
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0319AL381_3
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL381_3.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    -       -      L       9           -
LGA    -       -      K      10           -
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    A     106      D      21          2.339
LGA    E     107      N      22          2.318
LGA    -       -      F      23           -
LGA    G     108      P      24          1.667
LGA    E     109      L      25          2.263
LGA    M     110      Q      26          2.152
LGA    K     111      Y      27          1.425
LGA    C     112      D      28          0.629
LGA    R     113      G      29          1.188
LGA    N     114      S      30          1.739
LGA    C     115      K      31          1.056
LGA    G     116      C      32          2.082
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      P      72           -
LGA    -       -      P      73           -
LGA    -       -      T      74           -
LGA    -       -      K      75           -
LGA    -       -      P      76           -
LGA    -       -      S      77           -
LGA    -       -      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    -       -      M      90           -
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    -       -      L      93           -
LGA    -       -      N      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      H      97           -
LGA    -       -      T      98           -
LGA    -       -      L      99           -
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    H     117      E     109          1.327
LGA    I     118      M     110          0.787
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      I     121           -
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   13  135    5.0     13    1.71     0.00      9.068     0.718

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.147508 * X  +  -0.897657 * Y  +   0.415276 * Z  +   1.943617
  Y_new =  -0.026359 * X  +  -0.423288 * Y  +  -0.905612 * Z  +   4.986536
  Z_new =   0.988710 * X  +   0.122639 * Y  +  -0.086100 * Z  +   3.069282 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.182903   -0.958690  [ DEG:   125.0711    -54.9289 ]
  Theta =  -1.420385   -1.721208  [ DEG:   -81.3821    -98.6179 ]
  Phi   =  -0.176829    2.964763  [ DEG:   -10.1316    169.8684 ]
 
# 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: T0319AL381_3                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_3.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13  135   5.0   13   1.71    0.00   9.068
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_3
REMARK Aligment from pdb entry: 1dl6A
ATOM      1  N   ALA   106       8.129  -3.607   4.695  1.00  0.00              
ATOM      2  CA  ALA   106       6.990  -3.733   5.592  1.00  0.00              
ATOM      3  C   ALA   106       7.426  -3.523   7.035  1.00  0.00              
ATOM      4  O   ALA   106       8.294  -4.230   7.548  1.00  0.00              
ATOM      5  N   GLU   107       6.813  -2.545   7.678  1.00  0.00              
ATOM      6  CA  GLU   107       7.117  -2.214   9.069  1.00  0.00              
ATOM      7  C   GLU   107       8.441  -1.467   9.182  1.00  0.00              
ATOM      8  O   GLU   107       9.118  -1.534  10.208  1.00  0.00              
ATOM      9  N   GLY   108       8.804  -0.752   8.121  1.00  0.00              
ATOM     10  CA  GLY   108      10.046   0.001   8.124  1.00  0.00              
ATOM     11  C   GLY   108       9.829   1.493   7.958  1.00  0.00              
ATOM     12  O   GLY   108      10.727   2.290   8.230  1.00  0.00              
ATOM     13  N   GLU   109       8.634   1.877   7.512  1.00  0.00              
ATOM     14  CA  GLU   109       8.305   3.285   7.312  1.00  0.00              
ATOM     15  C   GLU   109       9.122   3.878   6.168  1.00  0.00              
ATOM     16  O   GLU   109       9.836   3.161   5.465  1.00  0.00              
ATOM     17  N   MET   110       9.011   5.190   5.988  1.00  0.00              
ATOM     18  CA  MET   110       9.740   5.882   4.932  1.00  0.00              
ATOM     19  C   MET   110      10.712   6.897   5.524  1.00  0.00              
ATOM     20  O   MET   110      10.303   7.833   6.210  1.00  0.00              
ATOM     21  N   LYS   111      12.003   6.701   5.267  1.00  0.00              
ATOM     22  CA  LYS   111      13.025   7.584   5.785  1.00  0.00              
ATOM     23  C   LYS   111      13.684   8.397   4.674  1.00  0.00              
ATOM     24  O   LYS   111      13.688   7.991   3.514  1.00  0.00              
ATOM     25  N   CYS   112      14.247   9.547   5.041  1.00  0.00              
ATOM     26  CA  CYS   112      14.915  10.412   4.073  1.00  0.00              
ATOM     27  C   CYS   112      16.432  10.228   4.145  1.00  0.00              
ATOM     28  O   CYS   112      17.000  10.152   5.232  1.00  0.00              
ATOM     29  N   ARG   113      17.109  10.145   2.984  1.00  0.00              
ATOM     30  CA  ARG   113      18.564   9.958   2.934  1.00  0.00              
ATOM     31  C   ARG   113      19.343  11.231   3.265  1.00  0.00              
ATOM     32  O   ARG   113      20.574  11.237   3.231  1.00  0.00              
ATOM     33  N   ASN   114      18.628  12.307   3.586  1.00  0.00              
ATOM     34  CA  ASN   114      19.266  13.574   3.919  1.00  0.00              
ATOM     35  C   ASN   114      18.999  13.956   5.375  1.00  0.00              
ATOM     36  O   ASN   114      19.866  13.789   6.232  1.00  0.00              
ATOM     37  N   CYS   115      17.798  14.465   5.658  1.00  0.00              
ATOM     38  CA  CYS   115      17.450  14.853   7.024  1.00  0.00              
ATOM     39  C   CYS   115      17.333  13.627   7.924  1.00  0.00              
ATOM     40  O   CYS   115      17.287  13.750   9.149  1.00  0.00              
ATOM     41  N   GLY   116      17.281  12.444   7.315  1.00  0.00              
ATOM     42  CA  GLY   116      17.166  11.224   8.088  1.00  0.00              
ATOM     43  C   GLY   116      15.899  11.190   8.914  1.00  0.00              
ATOM     44  O   GLY   116      15.946  10.990  10.129  1.00  0.00              
ATOM     45  N   HIS   117      14.760  11.386   8.257  1.00  0.00              
ATOM     46  CA  HIS   117      13.477  11.376   8.947  1.00  0.00              
ATOM     47  C   HIS   117      12.807  10.014   8.810  1.00  0.00              
ATOM     48  O   HIS   117      13.346   9.116   8.166  1.00  0.00              
ATOM     49  N   ILE   118      11.637   9.872   9.422  1.00  0.00              
ATOM     50  CA  ILE   118      10.893   8.620   9.373  1.00  0.00              
ATOM     51  C   ILE   118       9.389   8.876   9.368  1.00  0.00              
ATOM     52  O   ILE   118       8.766   8.993  10.423  1.00  0.00              
END
