
#######################################################
#                                                     #
#                        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_4_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_4_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          0.146
LGA    P     220      I     223          0.116
LGA    E     221      R     224          0.168
LGA    K     222      L     225          0.268
LGA    I     223      L     226          0.543
LGA    R     224      K     227          0.331
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    0.30     0.00      7.407     1.501

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.050312 * X  +   0.867339 * Y  +  -0.495168 * Z  + -55.183102
  Y_new =  -0.998184 * X  +  -0.027229 * Y  +   0.053727 * Z  +  51.792538
  Z_new =   0.033116 * X  +   0.496972 * Y  +   0.867134 * Z  +  51.881065 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.520420   -2.621172  [ DEG:    29.8179   -150.1821 ]
  Theta =  -0.033122   -3.108470  [ DEG:    -1.8978   -178.1022 ]
  Phi   =  -1.621157    1.520436  [ DEG:   -92.8855     87.1145 ]
 
# 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_4_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_4_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   0.30    0.00   7.407
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       5.325  58.508  78.393  1.00  0.20
ATOM   1471  CA  ASN   219       6.570  58.547  77.634  1.00  0.20
ATOM   1472  C   ASN   219       6.690  59.757  76.704  1.00  0.20
ATOM   1473  O   ASN   219       7.764  60.330  76.591  1.00  0.20
ATOM   1474  CB  ASN   219       6.791  57.279  76.840  1.00  0.20
ATOM   1475  CG  ASN   219       6.988  56.031  77.685  1.00  0.30
ATOM   1476  OD1 ASN   219       8.114  55.915  78.252  1.00  0.30
ATOM   1477  ND2 ASN   219       6.060  55.139  77.692  1.00  0.50
ATOM   1478  N   PRO   220       5.603  60.130  76.036  1.00  0.20
ATOM   1479  CA  PRO   220       5.638  61.261  75.116  1.00  0.20
ATOM   1480  C   PRO   220       5.773  62.564  75.902  1.00  0.20
ATOM   1481  O   PRO   220       6.576  63.411  75.558  1.00  0.20
ATOM   1482  CB  PRO   220       4.400  61.270  74.207  1.00  0.20
ATOM   1483  CG  PRO   220       3.412  60.131  74.438  1.00  0.30
ATOM   1484  CD  PRO   220       3.933  59.849  76.113  1.00  0.30
ATOM   1485  N   GLU   221       4.994  62.707  76.973  1.00  0.20
ATOM   1486  CA  GLU   221       5.070  63.847  77.870  1.00  0.20
ATOM   1487  C   GLU   221       6.490  64.128  78.369  1.00  0.20
ATOM   1488  O   GLU   221       6.933  65.288  78.401  1.00  0.20
ATOM   1489  CB  GLU   221       4.151  63.606  79.070  1.00  0.20
ATOM   1490  CG  GLU   221       2.793  63.553  78.673  1.00  0.30
ATOM   1491  CD  GLU   221       2.121  64.916  78.056  1.00  0.30
ATOM   1492  OE1 GLU   221       2.353  66.003  78.508  1.00  0.50
ATOM   1493  OE2 GLU   221       1.354  64.792  77.084  1.00  0.50
ATOM   1494  N   LYS   222       7.189  63.073  78.781  1.00  0.20
ATOM   1495  CA  LYS   222       8.567  63.172  79.285  1.00  0.20
ATOM   1496  C   LYS   222       9.573  63.493  78.178  1.00  0.20
ATOM   1497  O   LYS   222      10.651  64.058  78.437  1.00  0.20
ATOM   1498  CB  LYS   222       8.979  61.908  80.099  1.00  0.20
ATOM   1499  CG  LYS   222      10.370  62.048  80.676  1.00  0.30
ATOM   1500  CD  LYS   222      10.701  60.772  81.456  1.00  0.30
ATOM   1501  CE  LYS   222      10.877  59.514  80.697  1.00  0.50
ATOM   1502  NZ  LYS   222      12.072  59.550  79.774  1.00  0.50
ATOM   1503  N   ILE   223       8.924  62.928  77.213  1.00  0.20
ATOM   1504  CA  ILE   223       9.779  63.329  76.091  1.00  0.20
ATOM   1505  C   ILE   223       9.716  64.858  75.802  1.00  0.20
ATOM   1506  O   ILE   223      10.713  65.462  75.406  1.00  0.20
ATOM   1507  CB  ILE   223       9.357  62.500  74.881  1.00  0.20
ATOM   1508  CG1 ILE   223       9.572  61.005  74.944  1.00  0.30
ATOM   1509  CG2 ILE   223      10.022  63.119  73.644  1.00  0.30
ATOM   1510  CD1 ILE   223       8.993  60.165  73.922  1.00  0.50
ATOM   1511  N   ARG   224       8.564  65.479  76.045  1.00  0.20
ATOM   1512  CA  ARG   224       8.357  66.889  75.741  1.00  0.20
ATOM   1513  C   ARG   224       9.368  67.748  76.464  1.00  0.20
ATOM   1514  O   ARG   224       9.785  68.789  75.952  1.00  0.20
ATOM   1515  CB  ARG   224       6.958  67.363  76.105  1.00  0.20
ATOM   1516  CG  ARG   224       5.814  66.810  75.272  1.00  0.30
ATOM   1517  CD  ARG   224       4.564  67.364  75.902  1.00  0.30
ATOM   1518  NE  ARG   224       3.449  66.842  75.122  1.00  0.50
ATOM   1519  CZ  ARG   224       2.178  67.167  75.351  1.00  0.50
ATOM   1520  NH1 ARG   224       1.876  67.946  76.390  1.00  0.80
ATOM   1521  NH2 ARG   224       1.242  66.650  74.561  1.00  0.80
TER
END
