
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_2-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    K     290      L       9          1.330
LGA    Y     291      A      10          1.143
LGA    M     292      D      11          0.564
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    A     293      T      14          1.169
LGA    C     294      I      15          0.930
LGA    L     295      T      16          1.551
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    K     296      T      19          0.608
LGA    D     297      M      20          1.770
LGA    H     298      K      21          4.509
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    -       -      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)    9  126    5.0      9    1.88     0.00      6.715     0.454

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.757560 * X  +  -0.125016 * Y  +  -0.640682 * Z  +  76.589760
  Y_new =  -0.632453 * X  +  -0.102369 * Y  +   0.767805 * Z  +  60.857010
  Z_new =  -0.161574 * X  +   0.986859 * Y  +  -0.001516 * Z  + -41.920811 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.572333   -1.569260  [ DEG:    90.0880    -89.9120 ]
  Theta =   0.162286    2.979307  [ DEG:     9.2983    170.7017 ]
  Phi   =  -2.445957    0.695636  [ DEG:  -140.1430     39.8570 ]
 
# 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_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_2-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   1.88    0.00   6.715
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_2-D1
PFRMAT TS 
TARGET T0372
MODEL 2
PARENT 1QSM_A
ATOM   2963  H   LYS   290      52.409  49.570  12.568  1.00  0.00                              
ATOM   2965  N   LYS   290      51.614  50.065  12.730  1.00  0.00                              
ATOM   2967  CA  LYS   290      51.694  51.403  13.300  1.00  0.00                              
ATOM   2969  CB  LYS   290      52.539  51.387  14.572  1.00  0.00                              
ATOM   2971  C   LYS   290      52.196  52.462  12.322  1.00  0.00                              
ATOM   2973  O   LYS   290      52.971  52.163  11.409  1.00  0.00                              
ATOM   2975  CG  LYS   290      51.937  50.592  15.718  1.00  0.00                              
ATOM   2977  CD  LYS   290      52.826  50.669  16.951  1.00  0.00                              
ATOM   2979  CE  LYS   290      52.287  49.799  18.079  1.00  0.00                              
ATOM   2981  NZ  LYS   290      53.161  49.852  19.288  1.00  0.00                              
ATOM   2983  H   TYR   291      51.054  53.821  13.173  1.00  0.00                              
ATOM   2985  N   TYR   291      51.702  53.689  12.499  1.00  0.00                              
ATOM   2987  CA  TYR   291      52.122  54.848  11.713  1.00  0.00                              
ATOM   2989  CB  TYR   291      53.629  54.827  11.419  1.00  0.00                              
ATOM   2991  C   TYR   291      51.292  55.026  10.440  1.00  0.00                              
ATOM   2993  O   TYR   291      51.831  54.979   9.331  1.00  0.00                              
ATOM   2995  CG  TYR   291      54.488  54.703  12.659  1.00  0.00                              
ATOM   2997  CD1 TYR   291      53.935  54.801  13.937  1.00  0.00                              
ATOM   2999  CE1 TYR   291      54.740  54.744  15.072  1.00  0.00                              
ATOM   3001  CZ  TYR   291      56.111  54.610  14.927  1.00  0.00                              
ATOM   3003  CD2 TYR   291      55.852  54.446  12.550  1.00  0.00                              
ATOM   3005  CE2 TYR   291      56.662  54.382  13.680  1.00  0.00                              
ATOM   3007  OH  TYR   291      56.913  54.572  16.046  1.00  0.00                              
ATOM   3009  H   MET   292      49.634  55.220  11.480  1.00  0.00                              
ATOM   3011  N   MET   292      49.986  55.254  10.603  1.00  0.00                              
ATOM   3013  CA  MET   292      49.080  55.521   9.481  1.00  0.00                              
ATOM   3015  CB  MET   292      47.810  54.650   9.552  1.00  0.00                              
ATOM   3017  C   MET   292      48.697  57.003   9.437  1.00  0.00                              
ATOM   3019  O   MET   292      49.557  57.881   9.525  1.00  0.00                              
ATOM   3021  CG  MET   292      48.041  53.145   9.466  1.00  0.00                              
ATOM   3023  SD  MET   292      48.512  52.599   7.806  1.00  0.00                              
ATOM   3025  CE  MET   292      46.909  52.342   7.054  1.00  0.00                              
ATOM   3027  H   ALA   293      46.798  56.627   9.071  1.00  0.00                              
ATOM   3029  N   ALA   293      47.418  57.305   9.242  1.00  0.00                              
ATOM   3031  CA  ALA   293      46.980  58.699   9.265  1.00  0.00                              
