
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_1_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    -       -      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    K     290      G      71          1.498
LGA    Y     291      D      72          0.915
LGA    M     292      L      73          1.349
LGA    A     293      K      74          1.738
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    C     294      L      77          0.728
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    L     295      L      80          1.490
LGA    K     296      I      81          1.070
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    D     297      A      84          1.287
LGA    H     298      D      85          1.731
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    1.35    11.11      6.774     0.620

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.054275 * X  +   0.122645 * Y  +   0.990965 * Z  +  44.715038
  Y_new =   0.990058 * X  +  -0.135583 * Y  +  -0.037445 * Z  +  67.388100
  Z_new =   0.129765 * X  +   0.983146 * Y  +  -0.128784 * Z  +  -7.032236 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.701047   -1.440546  [ DEG:    97.4628    -82.5372 ]
  Theta =  -0.130132   -3.011461  [ DEG:    -7.4560   -172.5440 ]
  Phi   =   1.516031   -1.625561  [ DEG:    86.8622    -93.1378 ]
 
# 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_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_1_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   1.35   11.11   6.774
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      31.260  68.426   1.237  1.00  0.00
ATOM   1036  CA  LYS   290      31.775  67.112   1.130  1.00  0.00
ATOM   1037  C   LYS   290      31.126  66.568  -0.077  1.00  0.00
ATOM   1038  O   LYS   290      30.066  65.948  -0.012  1.00  0.00
ATOM   1039  CB  LYS   290      31.426  66.186   2.308  1.00  0.00
ATOM   1040  CG  LYS   290      32.394  66.286   3.489  1.00  0.00
ATOM   1041  CD  LYS   290      32.410  67.632   4.206  1.00  0.00
ATOM   1042  CE  LYS   290      33.367  67.656   5.398  1.00  0.00
ATOM   1043  NZ  LYS   290      32.958  66.632   6.386  1.00  0.00
ATOM   1044  N   TYR   291      31.760  66.812  -1.231  1.00  0.00
ATOM   1045  CA  TYR   291      31.196  66.238  -2.396  1.00  0.00
ATOM   1046  C   TYR   291      31.966  64.980  -2.484  1.00  0.00
ATOM   1047  O   TYR   291      33.025  64.920  -3.107  1.00  0.00
ATOM   1048  CB  TYR   291      31.447  67.058  -3.674  1.00  0.00
ATOM   1049  CG  TYR   291      30.693  66.406  -4.782  1.00  0.00
ATOM   1050  CD1 TYR   291      29.332  66.578  -4.879  1.00  0.00
ATOM   1051  CD2 TYR   291      31.336  65.639  -5.726  1.00  0.00
ATOM   1052  CE1 TYR   291      28.618  65.987  -5.894  1.00  0.00
ATOM   1053  CE2 TYR   291      30.627  65.045  -6.745  1.00  0.00
ATOM   1054  CZ  TYR   291      29.266  65.216  -6.827  1.00  0.00
ATOM   1055  OH  TYR   291      28.536  64.607  -7.870  1.00  0.00
ATOM   1056  N   MET   292      31.456  63.944  -1.797  1.00  0.00
ATOM   1057  CA  MET   292      32.181  62.722  -1.783  1.00  0.00
ATOM   1058  C   MET   292      31.601  61.858  -2.845  1.00  0.00
ATOM   1059  O   MET   292      30.960  60.847  -2.557  1.00  0.00
ATOM   1060  CB  MET   292      32.084  61.968  -0.442  1.00  0.00
