
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0319AL381_5
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL381_5.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    -       -      D      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      P      24           -
LGA    -       -      L      25           -
LGA    Q     102      Q      26          1.233
LGA    T     103      Y      27          0.817
LGA    S     104      D      28          0.672
LGA    I     105      G      29          0.673
LGA    A     106      S      30          0.893
LGA    E     107      K      31          1.697
LGA    G     108      C      32          2.071
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    E     109      E     109          1.389
LGA    M     110      M     110          1.103
LGA    K     111      K     111          0.652
LGA    C     112      C     112          0.495
LGA    R     113      R     113          0.352
LGA    N     114      N     114          0.931
LGA    C     115      C     115          0.836
LGA    G     116      G     116          0.670
LGA    H     117      H     117          0.783
LGA    I     118      I     118          1.063
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)   17  135    5.0     17    1.05    64.71     12.303     1.478

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.758061 * X  +   0.132668 * Y  +   0.638547 * Z  +  12.780232
  Y_new =   0.208227 * X  +   0.977082 * Y  +   0.044196 * Z  +   8.786755
  Z_new =  -0.618049 * X  +   0.166466 * Y  +  -0.768312 * Z  +  12.036155 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.928226   -0.213367  [ DEG:   167.7750    -12.2250 ]
  Theta =   0.666259    2.475334  [ DEG:    38.1738    141.8262 ]
  Phi   =   2.873521   -0.268072  [ DEG:   164.6406    -15.3594 ]
 
# 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_5                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_5.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  135   5.0   17   1.05   64.71  12.303
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_5
REMARK Aligment from pdb entry: 1pft
ATOM      1  N   GLN   102      10.507   3.205   6.754  1.00  0.00              
ATOM      2  CA  GLN   102      11.560   3.519   5.798  1.00  0.00              
ATOM      3  C   GLN   102      12.193   4.867   6.128  1.00  0.00              
ATOM      4  O   GLN   102      11.603   5.685   6.832  1.00  0.00              
ATOM      5  N   THR   103      13.453   5.017   5.731  1.00  0.00              
ATOM      6  CA  THR   103      14.268   6.145   6.159  1.00  0.00              
ATOM      7  C   THR   103      14.319   7.208   5.065  1.00  0.00              
ATOM      8  O   THR   103      13.890   6.970   3.937  1.00  0.00              
ATOM      9  N   SER   104      14.660   8.427   5.473  1.00  0.00              
ATOM     10  CA  SER   104      14.593   9.584   4.599  1.00  0.00              
ATOM     11  C   SER   104      15.807  10.501   4.853  1.00  0.00              
ATOM     12  O   SER   104      15.739  11.464   5.632  1.00  0.00              
ATOM     13  N   ILE   105      16.953  10.113   4.260  1.00  0.00              
ATOM     14  CA  ILE   105      18.257  10.767   4.536  1.00  0.00              
ATOM     15  C   ILE   105      18.278  12.256   4.189  1.00  0.00              
ATOM     16  O   ILE   105      19.254  12.950   4.468  1.00  0.00              
ATOM     17  N   ALA   106      17.317  12.649   3.359  1.00  0.00              
ATOM     18  CA  ALA   106      17.258  14.008   2.836  1.00  0.00              
ATOM     19  C   ALA   106      16.763  14.966   3.921  1.00  0.00              
ATOM     20  O   ALA   106      17.391  15.991   4.181  1.00  0.00              
ATOM     21  N   GLU   107      15.822  14.467   4.719  1.00  0.00              
