
#######################################################
#                                                     #
#                        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_3_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_3_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    N     219      K     249          1.026
LGA    P     220      E     250          2.367
LGA    E     221      G     251          0.574
LGA    K     222      E     252          0.661
LGA    I     223      T     253          2.431
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    R     224      T     299          1.368

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   81    5.0      6    1.59     0.00      6.942     0.355

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.269008 * X  +   0.945553 * Y  +  -0.183203 * Z  + -53.296612
  Y_new =   0.177018 * X  +  -0.138435 * Y  +  -0.974423 * Z  +  51.745975
  Z_new =  -0.946731 * X  +  -0.294558 * Y  +  -0.130140 * Z  +  88.926521 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.986823    1.154770  [ DEG:  -113.8366     66.1634 ]
  Theta =   1.242928    1.898665  [ DEG:    71.2145    108.7855 ]
  Phi   =   2.559586   -0.582007  [ DEG:   146.6535    -33.3465 ]
 
# 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_3_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_3_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   1.59    0.00   6.942
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219      12.450  48.387  78.567  1.00  0.50
ATOM   1471  CA  ASN   219      13.386  49.489  78.769  1.00  0.50
ATOM   1472  C   ASN   219      13.600  49.855  80.242  1.00  0.50
ATOM   1473  O   ASN   219      14.721  50.142  80.637  1.00  0.50
ATOM   1474  CB  ASN   219      12.986  50.724  77.996  1.00  0.50
ATOM   1475  CG  ASN   219      13.028  50.564  76.485  1.00  0.60
ATOM   1476  OD1 ASN   219      14.177  50.561  75.956  1.00  0.60
ATOM   1477  ND2 ASN   219      11.914  50.545  75.837  1.00  0.80
ATOM   1478  N   PRO   220      12.534  49.859  81.035  1.00  0.50
ATOM   1479  CA  PRO   220      12.650  50.216  82.444  1.00  0.50
ATOM   1480  C   PRO   220      13.382  49.109  83.200  1.00  0.50
ATOM   1481  O   PRO   220      14.273  49.383  83.982  1.00  0.50
ATOM   1482  CB  PRO   220      11.269  50.506  83.054  1.00  0.50
ATOM   1483  CG  PRO   220      10.091  50.368  82.096  1.00  0.60
ATOM   1484  CD  PRO   220      10.948  49.265  80.999  1.00  0.60
ATOM   1485  N   GLU   221      13.012  47.855  82.944  1.00  0.50
ATOM   1486  CA  GLU   221      13.672  46.694  83.514  1.00  0.50
ATOM   1487  C   GLU   221      15.192  46.709  83.320  1.00  0.50
ATOM   1488  O   GLU   221      15.952  46.410  84.256  1.00  0.50
ATOM   1489  CB  GLU   221      13.095  45.425  82.884  1.00  0.50
ATOM   1490  CG  GLU   221      11.729  45.262  83.220  1.00  0.60
ATOM   1491  CD  GLU   221      11.353  45.005  84.795  1.00  0.60
ATOM   1492  OE1 GLU   221      12.017  44.296  85.503  1.00  0.80
ATOM   1493  OE2 GLU   221      10.349  45.578  85.250  1.00  0.80
ATOM   1494  N   LYS   222      15.627  47.032  82.106  1.00  0.50
ATOM   1495  CA  LYS   222      17.054  47.097  81.758  1.00  0.50
ATOM   1496  C   LYS   222      17.761  48.291  82.402  1.00  0.50
ATOM   1497  O   LYS   222      18.986  48.267  82.619  1.00  0.50
ATOM   1498  CB  LYS   222      17.278  47.051  80.215  1.00  0.50
ATOM   1499  CG  LYS   222      18.749  47.044  79.867  1.00  0.60
ATOM   1500  CD  LYS   222      18.886  46.999  78.343  1.00  0.60
ATOM   1501  CE  LYS   222      18.459  48.184  77.567  1.00  0.80
ATOM   1502  NZ  LYS   222      19.304  49.405  77.850  1.00  0.80
ATOM   1503  N   ILE   223      16.985  49.328  82.704  1.00  0.50
ATOM   1504  CA  ILE   223      17.486  50.504  83.425  1.00  0.50
ATOM   1505  C   ILE   223      17.778  50.208  84.927  1.00  0.50
ATOM   1506  O   ILE   223      18.711  50.766  85.503  1.00  0.50
ATOM   1507  CB  ILE   223      16.454  51.616  83.251  1.00  0.50
ATOM   1508  CG1 ILE   223      16.230  52.154  81.856  1.00  0.60
ATOM   1509  CG2 ILE   223      16.810  52.733  84.241  1.00  0.60
ATOM   1510  CD1 ILE   223      15.119  53.045  81.613  1.00  0.80
ATOM   1511  N   ARG   224      16.118  49.261  85.711  1.00  0.50
ATOM   1512  CA  ARG   224      16.164  49.146  87.163  1.00  0.50
ATOM   1513  C   ARG   224      17.516  48.654  87.620  1.00  0.50
ATOM   1514  O   ARG   224      17.989  49.031  88.694  1.00  0.50
ATOM   1515  CB  ARG   224      15.090  48.214  87.706  1.00  0.50
ATOM   1516  CG  ARG   224      13.652  48.691  87.589  1.00  0.60
ATOM   1517  CD  ARG   224      12.817  47.552  88.110  1.00  0.60
ATOM   1518  NE  ARG   224      11.428  47.983  88.002  1.00  0.80
ATOM   1519  CZ  ARG   224      10.399  47.253  88.425  1.00  0.80
ATOM   1520  NH1 ARG   224      10.615  46.028  88.903  1.00  1.10
ATOM   1521  NH2 ARG   224       9.175  47.756  88.299  1.00  1.10
TER
END
