
#######################################################
#                                                     #
#                        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    9 (   86),  selected    9 , name T0372TS277_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_5-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    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
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    -       -      F      45           -
LGA    -       -      A      46           -
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    K     290      L      73          1.990
LGA    Y     291      K      74          3.306
LGA    M     292      A      75          2.082
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    A     293      K      79          1.136
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    C     294      E      82          2.356
LGA    L     295      D      83          0.911
LGA    K     296      A      84          1.648
LGA    D     297      D      85          2.830
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    H     298      N      90          2.983
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)    9  126    5.0      9    2.27    11.11      5.761     0.379

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.120731 * X  +   0.700028 * Y  +   0.703836 * Z  +  36.631714
  Y_new =  -0.946412 * X  +   0.132781 * Y  +  -0.294404 * Z  + 100.644264
  Z_new =  -0.299547 * X  +  -0.701662 * Y  +   0.646484 * Z  +  13.147194 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.826304    2.315288  [ DEG:   -47.3438    132.6562 ]
  Theta =   0.304218    2.837375  [ DEG:    17.4304    162.5696 ]
  Phi   =  -1.697678    1.443915  [ DEG:   -97.2698     82.7302 ]
 
# 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: T0372TS277_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_5-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.27   11.11   5.761
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_5-D1
PFRMAT TS 
TARGET T0372
MODEL 5
PARENT 1S7F_A
ATOM   2979  H   LYS   290      30.514  63.350  -3.055  1.00  0.00                              
ATOM   2981  N   LYS   290      30.856  62.465  -3.017  1.00  0.00                              
ATOM   2983  CA  LYS   290      30.116  61.391  -3.670  1.00  0.00                              
ATOM   2985  CB  LYS   290      28.663  61.808  -3.909  1.00  0.00                              
ATOM   2987  C   LYS   290      30.762  61.001  -4.994  1.00  0.00                              
ATOM   2989  O   LYS   290      31.187  61.874  -5.755  1.00  0.00                              
ATOM   2991  CG  LYS   290      27.823  60.738  -4.588  1.00  0.00                              
ATOM   2993  CD  LYS   290      26.360  61.152  -4.677  1.00  0.00                              
ATOM   2995  CE  LYS   290      25.503  60.064  -5.310  1.00  0.00                              
ATOM   2997  NZ  LYS   290      24.070  60.469  -5.402  1.00  0.00                              
ATOM   2999  H   TYR   291      30.586  59.083  -4.577  1.00  0.00                              
ATOM   3001  N   TYR   291      30.863  59.697  -5.238  1.00  0.00                              
ATOM   3003  CA  TYR   291      31.397  59.178  -6.490  1.00  0.00                              
ATOM   3005  CB  TYR   291      30.251  58.808  -7.431  1.00  0.00                              
ATOM   3007  C   TYR   291      32.308  60.184  -7.180  1.00  0.00                              
ATOM   3009  O   TYR   291      31.952  60.746  -8.220  1.00  0.00                              
ATOM   3011  CG  TYR   291      30.713  58.016  -8.629  1.00  0.00                              
ATOM   3013  CD1 TYR   291      31.990  57.459  -8.674  1.00  0.00                              
ATOM   3015  CE1 TYR   291      32.399  56.694  -9.763  1.00  0.00                              
ATOM   3017  CZ  TYR   291      31.502  56.433 -10.783  1.00  0.00                              
ATOM   3019  CD2 TYR   291      29.877  57.842  -9.730  1.00  0.00                              
ATOM   3021  CE2 TYR   291      30.272  57.067 -10.813  1.00  0.00                              
ATOM   3023  OH  TYR   291      31.886  55.640 -11.843  1.00  0.00                              
ATOM   3025  H   MET   292      33.751  59.851  -5.887  1.00  0.00                              
ATOM   3027  N   MET   292      33.508  60.372  -6.638  1.00  0.00                              
ATOM   3029  CA  MET   292      34.439  61.378  -7.142  1.00  0.00                              
ATOM   3031  CB  MET   292      35.107  62.100  -5.968  1.00  0.00                              
ATOM   3033  C   MET   292      35.529  60.829  -8.063  1.00  0.00                              
ATOM   3035  O   MET   292      35.700  61.324  -9.182  1.00  0.00                              
ATOM   3037  CG  MET   292      35.881  61.162  -5.052  1.00  0.00                              
ATOM   3039  SD  MET   292      34.776  60.097  -4.096  1.00  0.00                              
ATOM   3041  CE  MET   292      35.963  59.018  -3.317  1.00  0.00                              
