
#######################################################
#                                                     #
#                        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_2_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_2_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          3.126
LGA    P     220      T     255          2.744
LGA    E     221      G     256          1.290
LGA    K     222      T     257          3.000
LGA    I     223      Y     258          2.099
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    R     224      G     293          2.934
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    2.61     0.00      5.723     0.221

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.585963 * X  +  -0.529445 * Y  +   0.613462 * Z  +  57.330460
  Y_new =  -0.738224 * X  +   0.660973 * Y  +  -0.134683 * Z  +   4.214971
  Z_new =  -0.334175 * X  +  -0.531791 * Y  +  -0.778155 * Z  + 109.688538 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.542094    0.599498  [ DEG:  -145.6513     34.3487 ]
  Theta =   0.340729    2.800863  [ DEG:    19.5224    160.4776 ]
  Phi   =  -2.241713    0.899880  [ DEG:  -128.4407     51.5593 ]
 
# 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_2_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_2_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   2.61    0.00   5.723
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219      23.343  54.741  82.965  1.00  0.80
ATOM   1471  CA  ASN   219      22.281  55.486  83.633  1.00  0.80
ATOM   1472  C   ASN   219      22.761  56.299  84.839  1.00  0.80
ATOM   1473  O   ASN   219      22.308  57.417  85.035  1.00  0.80
ATOM   1474  CB  ASN   219      21.136  54.593  84.051  1.00  0.80
ATOM   1475  CG  ASN   219      20.379  53.954  82.898  1.00  0.90
ATOM   1476  OD1 ASN   219      19.598  54.714  82.255  1.00  0.90
ATOM   1477  ND2 ASN   219      20.497  52.685  82.712  1.00  1.10
ATOM   1478  N   PRO   220      23.655  55.734  85.646  1.00  0.80
ATOM   1479  CA  PRO   220      24.148  56.433  86.826  1.00  0.80
ATOM   1480  C   PRO   220      25.052  57.590  86.403  1.00  0.80
ATOM   1481  O   PRO   220      24.923  58.688  86.910  1.00  0.80
ATOM   1482  CB  PRO   220      24.868  55.466  87.778  1.00  0.80
ATOM   1483  CG  PRO   220      24.922  54.014  87.315  1.00  0.90
ATOM   1484  CD  PRO   220      24.726  54.421  85.596  1.00  0.90
ATOM   1485  N   GLU   221      25.953  57.337  85.455  1.00  0.80
ATOM   1486  CA  GLU   221      26.821  58.352  84.887  1.00  0.80
ATOM   1487  C   GLU   221      26.061  59.589  84.395  1.00  0.80
ATOM   1488  O   GLU   221      26.480  60.731  84.643  1.00  0.80
ATOM   1489  CB  GLU   221      27.610  57.748  83.723  1.00  0.80
ATOM   1490  CG  GLU   221      28.491  56.736  84.173  1.00  0.90
ATOM   1491  CD  GLU   221      29.721  57.174  85.164  1.00  0.90
ATOM   1492  OE1 GLU   221      30.343  58.188  84.999  1.00  1.10
ATOM   1493  OE2 GLU   221      29.994  56.418  86.112  1.00  1.10
ATOM   1494  N   LYS   222      24.962  59.358  83.680  1.00  0.80
ATOM   1495  CA  LYS   222      24.119  60.435  83.139  1.00  0.80
ATOM   1496  C   LYS   222      23.337  61.170  84.230  1.00  0.80
ATOM   1497  O   LYS   222      22.959  62.344  84.065  1.00  0.80
ATOM   1498  CB  LYS   222      23.187  59.923  81.999  1.00  0.80
ATOM   1499  CG  LYS   222      22.375  61.048  81.397  1.00  0.90
ATOM   1500  CD  LYS   222      21.490  60.470  80.292  1.00  0.90
ATOM   1501  CE  LYS   222      20.391  59.559  80.680  1.00  1.10
ATOM   1502  NZ  LYS   222      19.327  60.244  81.507  1.00  1.10
ATOM   1503  N   ILE   223      23.668  60.292  85.240  1.00  0.80
ATOM   1504  CA  ILE   223      23.014  60.945  86.379  1.00  0.80
ATOM   1505  C   ILE   223      23.955  61.937  87.125  1.00  0.80
ATOM   1506  O   ILE   223      23.507  62.967  87.628  1.00  0.80
ATOM   1507  CB  ILE   223      22.497  59.843  87.300  1.00  0.80
ATOM   1508  CG1 ILE   223      21.411  58.936  86.770  1.00  0.90
ATOM   1509  CG2 ILE   223      22.093  60.502  88.626  1.00  0.90
ATOM   1510  CD1 ILE   223      21.049  57.755  87.518  1.00  1.10
ATOM   1511  N   ARG   224      25.254  61.644  87.154  1.00  0.80
ATOM   1512  CA  ARG   224      26.221  62.451  87.886  1.00  0.80
ATOM   1513  C   ARG   224      26.202  63.881  87.403  1.00  0.80
ATOM   1514  O   ARG   224      26.427  64.809  88.183  1.00  0.80
ATOM   1515  CB  ARG   224      27.637  61.908  87.768  1.00  0.80
ATOM   1516  CG  ARG   224      27.919  60.584  88.458  1.00  0.90
ATOM   1517  CD  ARG   224      29.343  60.251  88.103  1.00  0.90
ATOM   1518  NE  ARG   224      29.637  58.977  88.750  1.00  1.10
ATOM   1519  CZ  ARG   224      30.831  58.391  88.707  1.00  1.10
ATOM   1520  NH1 ARG   224      31.804  58.936  87.976  1.00  1.40
ATOM   1521  NH2 ARG   224      30.994  57.242  89.354  1.00  1.40
TER
END
