
#######################################################
#                                                     #
#                        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 T0372TS349_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS349_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    K     290      L      52          0.858
LGA    Y     291      V      53          2.657
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    M     292      V      68          0.365
LGA    A     293      G      69          1.844
LGA    C     294      N      70          2.976
LGA    L     295      G      71          0.765
LGA    K     296      D      72          1.047
LGA    D     297      L      73          0.984
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    H     298      V      76          3.270
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    1.93     0.00      6.502     0.443

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624232 * X  +  -0.159591 * Y  +   0.764764 * Z  +  48.322212
  Y_new =   0.475722 * X  +   0.698845 * Y  +   0.534139 * Z  +  -9.818588
  Z_new =  -0.619695 * X  +   0.697242 * Y  +  -0.360321 * Z  +  -6.025139 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.047777   -1.093815  [ DEG:   117.3290    -62.6710 ]
  Theta =   0.668354    2.473238  [ DEG:    38.2939    141.7061 ]
  Phi   =   2.490398   -0.651195  [ DEG:   142.6893    -37.3107 ]
 
# 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: T0372TS349_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS349_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   1.93    0.00   6.502
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS349_5-D1
PFRMAT TS
TARGET T0372
MODEL  5  REFINED
PARENT 1YVO_B
ATOM   1090  N   LYS   290      41.344  58.833   2.422  1.00  0.00
ATOM   1091  CA  LYS   290      40.024  58.879   3.043  1.00  0.00
ATOM   1092  C   LYS   290      39.025  57.772   2.661  1.00  0.00
ATOM   1093  O   LYS   290      38.276  57.906   1.697  1.00  0.00
ATOM   1094  CB  LYS   290      39.407  60.221   3.394  1.00  0.00
ATOM   1095  CG  LYS   290      40.278  61.209   4.040  1.00  0.00
ATOM   1096  CD  LYS   290      40.476  60.843   5.463  1.00  0.00
ATOM   1097  CE  LYS   290      41.724  59.934   5.725  1.00  0.00
ATOM   1098  NZ  LYS   290      41.572  59.310   7.096  1.00  0.00
ATOM   1099  N   TYR   291      38.752  56.963   3.710  1.00  0.00
ATOM   1100  CA  TYR   291      37.778  55.891   3.706  1.00  0.00
ATOM   1101  C   TYR   291      36.402  56.578   4.088  1.00  0.00
ATOM   1102  O   TYR   291      35.369  56.203   3.499  1.00  0.00
ATOM   1103  CB  TYR   291      38.111  54.711   4.679  1.00  0.00
ATOM   1104  CG  TYR   291      36.917  53.717   4.626  1.00  0.00
ATOM   1105  CD1 TYR   291      35.756  53.932   5.367  1.00  0.00
ATOM   1106  CD2 TYR   291      36.967  52.602   3.824  1.00  0.00
ATOM   1107  CE1 TYR   291      34.686  53.069   5.297  1.00  0.00
ATOM   1108  CE2 TYR   291      35.909  51.679   3.746  1.00  0.00
ATOM   1109  CZ  TYR   291      34.794  51.935   4.492  1.00  0.00
ATOM   1110  OH  TYR   291      33.758  51.050   4.432  1.00  0.00
ATOM   1111  N   MET   292      36.371  57.390   5.178  1.00  0.00
ATOM   1112  CA  MET   292      35.192  58.164   5.655  1.00  0.00
ATOM   1113  C   MET   292      35.335  59.722   5.537  1.00  0.00
