
#######################################################
#                                                     #
#                        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 T0372TS028_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS028_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     290      K      55          1.684
LGA    Y     291      F      56          0.888
LGA    M     292      W      57          1.664
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    A     293      L      62          1.726
LGA    C     294      A      63          0.821
LGA    L     295      Y      64          1.940
LGA    K     296      M      65          1.556
LGA    D     297      M      66          1.139
LGA    H     298      P      67          2.672
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    1.66    11.11      6.781     0.513

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.318958 * X  +   0.632213 * Y  +  -0.706097 * Z  +  10.736265
  Y_new =   0.934739 * X  +  -0.332949 * Y  +   0.124130 * Z  +  59.441319
  Z_new =  -0.156617 * X  +  -0.699608 * Y  +  -0.697151 * Z  +  73.753784 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.354435    0.787158  [ DEG:  -134.8992     45.1008 ]
  Theta =   0.157265    2.984328  [ DEG:     9.0106    170.9894 ]
  Phi   =   1.241959   -1.899634  [ DEG:    71.1590   -108.8410 ]
 
# 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: T0372TS028_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS028_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   1.66   11.11   6.781
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS028_2-D1
PFRMAT TS
TARGET T0372
MODEL 2
PARENT 1yvo-A
ATOM   1061  N   LYS   290      39.799  50.680  -1.857  1.00  9.00
ATOM   1062  CA  LYS   290      39.533  49.241  -2.036  1.00  9.00
ATOM   1063  C   LYS   290      40.329  48.359  -1.066  1.00  9.00
ATOM   1064  O   LYS   290      41.470  48.668  -0.706  1.00  9.00
ATOM   1065  CB  LYS   290      39.918  48.820  -3.451  1.00  9.00
ATOM   1066  CG  LYS   290      39.057  49.472  -4.523  1.00  9.00
ATOM   1067  CD  LYS   290      39.503  49.040  -5.914  1.00  9.00
ATOM   1068  CE  LYS   290      38.694  49.732  -7.003  1.00  9.00
ATOM   1069  NZ  LYS   290      39.138  49.309  -8.340  1.00  9.00
ATOM   1070  N   TYR   291      39.717  47.250  -0.682  1.00  9.00
ATOM   1071  CA  TYR   291      40.392  46.204   0.108  1.00  9.00
ATOM   1072  C   TYR   291      39.656  44.877  -0.067  1.00  9.00
ATOM   1073  O   TYR   291      38.431  44.861  -0.239  1.00  9.00
ATOM   1074  CB  TYR   291      40.462  46.575   1.592  1.00  9.00
ATOM   1075  CG  TYR   291      39.153  46.486   2.375  1.00  9.00
ATOM   1076  CD1 TYR   291      38.872  45.363   3.145  1.00  9.00
ATOM   1077  CD2 TYR   291      38.247  47.536   2.334  1.00  9.00
ATOM   1078  CE1 TYR   291      37.682  45.285   3.856  1.00  9.00
ATOM   1079  CE2 TYR   291      37.059  47.462   3.046  1.00  9.00
ATOM   1080  CZ  TYR   291      36.778  46.337   3.804  1.00  9.00
ATOM   1081  OH  TYR   291      35.623  46.294   4.555  1.00  9.00
ATOM   1082  N   MET   292      40.418  43.790  -0.092  1.00  9.00
ATOM   1083  CA  MET   292      39.892  42.425  -0.297  1.00  9.00
ATOM   1084  C   MET   292      39.030  42.346  -1.557  1.00  9.00
ATOM   1085  O   MET   292      37.913  41.816  -1.530  1.00  9.00
