
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0358AL381_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL381_2-D1.T0358_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    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    V      40      W      53          1.614
LGA    V      41      N      54          2.326
LGA    R      42      F      55          1.273
LGA    D      43      E      56          0.678
LGA    T      44      P      57          0.905
LGA    E      45      D      58          0.530
LGA    G      46      A      59          2.419
LGA    R      47      G      60          2.104
LGA    M      48      E      61          1.869
LGA    V      49      G      62          2.153
LGA    W      50      L      63          2.239
LGA    R      51      N      64          4.548
LGA    A      52      R      65          3.865
LGA    W      53      Y      66          3.908
LGA    N      54      I      67          4.434
LGA    F      55      R      68          0.976
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   65    5.0     16    2.58     0.00     19.043     0.598

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.438148 * X  +  -0.888318 * Y  +   0.137540 * Z  +   1.964938
  Y_new =   0.706187 * X  +  -0.245490 * Y  +   0.664104 * Z  + -32.909309
  Z_new =  -0.556171 * X  +   0.388105 * Y  +   0.734880 * Z  +   3.718739 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.485890   -2.655702  [ DEG:    27.8395   -152.1605 ]
  Theta =   0.589771    2.551821  [ DEG:    33.7914    146.2086 ]
  Phi   =   2.126111   -1.015481  [ DEG:   121.8172    -58.1828 ]
 
# 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: T0358AL381_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_2-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   65   5.0   16   2.58    0.00  19.043
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_2-D1
REMARK Aligment from pdb entry: 2eql
ATOM      1  N   VAL    40      -0.058   8.837   2.140  1.00  0.00              
ATOM      2  CA  VAL    40       0.543   8.170   3.295  1.00  0.00              
ATOM      3  C   VAL    40       1.939   7.676   2.939  1.00  0.00              
ATOM      4  O   VAL    40       2.870   8.075   3.639  1.00  0.00              
ATOM      5  N   VAL    41       2.148   6.856   1.880  1.00  0.00              
ATOM      6  CA  VAL    41       3.481   6.275   1.529  1.00  0.00              
ATOM      7  C   VAL    41       4.622   7.282   1.399  1.00  0.00              
ATOM      8  O   VAL    41       5.784   6.891   1.330  1.00  0.00              
ATOM      9  N   ARG    42       4.212   8.533   1.224  1.00  0.00              
ATOM     10  CA  ARG    42       5.053   9.673   1.056  1.00  0.00              
ATOM     11  C   ARG    42       5.535  10.281   2.358  1.00  0.00              
ATOM     12  O   ARG    42       6.068  11.386   2.396  1.00  0.00              
ATOM     13  N   ASP    43       5.254   9.648   3.459  1.00  0.00              
ATOM     14  CA  ASP    43       5.845  10.103   4.672  1.00  0.00              
ATOM     15  C   ASP    43       7.121   9.250   4.844  1.00  0.00              
ATOM     16  O   ASP    43       7.328   8.242   4.147  1.00  0.00              
ATOM     17  N   THR    44       8.047   9.642   5.720  1.00  0.00              
ATOM     18  CA  THR    44       9.214   8.834   6.105  1.00  0.00              
ATOM     19  C   THR    44       8.970   7.383   6.503  1.00  0.00              
ATOM     20  O   THR    44       9.860   6.570   6.277  1.00  0.00              
ATOM     21  N   GLU    45       7.857   6.955   7.111  1.00  0.00              
ATOM     22  CA  GLU    45       7.663   5.532   7.380  1.00  0.00              
ATOM     23  C   GLU    45       7.441   4.776   6.075  1.00  0.00              
ATOM     24  O   GLU    45       7.644   3.548   6.093  1.00  0.00              
ATOM     25  N   GLY    46       7.015   5.375   4.958  1.00  0.00              
ATOM     26  CA  GLY    46       6.772   4.585   3.760  1.00  0.00              
ATOM     27  C   GLY    46       5.722   3.509   4.048  1.00  0.00              
ATOM     28  O   GLY    46       4.853   3.734   4.923  1.00  0.00              
ATOM     29  N   ARG    47       5.822   2.283   3.459  1.00  0.00              
ATOM     30  CA  ARG    47       4.774   1.294   3.731  1.00  0.00              
ATOM     31  C   ARG    47       4.774   0.650   5.086  1.00  0.00              
ATOM     32  O   ARG    47       3.899  -0.139   5.443  1.00  0.00              
ATOM     33  N   MET    48       5.688   1.161   5.886  1.00  0.00              
ATOM     34  CA  MET    48       5.832   0.679   7.227  1.00  0.00              
ATOM     35  C   MET    48       4.793   1.333   8.127  1.00  0.00              
ATOM     36  O   MET    48       4.559   0.917   9.280  1.00  0.00              
ATOM     37  N   VAL    49       4.071   2.309   7.541  1.00  0.00              
ATOM     38  CA  VAL    49       2.904   2.844   8.232  1.00  0.00              
ATOM     39  C   VAL    49       1.871   1.722   8.415  1.00  0.00              
ATOM     40  O   VAL    49       1.004   1.844   9.277  1.00  0.00              
ATOM     41  N   TRP    50       1.962   0.600   7.658  1.00  0.00              
ATOM     42  CA  TRP    50       1.035  -0.511   7.723  1.00  0.00              
ATOM     43  C   TRP    50       1.609  -1.744   8.356  1.00  0.00              
ATOM     44  O   TRP    50       2.214  -2.571   7.700  1.00  0.00              
ATOM     45  N   ARG    51       1.341  -1.948   9.633  1.00  0.00              
ATOM     46  CA  ARG    51       1.755  -3.110  10.446  1.00  0.00              
ATOM     47  C   ARG    51       1.589  -4.492   9.838  1.00  0.00              
ATOM     48  O   ARG    51       2.445  -5.364  10.045  1.00  0.00              
ATOM     49  N   ALA    52       0.519  -4.700   9.069  1.00  0.00              
ATOM     50  CA  ALA    52       0.307  -5.989   8.438  1.00  0.00              
ATOM     51  C   ALA    52       1.238  -6.193   7.254  1.00  0.00              
ATOM     52  O   ALA    52       1.637  -7.329   6.944  1.00  0.00              
ATOM     53  N   TRP    53       1.642  -5.090   6.605  1.00  0.00              
ATOM     54  CA  TRP    53       2.533  -5.172   5.477  1.00  0.00              
ATOM     55  C   TRP    53       3.875  -5.483   6.086  1.00  0.00              
ATOM     56  O   TRP    53       4.568  -6.365   5.602  1.00  0.00              
ATOM     57  N   ASN    54       4.296  -4.740   7.102  1.00  0.00              
ATOM     58  CA  ASN    54       5.562  -4.978   7.797  1.00  0.00              
ATOM     59  C   ASN    54       5.678  -6.442   8.204  1.00  0.00              
ATOM     60  O   ASN    54       6.664  -7.075   7.858  1.00  0.00              
ATOM     61  N   PHE    55       4.635  -6.980   8.857  1.00  0.00              
ATOM     62  CA  PHE    55       4.577  -8.347   9.327  1.00  0.00              
ATOM     63  C   PHE    55       4.324  -9.374   8.240  1.00  0.00              
ATOM     64  O   PHE    55       4.551 -10.571   8.417  1.00  0.00              
END
