
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0372TS383_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS383_4-D1.T0372_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    -       -      M       1           -
LGA    -       -      I       2           -
LGA    K     290      P       3          1.017
LGA    Y     291      F       4          0.814
LGA    C     294      K       5          0.938
LGA    L     295      D       6          0.508
LGA    K     296      I       7          2.863
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    D     297      F      45          2.532
LGA    H     298      A      46          1.471
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7  126    5.0      7    1.67     0.00      5.201     0.395

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.509571 * X  +   0.492511 * Y  +   0.705528 * Z  +  -2.551485
  Y_new =  -0.574125 * X  +   0.416116 * Y  +  -0.705144 * Z  +  59.924706
  Z_new =  -0.640873 * X  +  -0.764382 * Y  +   0.070722 * Z  +  29.425375 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.478537    1.663056  [ DEG:   -84.7139     95.2861 ]
  Theta =   0.695635    2.445958  [ DEG:    39.8569    140.1431 ]
  Phi   =  -2.296696    0.844896  [ DEG:  -131.5910     48.4090 ]
 
# 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: T0372TS383_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS383_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7  126   5.0    7   1.67    0.00   5.201
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS383_4-D1
PFRMAT TS
TARGET T0372
MODEL 4
PARENT 1cjwA
ATOM    505  N   LYS   290      46.394  56.564  -6.097  1.00  0.00
ATOM    506  CA  LYS   290      47.561  56.018  -5.404  1.00  0.00
ATOM    507  C   LYS   290      47.201  55.305  -4.102  1.00  0.00
ATOM    508  O   LYS   290      46.470  55.835  -3.260  1.00  0.00
ATOM    509  N   TYR   291      47.745  54.107  -3.938  1.00  0.00
ATOM    510  CA  TYR   291      47.500  53.310  -2.748  1.00  0.00
ATOM    511  C   TYR   291      48.828  53.024  -2.054  1.00  0.00
ATOM    512  O   TYR   291      49.837  52.768  -2.717  1.00  0.00
ATOM    513  N   CYS   294      48.840  53.149  -0.731  1.00  0.00
ATOM    514  CA  CYS   294      50.031  52.894   0.084  1.00  0.00
ATOM    515  C   CYS   294      49.573  52.057   1.272  1.00  0.00
ATOM    516  O   CYS   294      48.931  52.579   2.187  1.00  0.00
ATOM    517  N   LEU   295      49.888  50.764   1.260  1.00  0.00
ATOM    518  CA  LEU   295      49.472  49.900   2.347  1.00  0.00
ATOM    519  C   LEU   295      47.959  49.893   2.425  1.00  0.00
ATOM    520  O   LEU   295      47.292  49.713   1.407  1.00  0.00
ATOM    521  N   LYS   296      47.413  50.119   3.616  1.00  0.00
ATOM    522  CA  LYS   296      45.965  50.153   3.803  1.00  0.00
ATOM    523  C   LYS   296      45.433  51.589   3.865  1.00  0.00
ATOM    524  O   LYS   296      44.251  51.814   4.152  1.00  0.00
ATOM    525  N   ASP   297      46.304  52.553   3.579  1.00  0.00
ATOM    526  CA  ASP   297      45.943  53.971   3.598  1.00  0.00
ATOM    527  C   ASP   297      45.246  54.420   2.317  1.00  0.00
ATOM    528  O   ASP   297      45.606  53.987   1.222  1.00  0.00
ATOM    529  N   HIS   298      44.241  55.277   2.461  1.00  0.00
ATOM    530  CA  HIS   298      43.513  55.829   1.318  1.00  0.00
ATOM    531  C   HIS   298      43.635  57.352   1.432  1.00  0.00
ATOM    532  O   HIS   298      43.624  57.906   2.539  1.00  0.00
TER
END
