valine clusters

Gerard Kleijwegt gerard at rigel.bmc.uu.se
Fri Sep 29 10:38:36 EST 1995


In article <9509272257.AA06701 at bioc01.uthscsa.edu>, raman at BIOC01.UTHSCSA.EDU (C.S.RAMAN) writes:
|> Is anyone aware of sequential valine clusters in any of the solved
|> crystal structures? For example, VVVVVAA or VVVVVPA.  If yes, then what
|> type of secondary structure are they accomodated in?
|> 
|> Cheers
|> -raman
|> 
|> -- 

if we look at triplets only:
 VVV is beta 84%, alpha 15%  ( 69 observations)
 VVA is beta 58%, alpha 31%  (100 observations)
 VVP is beta 67%, alpha  2%  ( 51 observations)
(sec struct assignment is for the central residue)

looking for multiple sequential valines:


                             sequence   PDB ID  residues in PDB file
                             --------   ------  --------------------
 TUPLE LENGTH >>> (       6) 
 Found    7-  12|              VVVVAA| in 1CSE  146- 151
 Found    4-   9|              SGVVVV| in 1S01  145- 150

 TUPLE LENGTH >>> (       5) 
 Found    8-  12|               VVVAA| in 1THM  156- 160
 Found   18-  22|               VVVPA| in 4ICD    3-   7

 TUPLE LENGTH >>> (       4) 
 Found   19-  22|                VVPA| in 1ABK  166- 169
 Found    6-   9|                VVVV| in 1BLL   61-  64
 Found    6-   9|                VVVV| in 1CBP   31-  34
 Found    9-  12|                VVAA| in 1EFM   72-  75
 Found    9-  12|                VVAA| in 1FNA    5-   8
 Found    9-  12|                VVAA| in 1GDH  248- 251
 Found   18-  21|                VVVP| in 1HOC  247- 250
 Found   18-  21|                VVVP| in 1HSA  247- 250
 Found    6-   9|                VVVV| in 1LVL  349- 352
 Found    9-  12|                VVAA| in 1MEE  148- 151
 Found    8-  11|                VVVA| in 1NPX  238- 241
 Found   18-  21|                VVVP| in 1PFK  190- 193
 Found    8-  11|                VVVA| in 1PHP  266- 269
 Found    9-  12|                VVAA| in 1ST3  147- 150
 Found   18-  21|                VVVP| in 1VAA  247- 250
 Found    8-  11|                VVVA| in 3CMS  207- 210
 Found    8-  11|                VVVA| in 3GCT   60-  63
 Found    8-  11|                VVVA| in 3LAD  334- 337
 Found    8-  11|                VVVA| in 3YPI  159- 162
 Found    9-  12|                VVAA| in 4GPB  290- 293
 Found   18-  21|                VVVP| in 4ICD    3-   6

Predicted structure (CAs only) based on these hits
(the temp-factor is a sort of confidence score):

ATOM      6  CA  VAL 7           7.800   9.360  -1.848  1.00  7.00
ATOM      7  CA  VAL 8           9.218  12.733  -0.638  1.00  7.00
ATOM      8  CA  VAL 9           6.844  13.895   2.164  1.00  7.00
ATOM      9  CA  VAL 10          6.847  17.634   2.989  1.00  0.61
ATOM     10  CA  VAL 11          5.543  18.717   6.406  1.00  0.31
ATOM     11  CA  ALA 12          5.250  22.367   7.551  1.00 12.00
ATOM     12  CA  ALA 13          4.153  24.205  10.726  1.00 10.00

ATOM     16  CA  VAL 17         13.674  15.833  12.799  1.00  0.51
ATOM     17  CA  VAL 18         15.038  12.890  14.783  1.00  0.21
ATOM     18  CA  VAL 19         17.958  10.493  14.370  1.00  0.00
ATOM     19  CA  VAL 20         17.720   7.154  16.233  1.00  0.51
ATOM     20  CA  VAL 21         19.948   4.092  16.557  1.00  0.00
ATOM     21  CA  PRO 22         19.601   0.649  18.216  1.00  0.61
ATOM     22  CA  ALA 23         22.376  -0.134  20.751  1.00  0.21

so with both methods, my guess would be a beta strand

for what it's worth ;-)

--gerard




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