ATOM     22  CA  GLU   107      15.270  15.237   5.822  1.00  0.00              
ATOM     23  C   GLU   107      15.866  14.770   7.148  1.00  0.00              
ATOM     24  O   GLU   107      15.775  15.466   8.158  1.00  0.00              
ATOM     25  N   GLY   108      16.323  13.523   7.159  1.00  0.00              
ATOM     26  CA  GLY   108      16.693  12.846   8.394  1.00  0.00              
ATOM     27  C   GLY   108      15.465  12.206   9.037  1.00  0.00              
ATOM     28  O   GLY   108      15.281  12.276  10.250  1.00  0.00              
ATOM     29  N   GLU   109      14.575  11.704   8.188  1.00  0.00              
ATOM     30  CA  GLU   109      13.248  11.282   8.624  1.00  0.00              
ATOM     31  C   GLU   109      13.146   9.758   8.588  1.00  0.00              
ATOM     32  O   GLU   109      13.889   9.097   7.865  1.00  0.00              
ATOM     33  N   MET   110      12.104   9.244   9.230  1.00  0.00              
ATOM     34  CA  MET   110      11.718   7.847   9.082  1.00  0.00              
ATOM     35  C   MET   110      10.198   7.720   9.039  1.00  0.00              
ATOM     36  O   MET   110       9.507   8.080   9.988  1.00  0.00              
ATOM     37  N   LYS   111       9.697   7.258   7.899  1.00  0.00              
ATOM     38  CA  LYS   111       8.269   7.292   7.618  1.00  0.00              
ATOM     39  C   LYS   111       7.697   5.873   7.656  1.00  0.00              
ATOM     40  O   LYS   111       8.437   4.901   7.504  1.00  0.00              
ATOM     41  N   CYS   112       6.373   5.797   7.602  1.00  0.00              
ATOM     42  CA  CYS   112       5.680   4.549   7.297  1.00  0.00              
ATOM     43  C   CYS   112       5.849   4.204   5.820  1.00  0.00              
ATOM     44  O   CYS   112       5.842   5.087   4.964  1.00  0.00              
ATOM     45  N   ARG   113       5.822   2.906   5.534  1.00  0.00              
ATOM     46  CA  ARG   113       5.797   2.419   4.165  1.00  0.00              
ATOM     47  C   ARG   113       4.371   2.039   3.762  1.00  0.00              
ATOM     48  O   ARG   113       4.171   1.190   2.895  1.00  0.00              
ATOM     49  N   ASN   114       3.421   2.487   4.579  1.00  0.00              
ATOM     50  CA  ASN   114       2.027   2.111   4.415  1.00  0.00              
ATOM     51  C   ASN   114       1.133   3.342   4.377  1.00  0.00              
ATOM     52  O   ASN   114       0.770   3.822   3.300  1.00  0.00              
ATOM     53  N   CYS   115       1.022   4.009   5.531  1.00  0.00              
ATOM     54  CA  CYS   115       0.055   5.092   5.673  1.00  0.00              
ATOM     55  C   CYS   115       0.648   6.431   5.259  1.00  0.00              
ATOM     56  O   CYS   115      -0.040   7.455   5.290  1.00  0.00              
ATOM     57  N   GLY   116       1.982   6.459   5.171  1.00  0.00              
ATOM     58  CA  GLY   116       2.686   7.669   4.775  1.00  0.00              
ATOM     59  C   GLY   116       3.267   8.399   5.987  1.00  0.00              
ATOM     60  O   GLY   116       3.773   9.518   5.850  1.00  0.00              
ATOM     61  N   HIS   117       2.836   7.942   7.163  1.00  0.00              
ATOM     62  CA  HIS   117       3.079   8.658   8.407  1.00  0.00              
ATOM     63  C   HIS   117       4.573   8.661   8.730  1.00  0.00              
ATOM     64  O   HIS   117       5.149   7.608   9.009  1.00  0.00              
ATOM     65  N   ILE   118       5.099   9.862   8.958  1.00  0.00              
ATOM     66  CA  ILE   118       6.426  10.026   9.532  1.00  0.00              
ATOM     67  C   ILE   118       6.480   9.395  10.926  1.00  0.00              
ATOM     68  O   ILE   118       5.464   9.318  11.615  1.00  0.00              
END
