
#######################################################
#                                                     #
#                        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 (   24),  selected    6 , name T0295AL333_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_5-D2.T0295_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     181           -
LGA    -       -      N     182           -
LGA    -       -      F     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      L     190           -
LGA    -       -      R     191           -
LGA    -       -      I     192           -
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    -       -      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    E     266      K     199          0.890
LGA    F     267      T     200          1.969
LGA    N     268      L     201          1.635
LGA    K     269      H     202          0.876
LGA    K     270      A     203          0.241
LGA    G     271      I     204          1.147
LGA    -       -      F     205           -
LGA    -       -      K     206           -
LGA    -       -      R     207           -
LGA    -       -      N     208           -
LGA    -       -      A     209           -
LGA    -       -      V     210           -
LGA    -       -      L     211           -
LGA    -       -      N     212           -
LGA    -       -      M     213           -
LGA    -       -      L     214           -
LGA    -       -      E     215           -
LGA    -       -      H     216           -
LGA    -       -      N     217           -
LGA    -       -      Y     218           -
LGA    -       -      K     219           -
LGA    -       -      N     220           -
LGA    -       -      W     221           -
LGA    -       -      C     222           -
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      N     225           -
LGA    -       -      K     226           -
LGA    -       -      Q     227           -
LGA    -       -      V     228           -
LGA    -       -      P     229           -
LGA    -       -      V     230           -
LGA    -       -      N     231           -
LGA    -       -      F     232           -
LGA    -       -      P     233           -
LGA    -       -      F     234           -
LGA    -       -      K     235           -
LGA    -       -      K     236           -
LGA    -       -      Y     237           -
LGA    -       -      C     238           -
LGA    -       -      L     239           -
LGA    -       -      D     240           -
LGA    -       -      V     241           -
LGA    -       -      L     242           -
LGA    -       -      E     243           -
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    -       -      D     246           -
LGA    -       -      M     247           -
LGA    -       -      C     248           -
LGA    -       -      E     249           -
LGA    -       -      K     250           -
LGA    -       -      R     251           -
LGA    -       -      S     252           -
LGA    -       -      I     253           -
LGA    -       -      N     254           -
LGA    -       -      L     255           -
LGA    -       -      D     256           -
LGA    -       -      E     257           -
LGA    -       -      N     258           -
LGA    -       -      D     259           -
LGA    -       -      F     260           -
LGA    -       -      L     261           -
LGA    -       -      K     262           -
LGA    -       -      L     263           -
LGA    -       -      L     264           -
LGA    -       -      L     265           -
LGA    -       -      E     266           -
LGA    -       -      F     267           -
LGA    -       -      N     268           -
LGA    -       -      K     269           -
LGA    -       -      K     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   95    5.0      6    1.26     0.00      6.154     0.442

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.541585 * X  +  -0.661891 * Y  +   0.518253 * Z  +  -6.851432
  Y_new =   0.611283 * X  +   0.733280 * Y  +   0.297712 * Z  +  23.425690
  Z_new =  -0.577078 * X  +   0.155563 * Y  +   0.801737 * Z  + -15.423625 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.191651   -2.949942  [ DEG:    10.9808   -169.0192 ]
  Theta =   0.615146    2.526447  [ DEG:    35.2453    144.7547 ]
  Phi   =   0.845781   -2.295811  [ DEG:    48.4597   -131.5403 ]
 
# 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: T0295AL333_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_5-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   95   5.0    6   1.26    0.00   6.154
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_5-D2
REMARK Aligment from pdb entry: 1dl5_A
ATOM    585  N   GLU   266      12.844  15.873 -14.700  1.00  0.00              
ATOM    586  CA  GLU   266      14.277  15.620 -14.860  1.00  0.00              
ATOM    587  C   GLU   266      15.091  15.539 -13.581  1.00  0.00              
ATOM    588  O   GLU   266      14.768  16.166 -12.568  1.00  0.00              
ATOM    589  N   PHE   267      16.161  14.756 -13.650  1.00  0.00              
ATOM    590  CA  PHE   267      17.073  14.620 -12.528  1.00  0.00              
ATOM    591  C   PHE   267      18.323  15.390 -12.917  1.00  0.00              
ATOM    592  O   PHE   267      18.305  16.136 -13.902  1.00  0.00              
ATOM    593  N   ASN   268      19.407  15.223 -12.165  1.00  0.00              
ATOM    594  CA  ASN   268      20.632  15.930 -12.489  1.00  0.00              
ATOM    595  C   ASN   268      20.503  17.445 -12.420  1.00  0.00              
ATOM    596  O   ASN   268      19.676  17.977 -11.678  1.00  0.00              
ATOM    597  N   LYS   269      21.318  18.142 -13.205  1.00  0.00              
ATOM    598  CA  LYS   269      21.301  19.602 -13.221  1.00  0.00              
ATOM    599  C   LYS   269      20.069  20.190 -13.905  1.00  0.00              
ATOM    600  O   LYS   269      19.915  21.406 -13.967  1.00  0.00              
ATOM    601  N   LYS   270      19.190  19.334 -14.422  1.00  0.00              
ATOM    602  CA  LYS   270      17.975  19.834 -15.051  1.00  0.00              
ATOM    603  C   LYS   270      16.830  19.817 -14.040  1.00  0.00              
ATOM    604  O   LYS   270      15.699  20.171 -14.362  1.00  0.00              
ATOM    605  N   GLY   271      17.136  19.420 -12.806  1.00  0.00              
ATOM    606  CA  GLY   271      16.105  19.367 -11.781  1.00  0.00              
ATOM    607  C   GLY   271      16.515  19.926 -10.433  1.00  0.00              
ATOM    608  O   GLY   271      15.807  19.742  -9.442  1.00  0.00              
END