ATOM   3033  CB  ALA   293      47.494  59.458   8.045  1.00  0.00                              
ATOM   3035  C   ALA   293      45.464  58.818   9.363  1.00  0.00                              
ATOM   3037  O   ALA   293      44.947  59.889   9.692  1.00  0.00                              
ATOM   3039  H   CYS   294      45.206  56.927   8.921  1.00  0.00                              
ATOM   3041  N   CYS   294      44.758  57.720   9.114  1.00  0.00                              
ATOM   3043  CA  CYS   294      43.301  57.708   9.196  1.00  0.00                              
ATOM   3045  CB  CYS   294      42.753  56.479   8.472  1.00  0.00                              
ATOM   3047  C   CYS   294      42.866  57.662  10.653  1.00  0.00                              
ATOM   3049  O   CYS   294      43.680  57.343  11.521  1.00  0.00                              
ATOM   3051  SG  CYS   294      43.142  56.438   6.705  1.00  0.00                              
ATOM   3053  H   LEU   295      41.021  58.284  10.284  1.00  0.00                              
ATOM   3055  N   LEU   295      41.629  58.032  10.962  1.00  0.00                              
ATOM   3057  CA  LEU   295      41.214  58.047  12.360  1.00  0.00                              
ATOM   3059  CB  LEU   295      42.092  59.001  13.179  1.00  0.00                              
ATOM   3061  C   LEU   295      39.724  58.309  12.566  1.00  0.00                              
ATOM   3063  O   LEU   295      39.286  58.539  13.695  1.00  0.00                              
ATOM   3065  CG  LEU   295      41.984  60.509  12.914  1.00  0.00                              
ATOM   3067  CD1 LEU   295      43.235  60.996  12.193  1.00  0.00                              
ATOM   3069  CD2 LEU   295      40.739  60.844  12.105  1.00  0.00                              
ATOM   3071  H   LYS   296      39.347  58.045  10.652  1.00  0.00                              
ATOM   3073  N   LYS   296      38.945  58.218  11.494  1.00  0.00                              
ATOM   3075  CA  LYS   296      37.495  58.369  11.562  1.00  0.00                              
ATOM   3077  CB  LYS   296      36.815  57.051  11.957  1.00  0.00                              
ATOM   3079  C   LYS   296      37.016  59.504  12.465  1.00  0.00                              
ATOM   3081  O   LYS   296      36.905  60.647  12.008  1.00  0.00                              
ATOM   3083  CG  LYS   296      36.754  56.792  13.455  1.00  0.00                              
ATOM   3085  CD  LYS   296      36.501  55.321  13.757  1.00  0.00                              
ATOM   3087  CE  LYS   296      36.823  54.987  15.212  1.00  0.00                              
ATOM   3089  NZ  LYS   296      36.763  56.199  16.081  1.00  0.00                              
ATOM   3091  H   ASP   297      37.083  58.354  14.059  1.00  0.00                              
ATOM   3093  N   ASP   297      36.797  59.194  13.746  1.00  0.00                              
ATOM   3095  CA  ASP   297      36.202  60.130  14.704  1.00  0.00                              
ATOM   3097  CB  ASP   297      34.952  59.496  15.331  1.00  0.00                              
ATOM   3099  C   ASP   297      37.155  60.629  15.796  1.00  0.00                              
ATOM   3101  O   ASP   297      36.703  60.998  16.882  1.00  0.00                              
ATOM   3103  CG  ASP   297      33.967  60.502  15.902  1.00  0.00                              
ATOM   3105  OD1 ASP   297      34.059  61.699  15.556  1.00  0.00                              
ATOM   3107  OD2 ASP   297      33.083  60.098  16.690  1.00  0.00                              
ATOM   3109  H   HIS   298      38.756  60.326  14.682  1.00  0.00                              
ATOM   3111  N   HIS   298      38.457  60.650  15.520  1.00  0.00                              
ATOM   3113  CA  HIS   298      39.436  61.189  16.466  1.00  0.00                              
ATOM   3115  CB  HIS   298      38.951  61.085  17.920  1.00  0.00                              
ATOM   3117  C   HIS   298      40.803  60.537  16.284  1.00  0.00                              
ATOM   3119  O   HIS   298      40.868  59.378  15.877  1.00  0.00                              
ATOM   3121  CG  HIS   298      38.788  59.694  18.464  1.00  0.00                              
ATOM   3123  ND1 HIS   298      38.375  59.458  19.758  1.00  0.00                              
ATOM   3125  HD1 HIS   298      38.131  60.120  20.397  1.00  0.00                              
ATOM   3127  CE1 HIS   298      38.287  58.153  19.954  1.00  0.00                              
ATOM   3129  NE2 HIS   298      38.562  57.540  18.816  1.00  0.00                              
ATOM   3131  HE2 HIS   298      38.490  56.602  18.674  1.00  0.00                              
ATOM   3133  CD2 HIS   298      38.838  58.484  17.855  1.00  0.00                              
TER 
END
