
#######################################################
#                                                     #
#                        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    8 (   32),  selected    8 , name T0295AL333_4-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_4-D2.T0295_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    -       -      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    -       -      K     199           -
LGA    -       -      T     200           -
LGA    -       -      L     201           -
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    -       -      I     204           -
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    N     217      Y     237          2.565
LGA    Y     218      C     238          3.320
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    K     219      F     267          1.176
LGA    N     220      N     268          1.854
LGA    W     221      K     269          0.738
LGA    C     222      K     270          0.538
LGA    F     267      G     271          3.126
LGA    N     268      I     272          1.337
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8   95    5.0      8    2.09    12.50      7.202     0.366

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.990653 * X  +  -0.124286 * Y  +  -0.056207 * Z  +   7.757957
  Y_new =   0.118492 * X  +   0.579987 * Y  +   0.805962 * Z  + -19.700966
  Z_new =  -0.067570 * X  +  -0.805089 * Y  +   0.589293 * Z  +  17.279587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.938941    2.202652  [ DEG:   -53.7974    126.2026 ]
  Theta =   0.067622    3.073971  [ DEG:     3.8744    176.1255 ]
  Phi   =   0.119044   -3.022548  [ DEG:     6.8207   -173.1793 ]
 
# 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_4-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_4-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8   95   5.0    8   2.09   12.50   7.202
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_4-D2
REMARK Aligment from pdb entry: 1jg1_A
ATOM    585  N   ASN   217      30.348  26.355  -5.666  1.00  0.00              
ATOM    586  CA  ASN   217      30.294  24.941  -5.381  1.00  0.00              
ATOM    587  C   ASN   217      29.244  24.741  -4.325  1.00  0.00              
ATOM    588  O   ASN   217      29.460  25.162  -3.165  1.00  0.00              
ATOM    589  N   TYR   218      28.103  24.142  -4.637  1.00  0.00              
ATOM    590  CA  TYR   218      26.964  24.044  -3.735  1.00  0.00              
ATOM    591  C   TYR   218      26.878  22.602  -3.259  1.00  0.00              
ATOM    592  O   TYR   218      26.737  21.694  -4.114  1.00  0.00              
ATOM    593  N   LYS   219      26.997  22.386  -1.957  1.00  0.00              
ATOM    594  CA  LYS   219      26.869  21.001  -1.457  1.00  0.00              
ATOM    595  C   LYS   219      27.364  20.920  -0.019  1.00  0.00              
ATOM    596  O   LYS   219      27.635  21.930   0.613  1.00  0.00              
ATOM    597  N   ASN   220      27.466  19.655   0.412  1.00  0.00              
ATOM    598  CA  ASN   220      27.685  19.387   1.823  1.00  0.00              
ATOM    599  C   ASN   220      28.992  19.956   2.329  1.00  0.00              
ATOM    600  O   ASN   220      29.031  20.416   3.474  1.00  0.00              
ATOM    601  N   TRP   221      30.018  19.934   1.499  1.00  0.00              
ATOM    602  CA  TRP   221      31.329  20.501   1.872  1.00  0.00              
ATOM    603  C   TRP   221      31.602  21.733   1.008  1.00  0.00              
ATOM    604  O   TRP   221      32.769  22.138   0.899  1.00  0.00              
ATOM    605  N   CYS   222      30.567  22.334   0.438  1.00  0.00              
ATOM    606  CA  CYS   222      30.680  23.614  -0.219  1.00  0.00              
ATOM    607  C   CYS   222      29.739  24.620   0.447  1.00  0.00              
ATOM    608  O   CYS   222      29.572  24.644   1.678  1.00  0.00              
ATOM    609  N   PHE   267      29.116  25.459  -0.363  1.00  0.00              
ATOM    610  CA  PHE   267      28.144  26.433   0.053  1.00  0.00              
ATOM    611  C   PHE   267      26.795  25.755   0.294  1.00  0.00              
ATOM    612  O   PHE   267      26.372  24.872  -0.456  1.00  0.00              
ATOM    613  N   ASN   268      26.093  26.168   1.337  1.00  0.00              
ATOM    614  CA  ASN   268      24.706  25.658   1.455  1.00  0.00              
ATOM    615  C   ASN   268      23.795  26.186   0.354  1.00  0.00              
ATOM    616  O   ASN   268      24.051  27.238  -0.242  1.00  0.00              
END