ATOM   1061  CG  MET   292      32.982  60.729  -0.353  1.00  0.00
ATOM   1062  SD  MET   292      33.071  59.970   1.301  1.00  0.00
ATOM   1063  CE  MET   292      31.378  59.316   1.290  1.00  0.00
ATOM   1064  N   ALA   293      31.797  62.261  -4.115  1.00  0.00
ATOM   1065  CA  ALA   293      31.422  61.405  -5.196  1.00  0.00
ATOM   1066  C   ALA   293      32.535  60.411  -5.193  1.00  0.00
ATOM   1067  O   ALA   293      33.675  60.783  -4.918  1.00  0.00
ATOM   1068  CB  ALA   293      31.408  62.097  -6.571  1.00  0.00
ATOM   1069  N   CYS   294      32.260  59.139  -5.538  1.00  0.00
ATOM   1070  CA  CYS   294      33.272  58.157  -5.272  1.00  0.00
ATOM   1071  C   CYS   294      33.944  57.583  -6.494  1.00  0.00
ATOM   1072  O   CYS   294      33.933  58.155  -7.583  1.00  0.00
ATOM   1073  CB  CYS   294      32.740  56.973  -4.449  1.00  0.00
ATOM   1074  SG  CYS   294      32.161  57.486  -2.802  1.00  0.00
ATOM   1075  N   LEU   295      34.555  56.394  -6.264  1.00  0.00
ATOM   1076  CA  LEU   295      35.503  55.644  -7.059  1.00  0.00
ATOM   1077  C   LEU   295      34.943  54.796  -8.184  1.00  0.00
ATOM   1078  O   LEU   295      33.735  54.687  -8.376  1.00  0.00
ATOM   1079  CB  LEU   295      36.384  54.757  -6.147  1.00  0.00
ATOM   1080  CG  LEU   295      37.601  54.073  -6.800  1.00  0.00
ATOM   1081  CD1 LEU   295      38.616  55.105  -7.312  1.00  0.00
ATOM   1082  CD2 LEU   295      38.239  53.050  -5.849  1.00  0.00
ATOM   1083  N   LYS   296      35.871  54.226  -9.008  1.00  0.00
ATOM   1084  CA  LYS   296      35.606  53.361 -10.139  1.00  0.00
ATOM   1085  C   LYS   296      36.519  52.149 -10.114  1.00  0.00
ATOM   1086  O   LYS   296      37.622  52.183  -9.569  1.00  0.00
ATOM   1087  CB  LYS   296      35.813  54.051 -11.500  1.00  0.00
ATOM   1088  CG  LYS   296      35.682  53.083 -12.675  1.00  0.00
ATOM   1089  CD  LYS   296      34.294  52.453 -12.784  1.00  0.00
ATOM   1090  CE  LYS   296      34.275  51.165 -13.612  1.00  0.00
ATOM   1091  NZ  LYS   296      34.776  51.431 -14.976  1.00  0.00
ATOM   1092  N   ASP   297      36.057  51.047 -10.760  1.00  0.00
ATOM   1093  CA  ASP   297      36.649  49.726 -10.808  1.00  0.00
ATOM   1094  C   ASP   297      37.550  49.540 -11.990  1.00  0.00
ATOM   1095  O   ASP   297      38.611  50.149 -12.124  1.00  0.00
ATOM   1096  CB  ASP   297      35.613  48.600 -10.977  1.00  0.00
ATOM   1097  CG  ASP   297      34.813  48.451  -9.703  1.00  0.00
ATOM   1098  OD1 ASP   297      35.182  49.103  -8.693  1.00  0.00
ATOM   1099  OD2 ASP   297      33.825  47.671  -9.721  1.00  0.00
ATOM   1100  N   HIS   298      37.140  48.572 -12.837  1.00  0.00
ATOM   1101  CA  HIS   298      37.811  48.140 -14.031  1.00  0.00
ATOM   1102  C   HIS   298      37.864  49.300 -14.978  1.00  0.00
ATOM   1103  O   HIS   298      37.332  50.370 -14.699  1.00  0.00
ATOM   1104  CB  HIS   298      37.095  46.963 -14.715  1.00  0.00
ATOM   1105  CG  HIS   298      37.090  45.741 -13.849  1.00  0.00
ATOM   1106  ND1 HIS   298      36.190  45.522 -12.830  1.00  0.00
ATOM   1107  CD2 HIS   298      37.922  44.665 -13.848  1.00  0.00
ATOM   1108  CE1 HIS   298      36.522  44.335 -12.264  1.00  0.00
ATOM   1109  NE2 HIS   298      37.567  43.777 -12.848  1.00  0.00
TER
END
