
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0358AL381_1
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL381_1.T0358.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    V      40      R      51          2.991
LGA    V      41      A      52          4.443
LGA    R      42      -       -           -
LGA    D      43      W      53          2.661
LGA    E      45      N      54          4.501
LGA    G      46      F      55          3.113
LGA    R      47      E      56          2.783
LGA    M      48      P      57          3.778
LGA    -       -      D      58           -
LGA    V      49      A      59          4.180
LGA    W      50      G      60          1.952
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    R      51      N      64          2.422
LGA    A      52      R      65          3.236
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    W      53      R      68          0.333
LGA    N      54      T      69          1.817
LGA    F      55      S      70          1.888
LGA    E      56      G      71          2.314
LGA    P      57      I      72           -
LGA    D      58      R      73          4.954
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   66    5.0     16    3.18     0.00     14.983     0.487

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.380026 * X  +  -0.431577 * Y  +  -0.818120 * Z  + -26.438595
  Y_new =   0.890741 * X  +  -0.067653 * Y  +   0.449448 * Z  + -39.101818
  Z_new =  -0.249320 * X  +  -0.899535 * Y  +   0.358714 * Z  +  54.847488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.191345    1.950248  [ DEG:   -68.2590    111.7410 ]
  Theta =   0.251978    2.889615  [ DEG:    14.4373    165.5627 ]
  Phi   =   1.167537   -1.974055  [ DEG:    66.8950   -113.1050 ]
 
# 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_1                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_1.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   66   5.0   16   3.18    0.00  14.983
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_1
REMARK Aligment from pdb entry: 1zorA
ATOM      1  N   VAL    40      -2.637   4.546   4.569  1.00  0.00              
ATOM      2  CA  VAL    40      -1.577   4.468   3.549  1.00  0.00              
ATOM      3  C   VAL    40      -2.090   5.018   2.230  1.00  0.00              
ATOM      4  O   VAL    40      -1.513   5.948   1.663  1.00  0.00              
ATOM      5  N   VAL    41      -3.211   4.479   1.780  1.00  0.00              
ATOM      6  CA  VAL    41      -3.803   4.884   0.512  1.00  0.00              
ATOM      7  C   VAL    41      -4.163   6.379   0.451  1.00  0.00              
ATOM      8  O   VAL    41      -4.275   6.983  -0.627  1.00  0.00              
ATOM      9  N   ARG    42      -4.333   6.963   1.630  1.00  0.00              
ATOM     10  CA  ARG    42      -4.792   8.323   1.812  1.00  0.00              
ATOM     11  C   ARG    42      -3.603   9.288   1.939  1.00  0.00              
ATOM     12  O   ARG    42      -3.752  10.508   1.809  1.00  0.00              
ATOM     13  N   ASP    43      -2.423   8.743   2.211  1.00  0.00              
ATOM     14  CA  ASP    43      -1.260   9.559   2.588  1.00  0.00              
ATOM     15  C   ASP    43      -0.476  10.135   1.405  1.00  0.00              
ATOM     16  O   ASP    43      -0.763   9.835   0.244  1.00  0.00              
ATOM     17  N   GLU    45       0.515  10.964   1.728  1.00  0.00              
ATOM     18  CA  GLU    45       1.469  11.477   0.742  1.00  0.00              
ATOM     19  C   GLU    45       2.623  10.488   0.484  1.00  0.00              
ATOM     20  O   GLU    45       3.508  10.759  -0.329  1.00  0.00              
ATOM     21  N   GLY    46       2.582   9.341   1.167  1.00  0.00              
ATOM     22  CA  GLY    46       3.683   8.381   1.212  1.00  0.00              
ATOM     23  C   GLY    46       4.796   8.854   2.141  1.00  0.00              
