
#######################################################
#                                                     #
#                        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    9 (   36),  selected    9 , name T0378AL316_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL316_4-D1.T0378_D1.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    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    F       9      R      41          1.955
LGA    L      10      C      42          2.139
LGA    R      11      R      43          2.892
LGA    S      12      M      44          0.591
LGA    L      13      L      45          2.363
LGA    R      14      V      46          3.259
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    E      15      E      65          1.089
LGA    R      16      L      66          2.159
LGA    K      17      P      67          1.100
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9   89    5.0      9    2.12    33.33      8.414     0.406

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.047652 * X  +   0.236424 * Y  +   0.970481 * Z  + -24.644295
  Y_new =  -0.202842 * X  +  -0.953631 * Y  +   0.222359 * Z  +  16.464262
  Z_new =   0.978051 * X  +  -0.186259 * Y  +   0.093399 * Z  +  46.245682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.105990    2.035603  [ DEG:   -63.3686    116.6314 ]
  Theta =  -1.360894   -1.780699  [ DEG:   -77.9735   -102.0265 ]
  Phi   =  -1.801535    1.340058  [ DEG:  -103.2203     76.7797 ]
 
# 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: T0378AL316_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL316_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9   89   5.0    9   2.12   33.33   8.414
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL316_4-D1
REMARK Aligment from pdb entry: 1ipa_A
ATOM      1  N   PHE     9       5.378  13.441  55.148  1.00  0.00              
ATOM      2  CA  PHE     9       6.085  14.686  54.857  1.00  0.00              
ATOM      3  C   PHE     9       5.423  15.861  55.579  1.00  0.00              
ATOM      4  O   PHE     9       4.223  16.109  55.425  1.00  0.00              
ATOM      5  N   LEU    10       6.217  16.581  56.366  1.00  0.00              
ATOM      6  CA  LEU    10       5.726  17.718  57.138  1.00  0.00              
ATOM      7  C   LEU    10       5.726  19.029  56.353  1.00  0.00              
ATOM      8  O   LEU    10       5.939  20.098  56.928  1.00  0.00              
ATOM      9  N   ARG    11       5.493  18.949  55.047  1.00  0.00              
ATOM     10  CA  ARG    11       5.459  20.147  54.216  1.00  0.00              
ATOM     11  C   ARG    11       4.248  21.004  54.575  1.00  0.00              
ATOM     12  O   ARG    11       3.157  20.487  54.828  1.00  0.00              
ATOM     13  N   SER    12       4.445  22.318  54.603  1.00  0.00              
ATOM     14  CA  SER    12       3.365  23.227  54.941  1.00  0.00              
ATOM     15  C   SER    12       2.529  23.559  53.718  1.00  0.00              
ATOM     16  O   SER    12       2.970  23.379  52.582  1.00  0.00              
ATOM     17  N   LEU    13       1.320  24.052  53.960  1.00  0.00              
ATOM     18  CA  LEU    13       0.395  24.373  52.888  1.00  0.00              
ATOM     19  C   LEU    13      -0.101  25.812  52.882  1.00  0.00              
ATOM     20  O   LEU    13      -0.464  26.363  53.920  1.00  0.00              
ATOM     21  N   ARG    14      -0.097  26.411  51.694  1.00  0.00              
ATOM     22  CA  ARG    14      -0.588  27.771  51.488  1.00  0.00              
ATOM     23  C   ARG    14      -1.513  27.742  50.278  1.00  0.00              
ATOM     24  O   ARG    14      -1.113  27.359  49.175  1.00  0.00              
ATOM     25  N   GLU    15      -2.774  28.145  50.476  1.00  0.00              
ATOM     26  CA  GLU    15      -3.773  28.164  49.405  1.00  0.00              
ATOM     27  C   GLU    15      -3.349  28.908  48.144  1.00  0.00              
ATOM     28  O   GLU    15      -2.828  30.019  48.212  1.00  0.00              
ATOM     29  N   ARG    16      -3.577  28.289  46.993  1.00  0.00              
ATOM     30  CA  ARG    16      -3.239  28.911  45.724  1.00  0.00              
ATOM     31  C   ARG    16      -4.415  29.800  45.303  1.00  0.00              
ATOM     32  O   ARG    16      -5.506  29.690  45.852  1.00  0.00              
ATOM     33  N   LYS    17      -4.206  30.693  44.321  1.00  0.00              
ATOM     34  CA  LYS    17      -5.262  31.593  43.842  1.00  0.00              
ATOM     35  C   LYS    17      -6.522  30.911  43.294  1.00  0.00              
ATOM     36  O   LYS    17      -7.529  31.575  43.016  1.00  0.00              
END
