
#######################################################
#                                                     #
#                        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    8 (   32),  selected    8 , name T0304AL586_1-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL586_1-D1.T0304_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    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    V     110      L      69          0.769
LGA    Y     111      M      70          1.931
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    L     112      L      73          1.213
LGA    A     113      E      74          1.351
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    V     114      L      77          1.180
LGA    Y     115      T      78          0.557
LGA    P     116      S      79          0.975
LGA    T     117      G      80          2.434
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  101    5.0      8    1.42    12.50      7.469     0.525

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.808717 * X  +  -0.164121 * Y  +  -0.564837 * Z  +  48.983154
  Y_new =  -0.309777 * X  +   0.935158 * Y  +   0.171806 * Z  +  24.518143
  Z_new =   0.500015 * X  +   0.313916 * Y  +  -0.807119 * Z  +  46.530533 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.770663   -0.370930  [ DEG:   158.7473    -21.2527 ]
  Theta =  -0.523616   -2.617977  [ DEG:   -30.0010   -149.9990 ]
  Phi   =  -2.775785    0.365807  [ DEG:  -159.0408     20.9592 ]
 
# 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: T0304AL586_1-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL586_1-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  101   5.0    8   1.42   12.50   7.469
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL586_1-D1
REMARK Aligment from pdb entry: 1fmb
ATOM      1  N   VAL   110      52.620  25.470  38.132  1.00  0.00              
ATOM      2  CA  VAL   110      53.866  25.781  38.889  1.00  0.00              
ATOM      3  C   VAL   110      53.471  25.954  40.357  1.00  0.00              
ATOM      4  O   VAL   110      52.322  26.172  40.704  1.00  0.00              
ATOM      5  N   TYR   111      54.491  25.810  41.164  1.00  0.00              
ATOM      6  CA  TYR   111      54.381  25.839  42.613  1.00  0.00              
ATOM      7  C   TYR   111      55.137  27.005  43.201  1.00  0.00              
ATOM      8  O   TYR   111      56.280  27.199  42.863  1.00  0.00              
ATOM      9  N   LEU   112      54.494  27.749  44.104  1.00  0.00              
ATOM     10  CA  LEU   112      55.142  28.867  44.779  1.00  0.00              
ATOM     11  C   LEU   112      55.281  28.404  46.224  1.00  0.00              
ATOM     12  O   LEU   112      54.271  28.115  46.872  1.00  0.00              
ATOM     13  N   ALA   113      56.480  28.357  46.701  1.00  0.00              
ATOM     14  CA  ALA   113      56.881  27.902  48.027  1.00  0.00              
ATOM     15  C   ALA   113      56.910  29.025  49.068  1.00  0.00              
ATOM     16  O   ALA   113      57.293  28.802  50.229  1.00  0.00              
ATOM     17  N   VAL   114      56.539  30.228  48.584  1.00  0.00              
ATOM     18  CA  VAL   114      56.402  31.392  49.465  1.00  0.00              
ATOM     19  C   VAL   114      57.617  31.986  50.100  1.00  0.00              
ATOM     20  O   VAL   114      57.524  32.917  50.909  1.00  0.00              
ATOM     21  N   TYR   115      58.823  31.628  49.604  1.00  0.00              
ATOM     22  CA  TYR   115      60.066  32.293  49.978  1.00  0.00              
ATOM     23  C   TYR   115      60.037  33.738  49.432  1.00  0.00              
ATOM     24  O   TYR   115      60.648  34.616  50.043  1.00  0.00              
ATOM     25  N   PRO   116      59.345  33.921  48.324  1.00  0.00              
ATOM     26  CA  PRO   116      59.213  35.280  47.754  1.00  0.00              
ATOM     27  C   PRO   116      57.745  35.569  47.533  1.00  0.00              
ATOM     28  O   PRO   116      56.861  34.671  47.661  1.00  0.00              
ATOM     29  N   THR   117      57.358  36.856  47.297  1.00  0.00              
ATOM     30  CA  THR   117      55.894  37.029  47.105  1.00  0.00              
ATOM     31  C   THR   117      55.537  36.263  45.821  1.00  0.00              
ATOM     32  O   THR   117      56.330  36.358  44.855  1.00  0.00              
END
