
#######################################################
#                                                     #
#                        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    5 (   38),  selected    5 , name T0318TS389_5-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS389_5-D1.T0318_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    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    -       -      V       6           -
LGA    -       -      R       7           -
LGA    -       -      N       8           -
LGA    -       -      G       9           -
LGA    -       -      I      10           -
LGA    -       -      Q      11           -
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    -       -      P      78           -
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    V     151      N      85          0.437
LGA    C     152      T      86          0.378
LGA    D     153      P      87          0.144
LGA    K     154      T      88          0.263
LGA    L     155      N      89          0.314
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      L     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    -       -      H     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      A     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      F     131           -
LGA    -       -      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  154    5.0      5    0.32     0.00      3.247     1.181

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.210983 * X  +  -0.882371 * Y  +  -0.420603 * Z  +  17.716860
  Y_new =   0.207130 * X  +   0.380161 * Y  +  -0.901429 * Z  +  39.109032
  Z_new =   0.955292 * X  +  -0.277306 * Y  +   0.102558 * Z  +  40.539238 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.216558    1.925034  [ DEG:   -69.7037    110.2963 ]
  Theta =  -1.270647   -1.870946  [ DEG:   -72.8027   -107.1973 ]
  Phi   =   2.365408   -0.776185  [ DEG:   135.5279    -44.4721 ]
 
# 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: T0318TS389_5-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS389_5-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  154   5.0    5   0.32    0.00   3.247
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS389_5-D1
PFRMAT TS
TARGET T0318
MODEL  5
PARENT N/A
ATOM      2  N   VAL   151      11.472  41.048  33.348  1.00  0.00
ATOM      3  CA  VAL   151      12.897  41.399  33.347  1.00  0.00
ATOM      4  CB  VAL   151      13.483  41.386  34.771  1.00  0.00
ATOM      5  CG1 VAL   151      14.987  41.614  34.731  1.00  0.00
ATOM      6  CG2 VAL   151      12.852  42.478  35.619  1.00  0.00
ATOM      7  O   VAL   151      13.524  39.159  32.686  1.00  0.00
ATOM      8  C   VAL   151      13.621  40.350  32.475  1.00  0.00
ATOM      9  N   CYS   152      14.433  40.808  31.513  1.00  0.00
ATOM     10  CA  CYS   152      15.091  39.808  30.651  1.00  0.00
ATOM     11  CB  CYS   152      15.675  40.476  29.405  1.00  0.00
ATOM     12  SG  CYS   152      16.501  39.340  28.267  1.00  0.00
ATOM     13  O   CYS   152      17.203  39.752  31.804  1.00  0.00
ATOM     14  C   CYS   152      16.224  39.104  31.381  1.00  0.00
ATOM     15  N   ASP   153      16.120  37.799  31.486  1.00  0.00
ATOM     16  CA  ASP   153      17.200  37.005  32.142  1.00  0.00
ATOM     17  CB  ASP   153      16.921  35.508  32.007  1.00  0.00
ATOM     18  CG  ASP   153      15.780  35.044  32.892  1.00  0.00
ATOM     19  OD1 ASP   153      15.357  35.825  33.770  1.00  0.00
ATOM     20  OD2 ASP   153      15.311  33.902  32.708  1.00  0.00
ATOM     21  O   ASP   153      19.559  37.408  32.229  1.00  0.00
ATOM     22  C   ASP   153      18.557  37.292  31.510  1.00  0.00
ATOM     23  N   LYS   154      18.661  37.406  30.184  1.00  0.00
ATOM     24  CA  LYS   154      19.957  37.652  29.583  1.00  0.00
ATOM     25  CB  LYS   154      19.826  37.778  28.064  1.00  0.00
ATOM     26  CG  LYS   154      19.497  36.474  27.357  1.00  0.00
ATOM     27  CD  LYS   154      19.375  36.675  25.856  1.00  0.00
ATOM     28  CE  LYS   154      19.040  35.370  25.151  1.00  0.00
ATOM     29  NZ  LYS   154      18.887  35.556  23.682  1.00  0.00
ATOM     30  O   LYS   154      21.823  38.998  30.185  1.00  0.00
ATOM     31  C   LYS   154      20.603  38.935  30.094  1.00  0.00
ATOM     32  N   LEU   155      19.801  39.968  30.428  1.00  0.00
ATOM     33  CA  LEU   155      20.385  41.218  30.886  1.00  0.00
ATOM     34  CB  LEU   155      19.339  42.335  30.872  1.00  0.00
ATOM     35  CG  LEU   155      18.865  42.800  29.495  1.00  0.00
ATOM     36  CD1 LEU   155      17.706  43.778  29.628  1.00  0.00
ATOM     37  CD2 LEU   155      19.989  43.497  28.744  1.00  0.00
ATOM     38  O   LEU   155      21.956  41.550  32.653  1.00  0.00
ATOM     39  C   LEU   155      20.907  41.035  32.322  1.00  0.00
TER
END
