Contacts of the helix formed by residues 271 - 284 (chain C) in PDB entry 3N6J
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 SER 271 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 3.8 16.4 - - - -
271B SER* 3.9 7.6 - - - -
274B GLU* 2.5 41.3 + - - -
266C GLY* 3.5 3.8 - - - -
270C TYR* 1.3 76.8 - - - +
272C GLY* 1.3 66.4 - - - +
273C ARG* 3.7 5.4 + - - -
274C GLU* 2.7 26.3 + - - +
275C ILE* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 5.0 1.2 + - - -
265C ILE* 3.8 17.1 - - - +
266C GLY* 3.4 21.7 - - - +
271C SER* 1.3 75.0 - - - +
273C ARG* 1.3 55.4 + - - +
275C ILE* 3.0 3.8 + - - +
276C MSE 2.8 41.6 + - - +
292C ILE* 4.3 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLY 3.5 19.4 + - - -
270B TYR* 3.6 15.7 - - - -
274B GLU* 2.9 34.2 + - - +
271C SER* 3.3 6.2 + - - -
272C GLY* 1.3 76.4 - - - +
274C GLU* 1.3 56.8 + - - +
277C ALA* 3.2 9.4 + - - +
292C ILE* 2.5 66.3 + - + +
298C GLU* 3.3 48.5 + - - -
301C HIS* 3.9 3.9 - - - +
302C ALA* 3.7 14.8 - - + +
305C LEU* 3.5 18.5 - - + +
307C SER* 2.9 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B SER* 2.8 16.2 + - - -
273B ARG* 2.7 41.7 + - - +
274B GLU* 4.0 0.7 - - - +
301B HIS* 3.6 38.7 - - + +
305B LEU* 3.8 4.0 - - - +
270C TYR* 3.0 16.5 - - + -
271C SER* 2.7 36.6 + - - +
272C GLY 3.2 0.4 - - - -
273C ARG* 1.3 73.9 - - - +
275C ILE* 1.3 65.7 + - - +
277C ALA* 3.4 1.7 + - - +
278C GLU* 3.2 17.7 + - - +
305C LEU* 3.4 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 3.6 24.9 - - - +
243C LEU* 3.4 20.7 - - + +
264C CYS* 3.7 29.8 - - + +
265C ILE 3.6 24.0 - - - +
267C GLU* 3.5 30.3 - - + +
270C TYR* 4.0 13.7 - - + -
271C SER 3.0 16.7 + - - +
272C GLY 3.0 7.4 + - - +
274C GLU* 1.3 75.8 - - - +
276C MSE 1.3 57.0 + - - +
278C GLU* 3.2 9.1 + - - +
279C PHE* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ASP* 4.0 7.6 - - - +
263C PRO* 3.2 37.7 - - + -
264C CYS* 3.7 15.7 - - - +
272C GLY 2.8 19.8 + - - +
273C ARG 3.9 1.8 - - - +
275C ILE* 1.3 75.4 - - - +
277C ALA* 1.3 60.6 + - - +
278C GLU 3.1 0.2 - - - -
279C PHE* 3.1 7.4 + - - +
280C ARG* 2.9 30.5 + - - +
287C THR* 3.7 31.5 - - - +
288C ALA 3.8 16.8 - - - +
289C THR* 4.3 6.5 - - - -
292C ILE* 3.7 27.4 - - + -
307C SER* 3.8 15.2 - - - +
308C VAL* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B HIS* 4.8 4.5 - - + +
273C ARG 3.2 16.7 + - - +
274C GLU* 3.4 6.5 + - - +
276C MSE 1.3 77.0 - - - +
278C GLU* 1.3 57.9 + - - +
280C ARG* 3.6 2.7 + - - +
281C ARG* 3.1 46.0 + - - +
305C LEU* 3.3 31.4 - - + +
306C GLN 3.9 6.3 - - - +
307C SER* 3.6 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 2.9 51.9 + - - +
301B HIS* 2.7 33.2 + - + -
