349  1.00  5.84
ATOM   1504  CA  ARG   224      25.687  61.547  89.373  1.00  5.84
ATOM   1505  C   ARG   224      24.986  61.430  90.719  1.00  5.84
ATOM   1506  O   ARG   224      24.459  62.467  91.205  1.00  5.84
ATOM   1507  CB  ARG   224      26.487  62.850  89.319  1.00  5.84
ATOM   1508  CG  ARG   224      27.351  62.997  88.076  1.00  5.84
ATOM   1509  CD  ARG   224      28.094  64.322  88.075  1.00  5.84
ATOM   1510  NE  ARG   224      28.908  64.492  86.873  1.00  5.84
ATOM   1511  CZ  ARG   224      29.607  65.586  86.592  1.00  5.84
ATOM   1512  NH1 ARG   224      30.318  65.651  85.475  1.00  5.84
ATOM   1513  NH2 ARG   224      29.594  66.615  87.430  1.00  5.84
TER
END
