
#######################################################
#                                                     #
#                        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    6 (   53),  selected    6 , name T0347TS671_5-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS671_5-D1.T0347_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    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    M     103      G      25          1.419
LGA    D     104      F      26          1.315
LGA    H     105      R      27          2.589
LGA    -       -      E      28           -
LGA    R     106      V      29          1.499
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    N     107      K      32          0.828
LGA    L     108      R      33          1.243
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   89    5.0      6    1.58     0.00      6.402     0.358

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.535495 * X  +  -0.673610 * Y  +   0.509406 * Z  +  -6.691170
  Y_new =  -0.344095 * X  +  -0.376820 * Y  +  -0.860003 * Z  +  65.331131
  Z_new =   0.771261 * X  +  -0.635812 * Y  +  -0.030000 * Z  + -42.961872 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.617946    1.523647  [ DEG:   -92.7015     87.2985 ]
  Theta =  -0.880820   -2.260773  [ DEG:   -50.4673   -129.5327 ]
  Phi   =  -2.570456    0.571136  [ DEG:  -147.2763     32.7237 ]
 
# 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: T0347TS671_5-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS671_5-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   89   5.0    6   1.58    0.00   6.402
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS671_5-D1
PFRMAT TS
TARGET T0347
MODEL  5  REFINED
PARENT 1VZ0_A
ATOM      1  N   MET   103       9.890  55.486  -4.540  1.00  0.00
ATOM      2  CA  MET   103       9.191  54.196  -4.385  1.00  0.00
ATOM      3  C   MET   103       7.971  53.983  -5.347  1.00  0.00
ATOM      4  O   MET   103       7.357  52.905  -5.244  1.00  0.00
ATOM      5  CB  MET   103       8.668  54.176  -2.941  1.00  0.00
ATOM      6  CG  MET   103       9.740  53.831  -1.947  1.00  0.00
ATOM      7  SD  MET   103       9.088  53.934  -0.263  1.00  0.00
ATOM      8  CE  MET   103      10.436  54.840   0.364  1.00  0.00
ATOM      9  N   ASP   104       7.662  54.890  -6.257  1.00  0.00
ATOM     10  CA  ASP   104       6.497  54.688  -7.112  1.00  0.00
ATOM     11  C   ASP   104       6.849  54.361  -8.605  1.00  0.00
ATOM     12  O   ASP   104       5.896  54.202  -9.387  1.00  0.00
ATOM     13  CB  ASP   104       5.704  55.981  -7.035  1.00  0.00
ATOM     14  CG  ASP   104       4.360  55.861  -6.344  1.00  0.00
ATOM     15  OD1 ASP   104       3.506  56.763  -6.520  1.00  0.00
ATOM     16  OD2 ASP   104       4.177  54.876  -5.581  1.00  0.00
ATOM     17  N   HIS   105       8.065  53.909  -8.893  1.00  0.00
ATOM     18  CA  HIS   105       8.510  53.659 -10.196  1.00  0.00
ATOM     19  C   HIS   105       8.667  52.152 -10.514  1.00  0.00
ATOM     20  O   HIS   105       9.458  51.432  -9.887  1.00  0.00
ATOM     21  CB  HIS   105       9.922  54.274 -10.266  1.00  0.00
ATOM     22  CG  HIS   105       9.833  55.739 -10.662  1.00  0.00
ATOM     23  ND1 HIS   105       9.824  56.856  -9.886  1.00  0.00
ATOM     24  CD2 HIS   105       9.688  56.129 -11.949  1.00  0.00
ATOM     25  CE1 HIS   105       9.641  57.849 -10.708  1.00  0.00
ATOM     26  NE2 HIS   105       9.580  57.427 -11.907  1.00  0.00
ATOM     27  N   ARG   106       8.186  51.853 -11.699  1.00  0.00
ATOM     28  CA  ARG   106       8.265  50.551 -12.322  1.00  0.00
ATOM     29  C   ARG   106       9.644  50.564 -13.063  1.00  0.00
ATOM     30  O   ARG   106      10.069  51.632 -13.566  1.00  0.00
ATOM     31  CB  ARG   106       7.125  50.530 -13.342  1.00  0.00
ATOM     32  CG  ARG   106       6.900  49.154 -13.967  1.00  0.00
ATOM     33  CD  ARG   106       5.554  49.205 -14.664  1.00  0.00
ATOM     34  NE  ARG   106       4.504  49.250 -13.660  1.00  0.00
ATOM     35  CZ  ARG   106       3.208  49.176 -13.968  1.00  0.00
ATOM     36  NH1 ARG   106       2.769  49.066 -15.231  1.00  0.00
ATOM     37  NH2 ARG   106       2.330  49.185 -12.965  1.00  0.00
ATOM     38  N   ASN   107      10.451  49.475 -13.073  1.00  0.00
ATOM     39  CA  ASN   107      11.733  49.381 -13.775  1.00  0.00
ATOM     40  C   ASN   107      11.582  50.103 -15.159  1.00  0.00
ATOM     41  O   ASN   107      12.577  50.656 -15.593  1.00  0.00
ATOM     42  CB  ASN   107      12.058  47.870 -13.939  1.00  0.00
ATOM     43  CG  ASN   107      13.415  47.634 -14.548  1.00  0.00
ATOM     44  OD1 ASN   107      13.643  47.752 -15.765  1.00  0.00
ATOM     45  ND2 ASN   107      14.284  47.117 -13.749  1.00  0.00
ATOM     46  N   LEU   108      10.500  49.972 -15.857  1.00  0.00
ATOM     47  CA  LEU   108      10.241  50.620 -17.137  1.00  0.00
ATOM     48  C   LEU   108      10.695  52.165 -17.171  1.00  0.00
ATOM     49  O   LEU   108      11.578  52.474 -17.996  1.00  0.00
ATOM     50  CB  LEU   108       8.714  50.556 -17.336  1.00  0.00
ATOM     51  CG  LEU   108       8.004  49.217 -17.302  1.00  0.00
ATOM     52  CD1 LEU   108       6.505  49.394 -17.656  1.00  0.00
ATOM     53  CD2 LEU   108       8.664  48.240 -18.317  1.00  0.00
TER
END