243C LEU* 3.3 17.4 - - + +
270C TYR* 4.4 2.1 - - - -
274C GLU 3.2 9.7 + - - +
275C ILE* 3.2 10.0 + - - +
276C MSE 3.1 0.6 - - - -
277C ALA* 1.3 75.5 - - - +
279C PHE* 1.3 63.0 + - - +
281C ARG* 4.8 7.4 - - - +
282C ARG* 3.1 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LEU* 3.9 9.2 - - + -
246C ALA* 3.9 29.6 - - + -
247C ILE* 4.2 12.3 - - + -
250C CYS* 3.6 37.0 - - + -
260C ALA* 4.1 15.9 - - + -
263C PRO* 4.2 15.5 - - + -
264C CYS* 4.5 5.6 - - - -
275C ILE 2.9 13.7 + - - +
276C MSE 3.1 12.5 + - - +
278C GLU* 1.3 74.1 - - - +
280C ARG* 1.3 64.1 + - - +
282C ARG* 3.4 1.7 + - - +
283C THR* 2.7 53.5 + - + +
285C ILE* 4.3 9.4 - - + -
287C THR* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 3.5 42.0 + - - +
281A ARG* 5.9 8.9 - - - +
306A GLN* 5.1 1.4 + - - -
276C MSE 2.9 14.0 + - - +
277C ALA 3.8 4.9 - - - +
279C PHE* 1.3 77.7 - - - +
281C ARG* 1.3 64.8 + - - +
283C THR 3.1 0.7 + - - -
284C GLY* 2.6 37.9 + - - +
285C ILE 3.8 22.2 - - - +
286C PRO* 4.8 0.7 - - + -
287C THR* 3.8 14.4 - - + +
306C GLN* 3.7 31.9 + - - +
307C SER 4.1 5.8 - - - -
308C VAL 4.3 5.7 + - - -
309C ASP* 2.7 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ARG* 5.2 10.1 - - - +
306A GLN* 3.7 31.6 + - - +
308A VAL 5.6 0.4 - - - -
309A ASP* 5.0 9.3 - - - +
333A TRP 3.5 16.1 + - - +
334A GLY* 4.1 23.2 - - - +
335A LEU* 3.9 25.5 - - + +
300B CYS* 3.9 23.9 - - - -
301B HIS* 4.8 8.7 + - - -
304B MSE 5.3 5.3 - - - +
277C ALA* 3.1 34.5 + - - +
278C GLU* 4.5 7.5 - - - +
280C ARG* 1.3 85.8 - - - +
282C ARG* 1.3 62.0 + - + +
283C THR 3.5 0.4 - - - -
284C GLY* 4.6 1.6 + - - -
305C LEU 4.2 9.7 + - - -
306C GLN 4.7 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASN* 3.7 22.6 + - - -
332A GLU 4.9 4.6 + - - -
333A TRP 4.7 2.0 - - - -
334A GLY* 3.7 29.7 - - - +
297B ARG* 6.1 3.0 - - - +
243C LEU* 5.8 1.8 - - - -
247C ILE* 4.1 28.3 - - + +
278C GLU* 3.1 39.6 + - - +
279C PHE 4.2 0.4 - - - +
280C ARG 3.2 0.2 - - - -
281C ARG* 1.3 80.8 - - + +
283C THR* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ILE* 4.3 36.1 - - + +
250C CYS* 4.5 11.0 - - + +
251C LYS* 5.3 6.2 - - - +
254C ASN* 3.8 13.3 + - - -
279C PHE* 2.7 42.8 + - + +
280C ARG 4.0 0.2 + - - -
282C ARG* 1.3 84.6 - - - +
284C GLY* 1.3 57.2 + - - +
285C ILE* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLY 5.6 2.3 - - - +
254C ASN* 4.5 8.8 - - - +
280C ARG* 2.6 23.2 + - - +
281C ARG* 4.6 2.0 + - - -
282C ARG 3.9 0.4 - - - +
283C THR* 1.3 69.0 - - - +
285C ILE* 1.3 63.4 + - - +
286C PRO* 3.4 9.0 - - - +
----------------------------------------------------------
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