Contacts of the strand formed by residues 268 - 276 (chain C) in PDB entry 4PAR
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 LYS 268 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ASP* 3.0 24.6 + - + +
221C THR* 3.3 17.9 - - - +
222C LEU* 2.9 24.3 + - - +
266C PRO 4.2 2.4 - - - +
267C GLN* 1.3 87.1 - - + +
269C ARG* 1.3 66.4 + - - +
290C LEU* 4.0 26.7 - - + +
291C TYR 3.4 4.3 - - - +
292C GLU* 4.2 26.5 - - + -
307C VAL* 5.6 5.7 - - - +
308C LYS* 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 3.2 37.3 - - + +
224C TRP* 3.3 48.4 - - + +
247C GLU* 3.3 17.4 + - - -
262C TRP* 3.1 31.7 - - - +
266C PRO* 5.0 3.5 + - - +
268C LYS* 1.3 80.7 - - - +
270C ILE* 1.3 61.6 + - - +
271C VAL* 3.6 14.9 + - + +
290C LEU* 3.4 4.7 - - - +
291C TYR* 2.9 39.8 + - + +
304C TRP* 3.2 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PHE* 3.6 35.4 - - + -
215C HIS* 3.6 24.7 - - + +
221C THR* 3.5 16.4 - - + +
222C LEU 2.9 8.4 + - - +
223C ILE* 3.6 11.8 - - + +
224C TRP* 2.9 26.5 + - - +
269C ARG* 1.3 70.2 - - - +
271C VAL* 1.3 62.0 + - - +
272C PHE* 3.5 27.0 + - + -
287C PHE* 4.1 4.9 - - + -
289C GLY 3.7 3.4 - - - -
290C LEU* 3.8 11.0 - - + -
311C VAL* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C TRP* 3.6 21.8 - - + -
226C PRO* 3.8 26.9 - - + -
228C LEU* 5.3 0.2 - - + -
245C ILE* 4.4 13.0 - - + -
269C ARG* 3.7 16.6 - - + +
270C ILE* 1.3 76.5 - - - +
272C PHE* 1.3 69.0 + - - +
273C ALA* 4.3 2.0 - - + +
287C PHE* 3.6 4.5 - - - -
288C MET* 2.8 42.0 + - + -
289C GLY 2.9 16.2 + - - +
291C TYR* 3.7 23.3 - - + -
304C TRP* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ILE* 3.8 26.7 - - + -
189C VAL* 4.9 3.1 - - + -
191C LEU* 4.7 8.3 - - + -
197C VAL* 3.5 40.8 - - + -
201C PHE* 3.9 5.6 - + - -
223C ILE* 4.6 2.9 - - + -
224C TRP 2.9 8.3 + - - -
225C PHE* 3.1 40.2 - - + +
226C PRO* 4.0 2.0 - - - -
270C ILE* 3.5 30.3 - - + -
271C VAL* 1.3 75.5 - - - +
273C ALA* 1.3 63.3 + - - +
285C TYR* 3.9 19.2 - - + -
286C ARG 3.1 4.0 - - - +
287C PHE* 3.4 40.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C PRO* 3.5 9.0 - - + +
228C LEU* 3.6 38.1 - - + -
271C VAL* 4.1 2.0 + - + +
272C PHE* 1.3 72.3 - - - +
274C ARG* 1.3 64.2 + - - +
275C VAL* 3.4 9.5 + - + +
285C TYR* 3.3 4.9 - - - -
286C ARG 2.8 30.6 + - - +
288C MET* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C PHE 4.9 2.5 - - - +
226C PRO 3.0 18.1 + - - +
227C ARG* 3.1 54.1 - - + +
228C LEU 5.2 0.9 + - - -
229C TYR* 4.0 21.4 + - - +
272C PHE 3.8 2.0 + - - -
273C ALA* 1.3 71.8 - - - +
275C VAL* 1.3 66.3 + - - +
283C ALA* 3.8 27.8 - - + +
284C MET 3.5 5.6 - - - +
285C TYR* 3.6 33.2 + - + +
14E A 3.8 32.1 + - - +
15E G 4.7 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLU 3.6 5.2 - - - -
110C GLU 4.6 2.9 - - - +
111C ASP* 3.6 40.8 - - + +
112C ILE 5.0 2.2 - - - +
190C VAL* 4.8 3.6 - - + -
273C ALA* 3.7 18.6 - - + +
274C ARG* 1.3 82.4 - - - +
276C LYS* 1.3 65.6 + - - +
283C ALA* 3.7 3.3 - - - -
284C MET* 2.8 52.3 + - + +
285C TYR 4.6 1.1 - - - +
286C ARG* 4.6 12.1 - - + -
288C MET* 5.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLU* 2.9 50.9 + - + +
110C GLU* 3.5 33.6 + - - +
111C ASP* 3.6 21.4 + - - +
275C VAL* 1.3 77.4 - - - +
277C ASP* 1.3 66.0 + - - +
278C ASN* 3.5 1.6 + - - -
281C SER* 4.1 22.9 - - - +
282C ARG 3.9 4.3 - - - +
283C ALA* 4.9 1.3 - - - +
14F A 3.5 39.0 + - - -
15F G 5.6 1.6 + - - -
----------------------------------------------------------
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