
#######################################################
#                                                     #
#                        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 (   75),  selected    9 , name T0372TS249_5_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_5_2-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    -       -      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    K     290      N      99          1.653
LGA    Y     291      M     100          3.287
LGA    M     292      R     101          1.460
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    A     293      L     104          1.700
LGA    C     294      E     105          1.123
LGA    L     295      A     106          0.917
LGA    K     296      I     107          1.044
LGA    D     297      L     108          0.797
LGA    H     298      P     109          2.356
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    1.76     0.00      6.562     0.483

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.051780 * X  +   0.874688 * Y  +  -0.481912 * Z  +  26.166107
  Y_new =   0.442680 * X  +  -0.452663 * Y  +  -0.774035 * Z  +  55.608097
  Z_new =  -0.895183 * X  +  -0.173253 * Y  +  -0.410646 * Z  +  -2.811727 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.742348    0.399245  [ DEG:  -157.1250     22.8750 ]
  Theta =   1.108843    2.032750  [ DEG:    63.5320    116.4680 ]
  Phi   =   1.454355   -1.687238  [ DEG:    83.3284    -96.6716 ]
 
# 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: T0372TS249_5_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_5_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   1.76    0.00   6.562
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      24.343  57.853   7.056  1.00  0.00
ATOM   1036  CA  LYS   290      23.887  56.500   7.141  1.00  0.00
ATOM   1037  C   LYS   290      23.199  56.214   5.871  1.00  0.00
ATOM   1038  O   LYS   290      22.941  55.050   5.558  1.00  0.00
ATOM   1039  CB  LYS   290      22.868  56.247   8.261  1.00  0.00
ATOM   1040  CG  LYS   290      23.480  56.269   9.658  1.00  0.00
ATOM   1041  CD  LYS   290      22.433  56.274  10.768  1.00  0.00
ATOM   1042  CE  LYS   290      23.033  56.088  12.162  1.00  0.00
ATOM   1043  NZ  LYS   290      23.691  54.765  12.256  1.00  0.00
ATOM   1044  N   TYR   291      22.789  57.289   5.168  1.00  0.00
ATOM   1045  CA  TYR   291      22.218  57.074   3.886  1.00  0.00
ATOM   1046  C   TYR   291      23.306  56.351   3.219  1.00  0.00
ATOM   1047  O   TYR   291      24.479  56.706   3.341  1.00  0.00
ATOM   1048  CB  TYR   291      21.958  58.356   3.086  1.00  0.00
ATOM   1049  CG  TYR   291      21.261  59.265   4.030  1.00  0.00
ATOM   1050  CD1 TYR   291      20.009  58.982   4.522  1.00  0.00
ATOM   1051  CD2 TYR   291      21.881  60.430   4.405  1.00  0.00
ATOM   1052  CE1 TYR   291      19.399  59.848   5.399  1.00  0.00
ATOM   1053  CE2 TYR   291      21.281  61.299   5.279  1.00  0.00
ATOM   1054  CZ  TYR   291      20.037  61.004   5.779  1.00  0.00
ATOM   1055  OH  TYR   291      19.412  61.891   6.680  1.00  0.00
ATOM   1056  N   MET   292      22.966  55.243   2.573  1.00  0.00
ATOM   1057  CA  MET   292      24.044  54.613   1.921  1.00  0.00
ATOM   1058  C   MET   292      24.217  55.505   0.756  1.00  0.00
ATOM   1059  O   MET   292      24.563  56.684   0.821  1.00  0.00
