Contacts of the strand formed by residues 342 - 347 (chain D) in PDB entry 6WNX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 342 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ILE* 5.7 0.2 - - - +
107D GLU* 2.5 33.1 + - - -
110D TRP* 3.7 54.8 - - - +
338D PHE* 3.1 6.5 - - - +
339D ASP* 3.0 50.1 + - - +
340D ASN 3.7 1.0 - - - -
341D LYS* 1.3 95.2 - - - +
343D ILE* 1.3 66.0 + - - +
344D VAL* 4.7 1.1 - - + -
354D VAL* 3.6 22.9 - - + -
355D TRP 3.0 17.7 - - - +
356D ASP* 5.0 0.4 - - - -
357D LEU* 3.8 5.8 - - - +
372D LEU* 5.4 6.7 - - + +
387D PHE* 3.6 13.0 - - + -
388D ASP 4.2 3.4 + - - -
389D GLU* 4.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D VAL* 3.7 31.9 - - + -
312D ILE* 4.9 2.7 - - + -
314D LEU* 4.0 15.5 - - + -
326D LEU* 4.2 9.4 - - + -
336D ILE* 3.9 25.6 - - + -
337D ARG 3.4 12.1 - - - +
338D PHE* 4.0 4.9 - - + -
342D ARG* 1.3 75.9 - - - +
344D VAL* 1.3 64.6 + - - +
354D VAL* 3.4 3.1 - - - -
355D TRP* 2.8 55.6 + - + -
357D LEU* 3.9 26.0 - - + -
360D ALA* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TRP* 4.5 11.4 - - + -
336D ILE* 3.4 2.0 - - - -
337D ARG 2.9 30.1 + - - -
342D ARG* 4.7 2.9 - - + -
343D ILE* 1.3 79.7 - - - +
345D SER* 1.3 61.0 + - - +
352D ILE* 3.7 20.6 - - + -
353D LYS 3.3 10.3 - - - +
354D VAL* 4.4 4.9 - - + -
385D LEU* 3.6 25.4 - - + +
387D PHE* 3.6 39.3 - - + -
392D ILE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ILE* 3.5 19.9 - - - +
329D HIS* 2.8 27.3 + - - -
333D VAL* 4.0 5.2 - - - -
335D CYS 3.5 9.6 - - - -
336D ILE* 4.2 6.1 - - - +
343D ILE 4.2 0.4 - - - -
344D VAL* 1.3 73.1 - - - +
346D GLY* 1.3 58.3 + - - +
352D ILE* 3.2 7.3 - - - +
353D LYS 2.9 30.0 + - - -
355D TRP* 2.8 21.4 + - - -
385D LEU* 3.8 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D HIS* 4.6 1.1 - - - -
333D VAL* 3.7 2.6 - - - +
334D ARG 2.9 23.0 + - - -
335D CYS* 2.9 28.0 + - - +
345D SER* 1.3 74.3 - - - +
347D ALA* 1.3 60.3 + - - +
351D LYS 3.6 6.7 - - - -
352D ILE* 4.2 2.0 - - - -
382D VAL* 4.0 16.2 - - - -
385D LEU* 3.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D HIS* 3.4 33.7 - - + +
331D GLU 4.2 5.2 - - - +
332D LEU 3.1 16.8 - - - +
334D ARG* 4.2 1.3 - - - +
346D GLY* 1.3 73.8 - - - -
348D TYR* 1.3 55.9 + - - +
349D ASP* 3.1 16.6 - - - +
350D GLY* 2.9 24.9 + - - -
351D LYS 3.1 7.0 + - - +
382D VAL* 3.3 16.9 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il