Contacts of the strand formed by residues 278 - 283 (chain S) in PDB entry 6O81
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 VAL 278 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262S PHE* 3.0 40.4 + - + +
263S ASP 5.0 0.2 - - - -
264S VAL* 3.9 29.7 - - + +
276S GLY* 3.7 1.0 - - - -
277S GLY* 1.3 72.4 - - - +
279S ALA* 1.3 63.1 + - - +
339S VAL 3.6 6.5 - - - -
340S GLY* 3.9 10.5 - - - +
348S CYS* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S VAL* 5.2 9.2 - - + -
260S ARG 4.2 0.2 - - - -
261S SER* 4.3 18.4 - - - +
262S PHE* 5.6 1.1 - - - -
277S GLY 3.2 5.0 + - - +
278S VAL* 1.3 77.9 - - - +
280S GLY* 1.3 59.4 + - - +
338S GLY* 3.4 3.5 - - - -
339S VAL* 2.9 35.7 + - + +
348S CYS* 5.7 4.0 - - + -
353S MET* 5.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 280 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258S VAL* 3.8 5.2 - - - +
259S ILE* 3.1 4.4 + - - -
260S ARG* 2.9 41.3 + - - +
262S PHE* 5.3 4.0 - - - -
279S ALA* 1.3 78.2 - - - +
281S GLY* 1.3 57.7 + - - -
337S ILE 3.5 8.5 - - - -
338S GLY* 4.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 281 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S TYR* 4.9 3.8 - - - -
256S LEU* 5.6 4.0 - - - +
257S ILE 3.2 14.4 - - - -
258S VAL* 4.0 2.0 - - - -
259S ILE* 3.7 11.2 - - - -
280S GLY* 1.3 74.4 - - - -
282S SER* 1.3 61.1 + - - -
336S LEU* 3.5 9.4 - - - +
337S ILE* 2.9 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S TYR* 3.9 25.6 - - - -
255S ARG 3.6 0.5 - - - +
256S LEU* 4.3 3.6 - - - -
257S ILE* 2.9 37.7 + - - +
259S ILE* 5.4 2.0 - - - +
281S GLY* 1.3 75.4 - - - -
283S ILE* 1.3 65.5 + - - +
284S LEU* 3.7 1.0 + - - +
335S GLY 3.9 11.0 - - - -
337S ILE* 5.3 0.7 - - - -
410S SER* 5.8 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 283 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254S PRO* 6.4 1.3 - - + -
255S ARG 3.4 10.3 - - - +
256S LEU* 4.3 5.8 - - + +
282S SER* 1.3 74.1 - - - +
284S LEU* 1.3 64.4 + - - +
285S LYS 4.9 5.4 - - - +
286S GLY 5.4 2.7 - - - +
288S LEU* 6.3 2.9 - - + -
331S ALA 5.9 1.1 - - - +
332S ALA 4.3 7.6 - - - +
333S PRO* 3.4 34.7 - - + +
334S GLY 4.2 4.0 + - - +
335S GLY 4.4 5.5 + - - +
337S ILE* 4.8 11.6 - - + +
----------------------------------------------------------
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