ATOM   1060  CB  MET   292      23.693  53.221   1.364  1.00  0.00
ATOM   1061  CG  MET   292      23.258  52.229   2.441  1.00  0.00
ATOM   1062  SD  MET   292      24.564  51.722   3.596  1.00  0.00
ATOM   1063  CE  MET   292      25.211  50.410   2.519  1.00  0.00
ATOM   1064  N   ALA   293      24.077  54.885  -0.387  1.00  0.00
ATOM   1065  CA  ALA   293      24.095  55.554  -1.623  1.00  0.00
ATOM   1066  C   ALA   293      22.812  56.266  -1.930  1.00  0.00
ATOM   1067  O   ALA   293      22.787  57.095  -2.833  1.00  0.00
ATOM   1068  CB  ALA   293      24.580  54.623  -2.728  1.00  0.00
ATOM   1069  N   CYS   294      21.710  55.962  -1.210  1.00  0.00
ATOM   1070  CA  CYS   294      20.393  56.308  -1.672  1.00  0.00
ATOM   1071  C   CYS   294      20.218  57.705  -2.151  1.00  0.00
ATOM   1072  O   CYS   294      19.952  57.879  -3.341  1.00  0.00
ATOM   1073  CB  CYS   294      19.315  56.020  -0.616  1.00  0.00
ATOM   1074  SG  CYS   294      19.734  56.714   1.007  1.00  0.00
ATOM   1075  N   LEU   295      20.422  58.728  -1.309  1.00  0.00
ATOM   1076  CA  LEU   295      20.052  60.023  -1.793  1.00  0.00
ATOM   1077  C   LEU   295      20.885  60.393  -2.955  1.00  0.00
ATOM   1078  O   LEU   295      20.400  60.669  -4.053  1.00  0.00
ATOM   1079  CB  LEU   295      20.238  61.133  -0.751  1.00  0.00
ATOM   1080  CG  LEU   295      19.419  60.917   0.531  1.00  0.00
ATOM   1081  CD1 LEU   295      19.982  59.755   1.365  1.00  0.00
ATOM   1082  CD2 LEU   295      19.279  62.216   1.330  1.00  0.00
ATOM   1083  N   LYS   296      22.191  60.304  -2.761  1.00  0.00
ATOM   1084  CA  LYS   296      22.953  60.910  -3.777  1.00  0.00
ATOM   1085  C   LYS   296      23.053  60.137  -5.036  1.00  0.00
ATOM   1086  O   LYS   296      23.412  60.735  -6.032  1.00  0.00
ATOM   1087  CB  LYS   296      24.339  61.373  -3.342  1.00  0.00
ATOM   1088  CG  LYS   296      24.714  62.619  -4.138  1.00  0.00
ATOM   1089  CD  LYS   296      23.822  63.814  -3.771  1.00  0.00
ATOM   1090  CE  LYS   296      22.672  64.115  -4.742  1.00  0.00
ATOM   1091  NZ  LYS   296      21.465  63.311  -4.432  1.00  0.00
ATOM   1092  N   ASP   297      22.849  58.806  -5.040  1.00  0.00
ATOM   1093  CA  ASP   297      23.120  58.001  -6.212  1.00  0.00
ATOM   1094  C   ASP   297      22.280  58.465  -7.280  1.00  0.00
ATOM   1095  O   ASP   297      22.575  58.338  -8.466  1.00  0.00
ATOM   1096  CB  ASP   297      22.546  56.595  -6.158  1.00  0.00
ATOM   1097  CG  ASP   297      23.339  55.809  -5.192  1.00  0.00
ATOM   1098  OD1 ASP   297      24.483  56.249  -4.894  1.00  0.00
ATOM   1099  OD2 ASP   297      22.818  54.736  -4.785  1.00  0.00
ATOM   1100  N   HIS   298      21.130  58.916  -6.844  1.00  0.00
ATOM   1101  CA  HIS   298      20.191  59.351  -7.774  1.00  0.00
ATOM   1102  C   HIS   298      20.726  60.573  -8.457  1.00  0.00
ATOM   1103  O   HIS   298      20.441  60.671  -9.645  1.00  0.00
ATOM   1104  CB  HIS   298      18.861  59.678  -7.073  1.00  0.00
ATOM   1105  CG  HIS   298      17.689  60.006  -7.950  1.00  0.00
ATOM   1106  ND1 HIS   298      16.851  61.077  -7.729  1.00  0.00
ATOM   1107  CD2 HIS   298      17.190  59.366  -9.041  1.00  0.00
ATOM   1108  CE1 HIS   298      15.890  61.022  -8.683  1.00  0.00
ATOM   1109  NE2 HIS   298      16.054  60.002  -9.504  1.00  0.00
TER
END