ATOM     24  O   GLY    46       4.593   9.762   2.949  1.00  0.00              
ATOM     25  N   ARG    47       5.986   8.257   2.025  1.00  0.00              
ATOM     26  CA  ARG    47       7.147   8.776   2.727  1.00  0.00              
ATOM     27  C   ARG    47       7.566   8.036   3.977  1.00  0.00              
ATOM     28  O   ARG    47       8.517   8.452   4.627  1.00  0.00              
ATOM     29  N   MET    48       6.877   6.941   4.306  1.00  0.00              
ATOM     30  CA  MET    48       7.129   6.201   5.521  1.00  0.00              
ATOM     31  C   MET    48       7.567   4.764   5.199  1.00  0.00              
ATOM     32  O   MET    48       7.347   4.258   4.090  1.00  0.00              
ATOM     33  N   VAL    49       8.202   4.127   6.175  1.00  0.00              
ATOM     34  CA  VAL    49       8.355   2.671   6.176  1.00  0.00              
ATOM     35  C   VAL    49       7.101   2.052   6.767  1.00  0.00              
ATOM     36  O   VAL    49       6.730   2.373   7.892  1.00  0.00              
ATOM     37  N   TRP    50       6.447   1.177   6.008  1.00  0.00              
ATOM     38  CA  TRP    50       5.346   0.373   6.547  1.00  0.00              
ATOM     39  C   TRP    50       5.849  -1.038   6.835  1.00  0.00              
ATOM     40  O   TRP    50       6.016  -1.853   5.929  1.00  0.00              
ATOM     41  N   ARG    51       6.064  -1.327   8.111  1.00  0.00              
ATOM     42  CA  ARG    51       6.513  -2.628   8.556  1.00  0.00              
ATOM     43  C   ARG    51       5.276  -3.535   8.641  1.00  0.00              
ATOM     44  O   ARG    51       4.258  -3.154   9.227  1.00  0.00              
ATOM     45  N   ALA    52       5.351  -4.717   8.038  1.00  0.00              
ATOM     46  CA  ALA    52       4.188  -5.605   7.951  1.00  0.00              
ATOM     47  C   ALA    52       4.548  -6.999   8.443  1.00  0.00              
ATOM     48  O   ALA    52       5.650  -7.473   8.188  1.00  0.00              
ATOM     49  N   TRP    53       3.604  -7.657   9.104  1.00  0.00              
ATOM     50  CA  TRP    53       3.733  -9.077   9.400  1.00  0.00              
ATOM     51  C   TRP    53       3.754  -9.860   8.087  1.00  0.00              
ATOM     52  O   TRP    53       3.499  -9.303   7.030  1.00  0.00              
ATOM     53  N   ASN    54       4.032 -11.157   8.162  1.00  0.00              
ATOM     54  CA  ASN    54       4.401 -11.947   6.989  1.00  0.00              
ATOM     55  C   ASN    54       3.377 -11.933   5.810  1.00  0.00              
ATOM     56  O   ASN    54       3.710 -11.553   4.679  1.00  0.00              
ATOM     57  N   PHE    55       2.148 -12.354   6.094  1.00  0.00              
ATOM     58  CA  PHE    55       1.068 -12.427   5.119  1.00  0.00              
ATOM     59  C   PHE    55       0.694 -11.067   4.518  1.00  0.00              
ATOM     60  O   PHE    55       0.678 -10.912   3.296  1.00  0.00              
ATOM     61  N   GLU    56       0.425 -10.095   5.383  1.00  0.00              
ATOM     62  CA  GLU    56       0.157  -8.718   4.996  1.00  0.00              
ATOM     63  C   GLU    56       1.282  -8.140   4.141  1.00  0.00              
ATOM     64  O   GLU    56       1.017  -7.437   3.179  1.00  0.00              
ATOM     65  N   PRO    57       2.532  -8.412   4.518  1.00  0.00              
ATOM     66  CA  PRO    57       3.706  -7.911   3.787  1.00  0.00              
ATOM     67  C   PRO    57       3.807  -8.554   2.416  1.00  0.00              
ATOM     68  O   PRO    57       4.180  -7.896   1.465  1.00  0.00              
ATOM     69  N   ASP    58       3.457  -9.838   2.317  1.00  0.00              
ATOM     70  CA  ASP    58       3.411 -10.533   1.031  1.00  0.00              
ATOM     71  C   ASP    58       2.422  -9.806   0.112  1.00  0.00              
ATOM     72  O   ASP    58       2.771  -9.414  -0.997  1.00  0.00              
END
