
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0319AL381_4
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL381_4.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    E     107      N       7          1.764
LGA    -       -      F       8           -
LGA    G     108      L       9          3.347
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    E     109      L      25          1.206
LGA    M     110      Q      26          1.044
LGA    K     111      Y      27          0.369
LGA    C     112      D      28          0.635
LGA    R     113      G      29          0.739
LGA    N     114      S      30          1.238
LGA    C     115      K      31          0.745
LGA    G     116      C      32          2.661
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          1.165
LGA    I     118      M     110          1.099
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)   12  135    5.0     12    1.57     0.00      8.291     0.717

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.670611 * X  +  -0.511048 * Y  +   0.537690 * Z  +   7.175407
  Y_new =  -0.270167 * X  +  -0.843315 * Y  +  -0.464575 * Z  +   2.872836
  Z_new =   0.690862 * X  +   0.166283 * Y  +  -0.703605 * Z  +   4.762155 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.909521   -0.232072  [ DEG:   166.7033    -13.2967 ]
  Theta =  -0.762681   -2.378912  [ DEG:   -43.6984   -136.3016 ]
  Phi   =  -0.382975    2.758617  [ DEG:   -21.9429    158.0571 ]
 
# 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_4                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_4.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  135   5.0   12   1.57    0.00   8.291
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_4
REMARK Aligment from pdb entry: 1rlyA
ATOM      1  N   GLU   107      16.386  -0.050  11.545  1.00  0.00              
ATOM      2  CA  GLU   107      15.497  -0.944  12.290  1.00  0.00              
ATOM      3  C   GLU   107      14.203  -0.222  12.650  1.00  0.00              
ATOM      4  O   GLU   107      13.629  -0.444  13.716  1.00  0.00              
ATOM      5  N   GLY   108      13.751   0.650  11.748  1.00  0.00              
ATOM      6  CA  GLY   108      12.530   1.398  11.985  1.00  0.00              
ATOM      7  C   GLY   108      11.637   1.478  10.758  1.00  0.00              
ATOM      8  O   GLY   108      11.354   0.466  10.119  1.00  0.00              
ATOM      9  N   GLU   109      11.181   2.689  10.446  1.00  0.00              
ATOM     10  CA  GLU   109      10.299   2.916   9.300  1.00  0.00              
ATOM     11  C   GLU   109      11.087   3.410   8.081  1.00  0.00              
ATOM     12  O   GLU   109      12.182   2.926   7.812  1.00  0.00              
ATOM     13  N   MET   110      10.524   4.355   7.331  1.00  0.00              
ATOM     14  CA  MET   110      11.176   4.877   6.134  1.00  0.00              
ATOM     15  C   MET   110      12.060   6.084   6.453  1.00  0.00              
ATOM     16  O   MET   110      11.582   7.136   6.844  1.00  0.00              
ATOM     17  N   LYS   111      13.356   5.887   6.345  1.00  0.00              
ATOM     18  CA  LYS   111      14.329   6.911   6.690  1.00  0.00              
ATOM     19  C   LYS   111      14.815   7.702   5.481  1.00  0.00              
ATOM     20  O   LYS   111      15.409   7.160   4.558  1.00  0.00              
ATOM     21  N   CYS   112      14.562   8.999   5.501  1.00  0.00              
ATOM     22  CA  CYS   112      14.984   9.858   4.417  1.00  0.00              
ATOM     23  C   CYS   112      16.461  10.213   4.571  1.00  0.00              
ATOM     24  O   CYS   112      16.818  11.017   5.415  1.00  0.00              
ATOM     25  N   ARG   113      17.340   9.641   3.743  1.00  0.00              
ATOM     26  CA  ARG   113      18.781   9.883   3.833  1.00  0.00              
ATOM     27  C   ARG   113      19.181  11.344   3.973  1.00  0.00              
ATOM     28  O   ARG   113      20.312  11.634   4.359  1.00  0.00              
ATOM     29  N   ASN   114      18.289  12.268   3.660  1.00  0.00              
ATOM     30  CA  ASN   114      18.639  13.680   3.753  1.00  0.00              
ATOM     31  C   ASN   114      18.093  14.338   5.003  1.00  0.00              
ATOM     32  O   ASN   114      18.863  14.904   5.766  1.00  0.00              
ATOM     33  N   CYS   115      16.808  14.194   5.302  1.00  0.00              
ATOM     34  CA  CYS   115      16.326  14.748   6.559  1.00  0.00              
ATOM     35  C   CYS   115      16.332  13.619   7.555  1.00  0.00              
ATOM     36  O   CYS   115      16.217  13.830   8.748  1.00  0.00              
ATOM     37  N   GLY   116      16.482  12.412   7.016  1.00  0.00              
ATOM     38  CA  GLY   116      16.536  11.202   7.802  1.00  0.00              
ATOM     39  C   GLY   116      15.253  10.905   8.548  1.00  0.00              
ATOM     40  O   GLY   116      15.245  10.197   9.557  1.00  0.00              
ATOM     41  N   HIS   117      14.180  11.476   8.045  1.00  0.00              
ATOM     42  CA  HIS   117      12.857  11.333   8.630  1.00  0.00              
ATOM     43  C   HIS   117      12.359   9.895   8.544  1.00  0.00              
ATOM     44  O   HIS   117      12.642   9.195   7.575  1.00  0.00              
ATOM     45  N   ILE   118      11.634   9.458   9.567  1.00  0.00              
ATOM     46  CA  ILE   118      11.116   8.108   9.609  1.00  0.00              
ATOM     47  C   ILE   118       9.598   8.097   9.493  1.00  0.00              
ATOM     48  O   ILE   118       8.901   8.730  10.285  1.00  0.00              
END
