
#######################################################
#                                                     #
#                        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   28 (   28),  selected   28 , name T0301TS464_3_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_3_2-D1.T0301_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    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    Q       6      V      22           #
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    I       7      R      46          4.627
LGA    R       8      V      47          3.262
LGA    -       -      I      48           -
LGA    I       9      G      49          2.814
LGA    P      10      S      50          3.168
LGA    F      24      P      51           -
LGA    R      25      D      52           #
LGA    L      26      P      53          2.809
LGA    E      27      Y      54          4.305
LGA    D      28      A      55          5.294
LGA    L      29      A      56          5.399
LGA    P      30      H      57          2.453
LGA    E      31      I      58          3.142
LGA    S      32      D      59          1.999
LGA    C      33      G      60          2.664
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    E     128      T      65          2.083
LGA    D     129      S      66           -
LGA    G     130      S      67           -
LGA    I     131      T      68           -
LGA    C     132      S      69          2.834
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    E     133      V      91          1.105
LGA    V     134      S      92          1.870
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    R     135      F      97          1.999
LGA    I     141      -       -           -
LGA    G     142      -       -           -
LGA    K     143      -       -           -
LGA    T     144      V      98          3.767
LGA    I     145      D      99          1.900
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      T     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    -       -      A     172           -
LGA    -       -      E     173           -
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28  200    5.0     19    3.24     0.00      5.823     0.569

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.667803 * X  +   0.250403 * Y  +  -0.700954 * Z  + 100.491653
  Y_new =  -0.592435 * X  +   0.748923 * Y  +  -0.296877 * Z  +  34.750484
  Z_new =   0.450622 * X  +   0.613525 * Y  +   0.648481 * Z  + -104.122169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.757707   -2.383886  [ DEG:    43.4134   -136.5866 ]
  Theta =  -0.467461   -2.674131  [ DEG:   -26.7836   -153.2164 ]
  Phi   =  -0.725664    2.415929  [ DEG:   -41.5775    138.4225 ]
 
# 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: T0301TS464_3_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28  200   5.0   19   3.24    0.00   5.823
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  GLN     6      74.345  40.799  12.478  1.00  0.00
ATOM      2  CA  ILE     7      75.879  42.573   9.463  1.00  0.00
ATOM      3  CA  ARG     8      78.459  40.227   7.895  1.00  0.00
ATOM      4  CA  ILE     9      81.915  40.992   6.486  1.00  0.00
ATOM      5  CA  PRO    10      83.343  39.152   3.496  1.00  0.00
ATOM      6  CA  PHE    24      93.025  44.164  12.503  1.00  0.00
ATOM      7  CA  ARG    25      90.907  47.019  11.154  1.00  0.00
ATOM      8  CA  LEU    26      89.151  44.533   8.874  1.00  0.00
ATOM      9  CA  GLU    27      88.281  42.291  11.827  1.00  0.00
ATOM     10  CA  ASP    28      86.709  45.253  13.665  1.00  0.00
ATOM     11  CA  LEU    29      84.566  45.978  10.597  1.00  0.00
ATOM     12  CA  PRO    30      83.598  42.344   9.978  1.00  0.00
ATOM     13  CA  GLU    31      82.805  41.790  13.670  1.00  0.00
ATOM     14  CA  SER    32      80.757  44.973  13.931  1.00  0.00
ATOM     15  CA  CYS    33      79.257  44.248  10.509  1.00  0.00
ATOM     16  CA  GLU   128      89.766  34.656  12.766  1.00  0.00
ATOM     17  CA  ASP   129      89.805  38.442  12.917  1.00  0.00
ATOM     18  CA  GLY   130      86.181  39.181  12.001  1.00  0.00
ATOM     19  CA  ILE   131      85.559  37.942   8.442  1.00  0.00
ATOM     20  CA  CYS   132      82.424  35.819   7.985  1.00  0.00
ATOM     21  CA  GLU   133      83.351  34.872   4.451  1.00  0.00
ATOM     22  CA  VAL   134      86.274  35.007   2.030  1.00  0.00
ATOM     23  CA  ARG   135      85.945  36.304  -1.510  1.00  0.00
ATOM     24  CA  ILE   141      82.359  26.064   8.499  1.00  0.00
ATOM     25  CA  GLY   142      78.948  27.618   7.895  1.00  0.00
ATOM     26  CA  LYS   143      80.342  30.292   5.568  1.00  0.00
ATOM     27  CA  THR   144      79.396  31.444   2.079  1.00  0.00
ATOM     28  CA  ILE   145      81.317  30.757  -1.107  1.00  0.00
TER
END
