
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0321TS464_3_2
# Molecule2: number of CA atoms  244 ( 1840),  selected  244 , name T0321.pdb
# PARAMETERS: T0321TS464_3_2.T0321.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    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    A      84      T      26          3.665
LGA    Y      85      H      27          3.251
LGA    Y      86      S      28          2.320
LGA    N      87      V      29          3.898
LGA    N      88      I      30          2.572
LGA    P      89      R      31          3.674
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    Q      90      G      37          4.665
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    R     104      M      48          1.569
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    V     105      L      51          2.972
LGA    E     106      T      52          2.742
LGA    D     107      Q      53          3.488
LGA    R     108      N      54          2.819
LGA    M     109      L      55          1.607
LGA    N     110      L      56          0.455
LGA    D     111      G      57          3.855
LGA    P     112      -       -           -
LGA    F     113      -       -           -
LGA    I     114      -       -           -
LGA    M     115      -       -           -
LGA    F     220      -       -           -
LGA    M     221      -       -           -
LGA    V     222      -       -           -
LGA    K     223      -       -           -
LGA    D     224      -       -           -
LGA    N     225      -       -           -
LGA    A     226      L      58          4.902
LGA    R     227      P      59          3.661
LGA    A     228      L      60          1.454
LGA    -       -      R      61           -
LGA    F     229      V      62          2.269
LGA    R     230      A      63          3.071
LGA    -       -      A      64           -
LGA    I     231      G      65          1.935
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    -       -      A      80           -
LGA    -       -      A      81           -
LGA    -       -      I      82           -
LGA    -       -      N      83           -
LGA    -       -      A      84           -
LGA    -       -      Y      85           -
LGA    -       -      Y      86           -
LGA    -       -      N      87           -
LGA    -       -      N      88           -
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      H      95           -
LGA    -       -      G      96           -
LGA    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      N     110           -
LGA    -       -      D     111           -
LGA    -       -      P     112           -
LGA    -       -      F     113           -
LGA    -       -      I     114           -
LGA    -       -      M     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    -       -      K     121           -
LGA    -       -      G     122           -
LGA    -       -      K     123           -
LGA    -       -      K     124           -
LGA    -       -      V     125           -
LGA    -       -      G     126           -
LGA    -       -      V     127           -
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    -       -      V     171           -
LGA    -       -      Y     172           -
LGA    -       -      I     173           -
LGA    -       -      T     174           -
LGA    -       -      C     175           -
LGA    -       -      A     176           -
LGA    -       -      S     177           -
LGA    -       -      V     178           -
LGA    -       -      V     179           -
LGA    -       -      D     180           -
LGA    -       -      K     181           -
LGA    -       -      T     182           -
LGA    -       -      L     183           -
LGA    -       -      P     184           -
LGA    -       -      R     185           -
LGA    -       -      L     186           -
LGA    -       -      L     187           -
LGA    -       -      E     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      R     191           -
LGA    -       -      N     192           -
LGA    -       -      A     193           -
LGA    -       -      R     194           -
LGA    -       -      R     195           -
LGA    -       -      I     196           -
LGA    -       -      T     197           -
LGA    -       -      L     198           -
LGA    -       -      V     199           -
LGA    -       -      G     200           -
LGA    -       -      P     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      P     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      P     207           -
LGA    -       -      V     208           -
LGA    -       -      L     209           -
LGA    -       -      F     210           -
LGA    -       -      E     211           -
LGA    -       -      H     212           -
LGA    -       -      G     213           -
LGA    -       -      L     214           -
LGA    -       -      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31  244    5.0     21    3.09     0.00      5.175     0.658

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.975063 * X  +   0.209380 * Y  +   0.073571 * Z  + -65.859756
  Y_new =   0.001769 * X  +  -0.338829 * Y  +   0.940846 * Z  +  17.965351
  Z_new =   0.221922 * X  +  -0.917254 * Y  +  -0.330750 * Z  +  55.893597 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.916871    1.224721  [ DEG:  -109.8286     70.1714 ]
  Theta =  -0.223785   -2.917807  [ DEG:   -12.8220   -167.1780 ]
  Phi   =   0.001814   -3.139779  [ DEG:     0.1039   -179.8961 ]
 
# 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: T0321TS464_3_2                                
REMARK     2: T0321.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_3_2.T0321.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31  244   5.0   21   3.09    0.00   5.175
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  ALA    84       0.861  59.087  64.134  1.00  0.00
ATOM      2  CA  TYR    85      -1.807  60.304  61.738  1.00  0.00
ATOM      3  CA  TYR    86      -5.311  59.360  62.836  1.00  0.00
ATOM      4  CA  ASN    87      -7.458  61.396  65.198  1.00  0.00
ATOM      5  CA  ASN    88     -10.049  58.577  65.093  1.00  0.00
ATOM      6  CA  PRO    89      -9.582  55.475  67.223  1.00  0.00
ATOM      7  CA  GLN    90      -7.983  52.553  65.397  1.00  0.00
ATOM      8  CA  ARG   104      -7.881  61.312  53.862  1.00  0.00
ATOM      9  CA  VAL   105      -9.483  58.159  55.230  1.00  0.00
ATOM     10  CA  GLU   106      -9.232  59.483  58.793  1.00  0.00
ATOM     11  CA  ASP   107     -11.002  62.706  57.732  1.00  0.00
ATOM     12  CA  ARG   108     -13.962  60.817  56.251  1.00  0.00
ATOM     13  CA  MET   109     -14.202  58.412  59.189  1.00  0.00
ATOM     14  CA  ASN   110     -16.797  58.986  61.908  1.00  0.00
ATOM     15  CA  ASP   111     -16.648  55.524  63.513  1.00  0.00
ATOM     16  CA  PRO   112     -13.070  54.199  63.596  1.00  0.00
ATOM     17  CA  PHE   113     -10.269  53.286  61.210  1.00  0.00
ATOM     18  CA  ILE   114      -9.878  49.567  60.604  1.00  0.00
ATOM     19  CA  MET   115      -6.327  48.398  59.867  1.00  0.00
ATOM     20  CA  PHE   220     -25.403  56.506  58.371  1.00  0.00
ATOM     21  CA  MET   221     -23.424  54.030  60.458  1.00  0.00
ATOM     22  CA  VAL   222     -21.608  56.748  62.381  1.00  0.00
ATOM     23  CA  LYS   223     -24.932  58.494  62.996  1.00  0.00
ATOM     24  CA  ASP   224     -26.562  55.405  64.404  1.00  0.00
ATOM     25  CA  ASN   225     -24.064  54.472  67.050  1.00  0.00
ATOM     26  CA  ALA   226     -21.696  52.126  65.219  1.00  0.00
ATOM     27  CA  ARG   227     -18.386  52.395  67.080  1.00  0.00
ATOM     28  CA  ALA   228     -15.990  51.848  64.206  1.00  0.00
ATOM     29  CA  PHE   229     -15.853  50.910  60.533  1.00  0.00
ATOM     30  CA  ARG   230     -13.250  48.330  59.640  1.00  0.00
ATOM     31  CA  ILE   231     -11.725  48.412  56.156  1.00  0.00
TER
END
