
#######################################################
#                                                     #
#                        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 T0386TS074_1_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_1_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    N     219      K     222          0.111
LGA    P     220      I     223          0.100
LGA    E     221      R     224          0.102
LGA    K     222      L     225          0.125
LGA    I     223      L     226          0.357
LGA    R     224      K     227          0.372
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    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
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    -       -      D     294           -
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    0.23     0.00      7.407     1.825

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.045458 * X  +   0.884127 * Y  +  -0.465029 * Z  + -55.774445
  Y_new =  -0.997246 * X  +  -0.012856 * Y  +   0.073042 * Z  +  51.181942
  Z_new =   0.058600 * X  +   0.467069 * Y  +   0.882277 * Z  +  54.293133 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.486883   -2.654710  [ DEG:    27.8963   -152.1037 ]
  Theta =  -0.058634   -3.082959  [ DEG:    -3.3595   -176.6405 ]
  Phi   =  -1.616348    1.525244  [ DEG:   -92.6099     87.3901 ]
 
# 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: T0386TS074_1_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_1_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   0.23    0.00   7.407
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       5.275  58.398  78.362  1.00  0.90
ATOM   1471  CA  ASN   219       6.532  58.473  77.624  1.00  0.90
ATOM   1472  C   ASN   219       6.651  59.712  76.731  1.00  0.90
ATOM   1473  O   ASN   219       7.719  60.301  76.651  1.00  0.90
ATOM   1474  CB  ASN   219       6.781  57.232  76.799  1.00  0.90
ATOM   1475  CG  ASN   219       6.981  55.963  77.611  1.00  1.00
ATOM   1476  OD1 ASN   219       6.156  55.027  77.397  1.00  1.00
ATOM   1477  ND2 ASN   219       7.895  55.951  78.520  1.00  1.20
ATOM   1478  N   PRO   220       5.569  60.090  76.056  1.00  0.90
ATOM   1479  CA  PRO   220       5.605  61.247  75.170  1.00  0.90
ATOM   1480  C   PRO   220       5.711  62.528  75.995  1.00  0.90
ATOM   1481  O   PRO   220       6.508  63.394  75.687  1.00  0.90
ATOM   1482  CB  PRO   220       4.382  61.266  74.240  1.00  0.90
ATOM   1483  CG  PRO   220       3.405  60.109  74.423  1.00  1.00
ATOM   1484  CD  PRO   220       3.903  59.787  76.098  1.00  1.00
ATOM   1485  N   GLU   221       4.913  62.631  77.056  1.00  0.90
ATOM   1486  CA  GLU   221       4.959  63.745  77.986  1.00  0.90
ATOM   1487  C   GLU   221       6.368  64.030  78.517  1.00  0.90
ATOM   1488  O   GLU   221       6.796  65.194  78.588  1.00  0.90
ATOM   1489  CB  GLU   221       4.024  63.460  79.163  1.00  0.90
ATOM   1490  CG  GLU   221       2.674  63.401  78.742  1.00  1.00
ATOM   1491  CD  GLU   221       1.995  64.772  78.153  1.00  1.00
ATOM   1492  OE1 GLU   221       2.206  65.849  78.640  1.00  1.20
ATOM   1493  OE2 GLU   221       1.246  64.667  77.166  1.00  1.20
ATOM   1494  N   LYS   222       7.074  62.972  78.909  1.00  0.90
ATOM   1495  CA  LYS   222       8.442  63.074  79.438  1.00  0.90
ATOM   1496  C   LYS   222       9.462  63.438  78.357  1.00  0.90
ATOM   1497  O   LYS   222      10.528  64.010  78.650  1.00  0.90
ATOM   1498  CB  LYS   222       8.857  61.793  80.222  1.00  0.90
ATOM   1499  CG  LYS   222      10.237  61.933  80.826  1.00  1.00
ATOM   1500  CD  LYS   222      10.571  60.641  81.575  1.00  1.00
ATOM   1501  CE  LYS   222      10.777  59.407  80.784  1.00  1.20
ATOM   1502  NZ  LYS   222      11.987  59.482  79.883  1.00  1.20
ATOM   1503  N   ILE   223       9.130  63.104  77.112  1.00  0.90
ATOM   1504  CA  ILE   223       9.945  63.480  75.952  1.00  0.90
ATOM   1505  C   ILE   223       9.866  65.001  75.629  1.00  0.90
ATOM   1506  O   ILE   223      10.846  65.598  75.184  1.00  0.90
ATOM   1507  CB  ILE   223       9.484  62.620  74.777  1.00  0.90
ATOM   1508  CG1 ILE   223       9.706  61.128  74.868  1.00  1.00
ATOM   1509  CG2 ILE   223      10.103  63.212  73.503  1.00  1.00
ATOM   1510  CD1 ILE   223       9.095  60.262  73.887  1.00  1.20
ATOM   1511  N   ARG   224       8.720  65.625  75.896  1.00  0.90
ATOM   1512  CA  ARG   224       8.498  67.027  75.567  1.00  0.90
ATOM   1513  C   ARG   224       9.530  67.905  76.233  1.00  0.90
ATOM   1514  O   ARG   224       9.925  68.935  75.683  1.00  0.90
ATOM   1515  CB  ARG   224       7.110  67.504  75.968  1.00  0.90
ATOM   1516  CG  ARG   224       5.941  66.928  75.188  1.00  1.00
ATOM   1517  CD  ARG   224       4.711  67.494  75.848  1.00  1.00
ATOM   1518  NE  ARG   224       3.571  66.950  75.120  1.00  1.20
ATOM   1519  CZ  ARG   224       2.308  67.277  75.385  1.00  1.20
ATOM   1520  NH1 ARG   224       2.040  68.080  76.414  1.00  1.50
ATOM   1521  NH2 ARG   224       1.348  66.738  74.641  1.00  1.50
TER
END
