
#######################################################
#                                                     #
#                        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    7 (   34),  selected    7 , name T0316TS102_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS102_5-D2.T0316_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    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    K     269      L     267          0.948
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    N     270      N     270          0.660
LGA    I     271      I     271          0.890
LGA    L     272      L     272          0.994
LGA    Y     273      Y     273          1.022
LGA    V     274      V     274          0.526
LGA    G     275      G     275          0.473
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   60    5.0      7    0.82    85.71     11.667     0.764

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.602070 * X  +  -0.542972 * Y  +  -0.585400 * Z  +  75.342407
  Y_new =   0.788216 * X  +   0.287216 * Y  +   0.544263 * Z  + -51.647030
  Z_new =  -0.127383 * X  +  -0.789106 * Y  +   0.600903 * Z  + -28.540226 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.919977    2.221616  [ DEG:   -52.7108    127.2892 ]
  Theta =   0.127730    3.013863  [ DEG:     7.3184    172.6816 ]
  Phi   =   0.918497   -2.223095  [ DEG:    52.6260   -127.3740 ]
 
# 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: T0316TS102_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   60   5.0    7   0.82   85.71  11.667
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_5-D2
PFRMAT TS
TARGET T0316
MODEL 5
PARENT 1jcm_P
ATOM    615  N   LYS   269      42.604  16.275 -13.202  1.00  1.00
ATOM    616  CA  LYS   269      42.587  15.764 -14.564  1.00  1.00
ATOM    617  C   LYS   269      43.393  16.629 -15.523  1.00  1.00
ATOM    618  O   LYS   269      43.634  17.809 -15.256  1.00  1.00
ATOM    619  CB  LYS   269      41.151  15.651 -15.058  1.00  1.00
ATOM    620  N   ASN   270      43.808  16.022 -16.637  1.00  1.00
ATOM    621  CA  ASN   270      44.581  16.704 -17.667  1.00  1.00
ATOM    622  C   ASN   270      43.656  17.522 -18.563  1.00  1.00
ATOM    623  O   ASN   270      44.073  18.504 -19.179  1.00  1.00
ATOM    624  CB  ASN   270      45.343  15.693 -18.531  1.00  1.00
ATOM    625  N   ILE   271      42.396  17.112 -18.625  1.00  1.00
ATOM    626  CA  ILE   271      41.456  17.808 -19.465  1.00  1.00
ATOM    627  C   ILE   271      40.017  17.522 -19.110  1.00  1.00
ATOM    628  O   ILE   271      39.724  16.732 -18.204  1.00  1.00
ATOM    629  CB  ILE   271      41.685  17.341 -20.915  1.00  1.00
ATOM    630  N   LEU   272      39.123  18.169 -19.850  1.00  1.00
ATOM    631  CA  LEU   272      37.687  18.058 -19.651  1.00  1.00
ATOM    632  C   LEU   272      36.944  17.866 -20.955  1.00  1.00
ATOM    633  O   LEU   272      37.367  18.342 -22.007  1.00  1.00
ATOM    634  CB  LEU   272      37.147  19.335 -19.015  1.00  1.00
ATOM    635  N   TYR   273      35.827  17.163 -20.860  1.00  1.00
ATOM    636  CA  TYR   273      34.961  16.946 -22.003  1.00  1.00
ATOM    637  C   TYR   273      33.667  17.594 -21.535  1.00  1.00
ATOM    638  O   TYR   273      33.007  17.109 -20.626  1.00  1.00
ATOM    639  CB  TYR   273      34.775  15.451 -22.283  1.00  1.00
ATOM    640  N   VAL   274      33.325  18.706 -22.164  1.00  1.00
ATOM    641  CA  VAL   274      32.155  19.494 -21.807  1.00  1.00
ATOM    642  C   VAL   274      31.131  19.554 -22.932  1.00  1.00
ATOM    643  O   VAL   274      31.463  19.927 -24.057  1.00  1.00
ATOM    644  CB  VAL   274      32.622  20.927 -21.448  1.00  1.00
ATOM    645  N   GLY   275      29.890  19.192 -22.614  1.00  1.00
ATOM    646  CA  GLY   275      28.821  19.216 -23.598  1.00  1.00
ATOM    647  C   GLY   275      27.757  20.271 -23.327  1.00  1.00
ATOM    648  O   GLY   275      27.798  21.362 -23.903  1.00  1.00
TER
END