ATOM   1114  O   MET   292      34.370  60.395   5.869  1.00  0.00
ATOM   1115  CB  MET   292      34.970  57.775   7.125  1.00  0.00
ATOM   1116  CG  MET   292      35.157  56.326   7.523  1.00  0.00
ATOM   1117  SD  MET   292      34.387  55.868   9.224  1.00  0.00
ATOM   1118  CE  MET   292      34.487  54.117   9.149  1.00  0.00
ATOM   1119  N   ALA   293      36.534  60.309   5.275  1.00  0.00
ATOM   1120  CA  ALA   293      36.554  61.746   5.091  1.00  0.00
ATOM   1121  C   ALA   293      35.770  61.996   3.815  1.00  0.00
ATOM   1122  O   ALA   293      36.167  61.426   2.790  1.00  0.00
ATOM   1123  CB  ALA   293      37.922  62.355   5.154  1.00  0.00
ATOM   1124  N   CYS   294      34.796  62.954   3.831  1.00  0.00
ATOM   1125  CA  CYS   294      33.991  63.105   2.644  1.00  0.00
ATOM   1126  C   CYS   294      33.294  64.516   2.487  1.00  0.00
ATOM   1127  O   CYS   294      32.694  65.049   3.424  1.00  0.00
ATOM   1128  CB  CYS   294      32.847  62.041   2.595  1.00  0.00
ATOM   1129  SG  CYS   294      33.555  60.387   2.819  1.00  0.00
ATOM   1130  N   LEU   295      33.289  64.961   1.205  1.00  0.00
ATOM   1131  CA  LEU   295      32.636  66.195   0.693  1.00  0.00
ATOM   1132  C   LEU   295      32.488  66.016  -0.860  1.00  0.00
ATOM   1133  O   LEU   295      33.554  65.792  -1.481  1.00  0.00
ATOM   1134  CB  LEU   295      33.493  67.439   1.092  1.00  0.00
ATOM   1135  CG  LEU   295      32.828  68.821   1.019  1.00  0.00
ATOM   1136  CD1 LEU   295      33.716  69.883   0.342  1.00  0.00
ATOM   1137  CD2 LEU   295      31.491  68.887   0.288  1.00  0.00
ATOM   1138  N   LYS   296      31.430  66.598  -1.496  1.00  0.00
ATOM   1139  CA  LYS   296      31.260  66.486  -2.936  1.00  0.00
ATOM   1140  C   LYS   296      31.380  64.991  -3.407  1.00  0.00
ATOM   1141  O   LYS   296      31.816  64.767  -4.538  1.00  0.00
ATOM   1142  CB  LYS   296      32.285  67.333  -3.612  1.00  0.00
ATOM   1143  CG  LYS   296      32.609  68.722  -3.233  1.00  0.00
ATOM   1144  CD  LYS   296      31.334  69.556  -3.191  1.00  0.00
ATOM   1145  CE  LYS   296      31.264  70.718  -2.199  1.00  0.00
ATOM   1146  NZ  LYS   296      30.060  71.579  -2.511  1.00  0.00
ATOM   1147  N   ASP   297      30.814  63.988  -2.705  1.00  0.00
ATOM   1148  CA  ASP   297      31.005  62.582  -3.073  1.00  0.00
ATOM   1149  C   ASP   297      32.549  62.239  -3.202  1.00  0.00
ATOM   1150  O   ASP   297      32.904  61.340  -3.962  1.00  0.00
ATOM   1151  CB  ASP   297      30.271  62.274  -4.378  1.00  0.00
ATOM   1152  CG  ASP   297      28.779  62.261  -4.177  1.00  0.00
ATOM   1153  OD1 ASP   297      28.297  61.759  -3.102  1.00  0.00
ATOM   1154  OD2 ASP   297      28.046  62.673  -5.037  1.00  0.00
ATOM   1155  N   HIS   298      33.407  62.775  -2.279  1.00  0.00
ATOM   1156  CA  HIS   298      34.938  62.680  -2.144  1.00  0.00
ATOM   1157  C   HIS   298      35.524  62.986  -0.644  1.00  0.00
ATOM   1158  O   HIS   298      34.746  62.658   0.181  1.00  0.00
ATOM   1159  CB  HIS   298      35.568  63.709  -3.081  1.00  0.00
ATOM   1160  CG  HIS   298      35.236  63.442  -4.522  1.00  0.00
ATOM   1161  ND1 HIS   298      35.794  62.447  -5.292  1.00  0.00
ATOM   1162  CD2 HIS   298      34.328  64.076  -5.331  1.00  0.00
ATOM   1163  CE1 HIS   298      35.236  62.506  -6.493  1.00  0.00
ATOM   1164  NE2 HIS   298      34.335  63.439  -6.552  1.00  0.00
TER
END
