Similar to distang, one can also do it with the gemmi contact program
and some
simple filtering with awk (or other tool). It will also look for
symmetry related
contacts and can read mmcif or pdb format. (One can adjust distance
thresholds etc with
parameters to gemmi
https://gemmi.readthedocs.io/en/latest/program.html#contact )
Here is a one-line script to find waters that contact more than one
chain (or a
water and a symmetry related copy of the same water that both contact a chain)
gemmi contact mycoords.cif | awk '/HOH/&&!/HOH(.*)HOH/{for
(i=1;i<=NF;i++){if ($i~/HOH/){HOH[$(i+1)$(i+2)]=HOH[$(i+1)$(i+2)] $0 "
| "}}}END{for (water in HOH){print water, HOH[water]}}' | sort
-k1.1,1.1 -k1.2,1.5n | awk '/([|].*[|])/{water=$1; for
(i=2;i<NF;i++){if ($i~/HOH/){contact[$(i-3)]=$(i-2);
HOHsym[$(i+4)]=$(i+4) water}} if
(length(contact)>1||length(HOHsym)>1){print $0} delete contact ;
delete HOHsym }' | tr -s "|" "\n"
The regex for the first awk finds lines that have a contact with water
and rejects
those that are between 2 waters. It puts these waters into an array
and then outputs
all of the contracts from each water as a single line. The second awk
script regex finds
those waters that have more than one contact and does additional
analysis to see if
it interacts with more than one chain id (or if the water and a
symmetry related copy
of the same water both have contacts e.g. on two sides of a protein or
with a water on
a special position).
Regards,
Mitch
Quoting Edward Berry <eaber...@gmail.com>:
Modification of Eleanor's suggestion-
It is fairly trivial to write a program (e.g.
https://www.cytbc1.com/berry/for/pdbdist3w.for) which;
reads coordinates from one pdb file into memory
reads a second pdb file, and for each atom/hetatm
checks whether it is within threshold distance of the first pdb
if so writes that atom out to"near.pdb"
if not, writes that atom out to "far.pdb"
So, you divide your protein into the two domains, one .pdb file for each
get all the waters in a third pdb file
run the program with domain1 and waters.pdb to get all waters
contacting domain 1 in near.pdb
run again with domain2 and near.pdb to get all of those waters that
also contact domain 2
every time it finds a contact, it prints out the two atoms and their
distance, so combining the two log files you can make a table of the
contacts of each water. Or run a third time with the second near.pdb
against the entire anhydrous protein to get all contacts of each
water.
eab
PS. if you do use the program linked above, notice it switches the
files compared to what is described above: the first file should be
the water to be sorted, and second the protein. I guess I was
skeptical about being able to store coordinates of a large pdb in
memory, and the waters file would be smaller)
Eleanor Dodson wrote on 11/7/2024 7:29 AM:
A very old fashioned hands on way to do it..
Run distang
Find those H2O which contact two protein molecules..
5od5.pdb has 3 chains..
distang xyzin CCP4_DOWNLOADED_FILES/5od5.pdb > d
You get a list like this
Atom I Atom J Dij Sym TX TY TZ occ(i)*occ(j) av_bi+bj
M 23 SD A S 40 OG A 2.954 X,Y,Z
1.00 69.64
I 26 N A N 148 OD1 A 2.702 X,Y,Z
1.00 39.22
S 27 N A K 38 O A 2.911 X,Y,Z
1.00 41.32
S 27 O A K 38 N A 2.789 X,Y,Z
1.00 38.33
S 29 N A L 36 O A 2.817 X,Y,Z
1.00 42.18
....
then for the HOH
O 502 O A I 231 O A 2.282 X,Y,Z
1.00 49.74
O 502 O A G 32 CA B 2.710 X,Y,Z [-1 0+1]
1.00 53.59
O 503 O A D 39 CG A 2.973 X,Y,Z
1.00 42.27
O 503 O A D 39 OD1 A 2.470 X,Y,Z
1.00 39.89
Here HOH all labelled 501 on A B or C
I cut out the HOH from d
got rid of HOH to HOH
checked for any with more than one link to protein
* O 502 O A I 231 O A 2.282 X,Y,Z
1.00 49.74*
* O. 502 O A G 32 CA B 2.710 X,Y,Z [-1 0+1]
1.00 53.59*
O 503 O A D 39 CG A 2.973 X,Y,Z
1.00 42.27
O 503 O A D 39 OD1 A 2.470 X,Y,Z
1.00 39.89
O 503 O A D 39 OD2 A 2.782 X,Y,Z
1.00 39.34
O 503 O A Y 123 OH A 2.823 X,Y,Z
1.00 41.69
*
O 504 O A D 62 OD1 A 2.520 X,Y,Z
1.00 32.93
O 504 O A K 52 NZ C 2.886 X,Y,Z
1.00 28.56*
O 505 O A D 248 OD2 A 2.526 X,Y,Z
1.00 38.18
O 506 O A I 189 N A 2.723 X,Y,Z
1.00 40.59
O 507 O A D 248 N A 2.919 X,Y,Z
1.00 30.24
*
O 510 O A D 65 OD2 A 2.636 X,Y,Z
1.00 32.75
O 510 O A D 111 OD2 C 2.795 X,Y,Z
1.00 34.55*
....
O 505 O C K 306 NZ A 2.896 X,Y,Z [0+1 0]
1.00 50.02
O 505 O C D 264 OD2 C 2.542 X,Y,Z
1.00 51.45
.....
* O 526 O C N 90 N A 2.854 X,Y,Z
1.00 28.44
O 526 O C N 90 ND2 A 2.928 X,Y,Z
1.00 30.82
O 526 O C Z 407 O3 C 2.744 X,Y,Z
1.00 34.91
*
On Thu, 7 Nov 2024 at 10:38, Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote:
Is it possible to extract this info from pdbepisa?
Best wishes, Jon Cooper.
Emeritus at UCL.
jon.b.coo...@protonmail.com <mailto:jon.b.coo...@protonmail.com>
Sent from Proton Mail Android
-------- Original Message --------
On 07/11/2024 09:31, Italo Carugo Oliviero __ wrote:
Dear Tommi,
you could write a program (perhaps with ChatGPT) that (i)
stores water molecules, (ii) stores protein atoms, and (iii)
searches, among the water molecules, for those that are close to
two protein atoms that belong to different chains.
Oliviero
Il giorno mer 6 nov 2024 alle ore 16:43 Kajander, Tommi A
<tommi.kajan...@helsinki.fi <mailto:tommi.kajan...@helsinki.fi>> ha
scritto:
Dear all,____
__ __
Is there a something available to automatically
analyse/identifiy/quantify bound (“bridging”) water molecules at
protein-protein interfaces? Could not find anyting right away.____
__ __
Thanks in advance,____
Best,____
__ __
Tommi____
__ __
__ __
__ __
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