ATOM   1086  CB  MET   292      39.071  42.012   0.924  1.00  9.00
ATOM   1087  CG  MET   292      39.888  42.048   2.214  1.00  9.00
ATOM   1088  SD  MET   292      41.234  40.848   2.353  1.00  9.00
ATOM   1089  CE  MET   292      40.260  39.325   2.372  1.00  9.00
ATOM   1090  N   ALA   293      39.563  42.914  -2.631  1.00  9.00
ATOM   1091  CA  ALA   293      38.877  43.084  -3.928  1.00  9.00
ATOM   1092  C   ALA   293      37.488  43.751  -3.894  1.00  9.00
ATOM   1093  O   ALA   293      36.660  43.453  -4.762  1.00  9.00
ATOM   1094  CB  ALA   293      38.770  41.722  -4.608  1.00  9.00
ATOM   1095  N   CYS   294      37.239  44.642  -2.942  1.00  9.00
ATOM   1096  CA  CYS   294      35.957  45.365  -2.897  1.00  9.00
ATOM   1097  C   CYS   294      36.129  46.847  -2.546  1.00  9.00
ATOM   1098  O   CYS   294      37.139  47.249  -1.958  1.00  9.00
ATOM   1099  CB  CYS   294      35.060  44.711  -1.850  1.00  9.00
ATOM   1100  SG  CYS   294      34.592  42.991  -2.156  1.00  9.00
ATOM   1101  N   LEU   295      35.152  47.642  -2.957  1.00  9.00
ATOM   1102  CA  LEU   295      35.106  49.095  -2.668  1.00  9.00
ATOM   1103  C   LEU   295      34.702  49.406  -1.219  1.00  9.00
ATOM   1104  O   LEU   295      34.028  48.596  -0.573  1.00  9.00
ATOM   1105  CB  LEU   295      34.079  49.722  -3.605  1.00  9.00
ATOM   1106  CG  LEU   295      34.553  49.749  -5.053  1.00  9.00
ATOM   1107  CD1 LEU   295      33.392  50.010  -6.006  1.00  9.00
ATOM   1108  CD2 LEU   295      35.652  50.788  -5.238  1.00  9.00
ATOM   1109  N   LYS   296      35.145  50.552  -0.712  1.00  9.00
ATOM   1110  CA  LYS   296      34.811  50.948   0.679  1.00  9.00
ATOM   1111  C   LYS   296      34.542  52.456   0.911  1.00  9.00
ATOM   1112  O   LYS   296      35.050  53.336   0.199  1.00  9.00
ATOM   1113  CB  LYS   296      35.966  50.510   1.562  1.00  9.00
ATOM   1114  CG  LYS   296      37.202  51.357   1.296  1.00  9.00
ATOM   1115  CD  LYS   296      38.389  50.911   2.133  1.00  9.00
ATOM   1116  CE  LYS   296      38.037  50.856   3.611  1.00  9.00
ATOM   1117  NZ  LYS   296      37.609  52.167   4.105  1.00  9.00
ATOM   1118  N   ASP   297      33.821  52.728   2.000  1.00  9.00
ATOM   1119  CA  ASP   297      33.321  54.093   2.360  1.00  9.00
ATOM   1120  C   ASP   297      34.029  54.693   3.610  1.00  9.00
ATOM   1121  O   ASP   297      34.588  53.911   4.382  1.00  9.00
ATOM   1122  CB  ASP   297      31.820  53.989   2.639  1.00  9.00
ATOM   1123  CG  ASP   297      30.985  53.444   1.472  1.00  9.00
ATOM   1124  OD1 ASP   297      31.503  53.390   0.366  1.00  9.00
ATOM   1125  OD2 ASP   297      29.791  53.302   1.673  1.00  9.00
ATOM   1126  N   HIS   298      33.903  56.008   3.862  1.00  9.00
ATOM   1127  CA  HIS   298      34.765  56.741   4.862  1.00  9.00
ATOM   1128  C   HIS   298      34.197  58.032   5.565  1.00  9.00
ATOM   1129  O   HIS   298      33.957  59.024   4.865  1.00  9.00
ATOM   1130  CB  HIS   298      35.982  57.267   4.089  1.00  9.00
ATOM   1131  CG  HIS   298      37.016  56.307   3.510  1.00  9.00
ATOM   1132  ND1 HIS   298      36.967  55.684   2.317  1.00  9.00
ATOM   1133  CD2 HIS   298      38.207  55.955   4.096  1.00  9.00
ATOM   1134  CE1 HIS   298      38.081  54.943   2.154  1.00  9.00
ATOM   1135  NE2 HIS   298      38.850  55.116   3.251  1.00  9.00
TER
END
