
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0363AL333_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_5-D1.T0363_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    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    I      42      T      37          2.986
LGA    T      43      V      38          2.476
LGA    -       -      Q      39           -
LGA    -       -      T      40           -
LGA    Q      44      A      41          1.845
LGA    S      45      I      42          2.864
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    G      46      S      45          1.272
LGA    I      47      G      46          0.887
LGA    -       -      I      47           -
LGA    -       -      L      48           -
LGA    L      48      S      49          1.882
LGA    S      49      Q      50          1.760
LGA    Q      50      F      51          3.893
LGA    F      51      P      52          4.689
LGA    P      52      E      53           #
LGA    E      53      -       -           -
LGA    I      54      -       -           -
LGA    D      55      I      54          3.374
LGA    L      56      D      55          2.978
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   46    5.0     12    2.79     0.00     18.774     0.416

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.078588 * X  +   0.989222 * Y  +   0.123549 * Z  +  45.326012
  Y_new =  -0.982125 * X  +  -0.055562 * Y  +  -0.179843 * Z  +  27.428844
  Z_new =  -0.171040 * X  +  -0.135473 * Y  +   0.975906 * Z  +  19.930445 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.137937    3.003656  [ DEG:    -7.9032    172.0968 ]
  Theta =   0.171885    2.969708  [ DEG:     9.8483    170.1517 ]
  Phi   =  -1.650644    1.490949  [ DEG:   -94.5749     85.4251 ]
 
# 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: T0363AL333_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_5-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   46   5.0   12   2.79    0.00  18.774
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_5-D1
REMARK Aligment from pdb entry: 1a62
ATOM      5  N   ILE    42      27.003  11.551  17.530  1.00  0.00              
ATOM      6  CA  ILE    42      26.318  11.687  16.265  1.00  0.00              
ATOM      7  C   ILE    42      27.347  11.283  15.204  1.00  0.00              
ATOM      8  O   ILE    42      28.546  11.580  15.333  1.00  0.00              
ATOM      9  N   THR    43      26.886  10.583  14.180  1.00  0.00              
ATOM     10  CA  THR    43      27.783  10.106  13.146  1.00  0.00              
ATOM     11  C   THR    43      27.453  10.642  11.775  1.00  0.00              
ATOM     12  O   THR    43      26.351  11.151  11.533  1.00  0.00              
ATOM     13  N   GLN    44      28.418  10.499  10.872  1.00  0.00              
ATOM     14  CA  GLN    44      28.245  10.936   9.499  1.00  0.00              
ATOM     15  C   GLN    44      29.189  10.153   8.592  1.00  0.00              
ATOM     16  O   GLN    44      30.076   9.443   9.071  1.00  0.00              
ATOM     17  N   SER    45      28.997  10.263   7.285  1.00  0.00              
ATOM     18  CA  SER    45      29.869   9.558   6.362  1.00  0.00              
ATOM     19  C   SER    45      29.818  10.200   4.991  1.00  0.00              
ATOM     20  O   SER    45      28.948  11.018   4.701  1.00  0.00              
ATOM     21  N   GLY    46      30.767   9.843   4.142  1.00  0.00              
ATOM     22  CA  GLY    46      30.772  10.420   2.813  1.00  0.00              
ATOM     23  C   GLY    46      32.057  10.149   2.073  1.00  0.00              
ATOM     24  O   GLY    46      32.961   9.495   2.591  1.00  0.00              
ATOM     25  N   ILE    47      32.125  10.649   0.847  1.00  0.00              
ATOM     26  CA  ILE    47      33.306  10.476   0.017  1.00  0.00              
ATOM     27  C   ILE    47      34.159  11.714   0.185  1.00  0.00              
ATOM     28  O   ILE    47      33.686  12.835   0.019  1.00  0.00              
ATOM     29  N   LEU    48      35.421  11.496   0.520  1.00  0.00              
ATOM     30  CA  LEU    48      36.325  12.599   0.749  1.00  0.00              
ATOM     31  C   LEU    48      36.906  13.198  -0.512  1.00  0.00              
ATOM     32  O   LEU    48      37.264  12.482  -1.457  1.00  0.00              
ATOM     33  N   SER    49      36.976  14.526  -0.524  1.00  0.00              
ATOM     34  CA  SER    49      37.600  15.273  -1.610  1.00  0.00              
ATOM     35  C   SER    49      38.474  16.298  -0.910  1.00  0.00              
ATOM     36  O   SER    49      37.977  17.137  -0.170  1.00  0.00              
ATOM     37  N   GLN    50      39.780  16.203  -1.112  1.00  0.00              
ATOM     38  CA  GLN    50      40.713  17.149  -0.517  1.00  0.00              
ATOM     39  C   GLN    50      40.845  18.313  -1.493  1.00  0.00              
ATOM     40  O   GLN    50      41.158  18.118  -2.669  1.00  0.00              
ATOM     41  N   PHE    51      40.592  19.526  -1.018  1.00  0.00              
ATOM     42  CA  PHE    51      40.686  20.697  -1.867  1.00  0.00              
ATOM     43  C   PHE    51      42.082  21.304  -1.856  1.00  0.00              
ATOM     44  O   PHE    51      42.983  20.807  -1.182  1.00  0.00              
ATOM     45  N   PRO    52      42.246  22.380  -2.616  1.00  0.00              
ATOM     46  CA  PRO    52      43.526  23.075  -2.739  1.00  0.00              
ATOM     47  C   PRO    52      44.191  23.442  -1.417  1.00  0.00              
ATOM     48  O   PRO    52      45.360  23.113  -1.187  1.00  0.00              
ATOM     49  N   GLU    53      43.454  24.131  -0.556  1.00  0.00              
ATOM     50  CA  GLU    53      43.986  24.559   0.730  1.00  0.00              
ATOM     51  C   GLU    53      44.502  23.420   1.615  1.00  0.00              
ATOM     52  O   GLU    53      45.176  23.667   2.612  1.00  0.00              
ATOM     53  N   ILE    54      30.595  17.391   5.254  1.00  0.00              
ATOM     54  CA  ILE    54      31.318  17.268   6.520  1.00  0.00              
ATOM     55  C   ILE    54      32.772  17.694   6.332  1.00  0.00              
ATOM     56  O   ILE    54      33.491  17.150   5.499  1.00  0.00              
ATOM     57  N   ASP    55      33.184  18.688   7.112  1.00  0.00              
ATOM     58  CA  ASP    55      34.543  19.210   7.052  1.00  0.00              
ATOM     59  C   ASP    55      35.565  18.246   7.621  1.00  0.00              
ATOM     60  O   ASP    55      35.364  17.690   8.701  1.00  0.00              
ATOM     61  N   LEU    56      36.671  18.064   6.900  1.00  0.00              
ATOM     62  CA  LEU    56      37.755  17.200   7.330  1.00  0.00              
ATOM     63  C   LEU    56      39.029  18.027   7.364  1.00  0.00              
ATOM     64  O   LEU    56      39.423  18.603   6.356  1.00  0.00              
END
