
#######################################################
#                                                     #
#                        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    5 (   37),  selected    5 , name T0320TS268_3_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_3_2-D2.T0320_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     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    N     228      I     252          0.598
LGA    N     229      H     253          0.421
LGA    S     230      A     254          0.633
LGA    L     231      F     255          0.406
LGA    P     232      G     256          0.418
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   73    5.0      5    0.51     0.00      6.849     0.826

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.192740 * X  +  -0.913643 * Y  +  -0.357922 * Z  +  31.394011
  Y_new =   0.839419 * X  +   0.035379 * Y  +  -0.542332 * Z  +  36.757763
  Z_new =   0.508161 * X  +  -0.404976 * Y  +   0.760110 * Z  + -63.327011 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.489531    2.652062  [ DEG:   -28.0480    151.9520 ]
  Theta =  -0.533048   -2.608545  [ DEG:   -30.5414   -149.4586 ]
  Phi   =   1.796495   -1.345098  [ DEG:   102.9316    -77.0684 ]
 
# 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: T0320TS268_3_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_3_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   73   5.0    5   0.51    0.00   6.849
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1sur
ATOM   1861  N   ASN   228      -4.765  24.799   8.229  1.00  0.00
ATOM   1862  CA  ASN   228      -4.523  23.668   9.078  1.00  0.00
ATOM   1863  C   ASN   228      -4.780  24.072  10.488  1.00  0.00
ATOM   1864  O   ASN   228      -4.453  25.186  10.895  1.00  0.00
ATOM   1865  CB  ASN   228      -3.074  23.195   8.939  1.00  0.00
ATOM   1866  CG  ASN   228      -2.795  22.563   7.590  1.00  0.00
ATOM   1867  OD1 ASN   228      -3.704  22.063   6.927  1.00  0.00
ATOM   1868  ND2 ASN   228      -1.532  22.583   7.179  1.00  0.00
ATOM   1869  N   ASN   229      -5.361  23.150  11.282  1.00  0.00
ATOM   1870  CA  ASN   229      -5.649  23.472  12.645  1.00  0.00
ATOM   1871  C   ASN   229      -4.347  23.827  13.272  1.00  0.00
ATOM   1872  O   ASN   229      -3.432  23.007  13.346  1.00  0.00
ATOM   1873  CB  ASN   229      -6.280  22.273  13.357  1.00  0.00
ATOM   1874  CG  ASN   229      -6.783  22.618  14.745  1.00  0.00
ATOM   1875  OD1 ASN   229      -6.343  23.595  15.349  1.00  0.00
ATOM   1876  ND2 ASN   229      -7.709  21.814  15.253  1.00  0.00
ATOM   1877  N   SER   230      -4.234  25.087  13.725  1.00  0.00
ATOM   1878  CA  SER   230      -3.007  25.536  14.304  1.00  0.00
ATOM   1879  C   SER   230      -3.345  26.745  15.112  1.00  0.00
ATOM   1880  O   SER   230      -4.498  27.171  15.154  1.00  0.00
ATOM   1881  CB  SER   230      -1.993  25.885  13.212  1.00  0.00
ATOM   1882  OG  SER   230      -2.399  27.033  12.488  1.00  0.00
ATOM   1883  N   LEU   231      -2.342  27.325  15.793  1.00  0.00
ATOM   1884  CA  LEU   231      -2.604  28.493  16.573  1.00  0.00
ATOM   1885  C   LEU   231      -2.929  29.578  15.605  1.00  0.00
ATOM   1886  O   LEU   231      -2.345  29.676  14.528  1.00  0.00
ATOM   1887  CB  LEU   231      -1.377  28.866  17.408  1.00  0.00
ATOM   1888  CG  LEU   231      -0.964  27.866  18.490  1.00  0.00
ATOM   1889  CD1 LEU   231       0.329  28.305  19.161  1.00  0.00
ATOM   1890  CD2 LEU   231      -2.040  27.756  19.558  1.00  0.00
ATOM   1891  N   PRO   232      -3.886  30.380  15.973  1.00  0.00
ATOM   1892  CA  PRO   232      -4.279  31.455  15.109  1.00  0.00
ATOM   1893  C   PRO   232      -3.397  32.631  15.349  1.00  0.00
ATOM   1894  O   PRO   232      -3.383  33.142  16.502  1.00  0.00
ATOM   1895  CB  PRO   232      -5.731  31.732  15.501  1.00  0.00
ATOM   1896  CG  PRO   232      -5.780  31.466  16.968  1.00  0.00
ATOM   1897  CD  PRO   232      -4.863  30.300  17.210  1.00  0.00
TER
END