ATOM   3043  H   ALA   293      36.135  59.497  -6.746  1.00  0.00                              
ATOM   3045  N   ALA   293      36.314  59.863  -7.587  1.00  0.00                              
ATOM   3047  CA  ALA   293      37.430  59.331  -8.375  1.00  0.00                              
ATOM   3049  CB  ALA   293      38.600  58.928  -7.477  1.00  0.00                              
ATOM   3051  C   ALA   293      36.977  58.139  -9.220  1.00  0.00                              
ATOM   3053  O   ALA   293      35.813  57.735  -9.156  1.00  0.00                              
ATOM   3055  H   CYS   294      38.720  57.935 -10.118  1.00  0.00                              
ATOM   3057  N   CYS   294      37.861  57.582 -10.051  1.00  0.00                              
ATOM   3059  CA  CYS   294      37.478  56.449 -10.894  1.00  0.00                              
ATOM   3061  CB  CYS   294      37.089  56.932 -12.292  1.00  0.00                              
ATOM   3063  C   CYS   294      38.565  55.380 -10.992  1.00  0.00                              
ATOM   3065  O   CYS   294      39.562  55.559 -11.698  1.00  0.00                              
ATOM   3067  SG  CYS   294      38.096  56.211 -13.612  1.00  0.00                              
ATOM   3069  H   LEU   295      37.522  54.125  -9.881  1.00  0.00                              
ATOM   3071  N   LEU   295      38.345  54.246 -10.330  1.00  0.00                              
ATOM   3073  CA  LEU   295      39.338  53.168 -10.296  1.00  0.00                              
ATOM   3075  CB  LEU   295      40.303  53.356  -9.117  1.00  0.00                              
ATOM   3077  C   LEU   295      38.720  51.767 -10.219  1.00  0.00                              
ATOM   3079  O   LEU   295      37.704  51.562  -9.552  1.00  0.00                              
ATOM   3081  CG  LEU   295      41.322  52.233  -8.900  1.00  0.00                              
ATOM   3083  CD1 LEU   295      42.282  52.163 -10.082  1.00  0.00                              
ATOM   3085  CD2 LEU   295      42.087  52.415  -7.591  1.00  0.00                              
ATOM   3087  H   LYS   296      40.015  51.077 -11.529  1.00  0.00                              
ATOM   3089  N   LYS   296      39.318  50.816 -10.937  1.00  0.00                              
ATOM   3091  CA  LYS   296      38.932  49.401 -10.897  1.00  0.00                              
ATOM   3093  CB  LYS   296      38.759  48.890  -9.464  1.00  0.00                              
ATOM   3095  C   LYS   296      37.724  49.061 -11.775  1.00  0.00                              
ATOM   3097  O   LYS   296      37.910  48.580 -12.896  1.00  0.00                              
ATOM   3099  CG  LYS   296      40.049  48.850  -8.656  1.00  0.00                              
ATOM   3101  CD  LYS   296      40.877  47.609  -8.963  1.00  0.00                              
ATOM   3103  CE  LYS   296      42.363  47.858  -8.739  1.00  0.00                              
ATOM   3105  NZ  LYS   296      43.206  46.937  -9.557  1.00  0.00                              
ATOM   3107  H   ASP   297      36.360  49.601 -10.433  1.00  0.00                              
ATOM   3109  N   ASP   297      36.491  49.250 -11.299  1.00  0.00                              
ATOM   3111  CA  ASP   297      35.343  48.938 -12.150  1.00  0.00                              
ATOM   3113  CB  ASP   297      35.380  47.471 -12.591  1.00  0.00                              
ATOM   3115  C   ASP   297      33.967  49.279 -11.566  1.00  0.00                              
ATOM   3117  O   ASP   297      33.300  50.176 -12.094  1.00  0.00                              
ATOM   3119  CG  ASP   297      34.825  47.264 -13.990  1.00  0.00                              
ATOM   3121  OD1 ASP   297      33.687  47.710 -14.257  1.00  0.00                              
ATOM   3123  OD2 ASP   297      35.527  46.664 -14.833  1.00  0.00                              
ATOM   3125  H   HIS   298      34.074  47.937 -10.103  1.00  0.00                              
ATOM   3127  N   HIS   298      33.516  48.577 -10.521  1.00  0.00                              
ATOM   3129  CA  HIS   298      32.152  48.786 -10.029  1.00  0.00                              
ATOM   3131  CB  HIS   298      31.225  47.787 -10.742  1.00  0.00                              
ATOM   3133  C   HIS   298      31.928  48.673  -8.515  1.00  0.00                              
ATOM   3135  O   HIS   298      31.955  49.682  -7.804  1.00  0.00                              
ATOM   3137  CG  HIS   298      29.774  47.948 -10.409  1.00  0.00                              
ATOM   3139  ND1 HIS   298      28.971  48.864 -11.047  1.00  0.00                              
ATOM   3141  HD1 HIS   298      29.248  49.484 -11.713  1.00  0.00                              
ATOM   3143  CE1 HIS   298      27.757  48.806 -10.529  1.00  0.00                              
ATOM   3145  NE2 HIS   298      27.706  47.771  -9.708  1.00  0.00                              
ATOM   3147  HE2 HIS   298      26.913  47.443  -9.298  1.00  0.00                              
ATOM   3149  CD2 HIS   298      28.947  47.192  -9.643  1.00  0.00                              
TER 
END
