Contacts of the helix formed by residues 282 - 294 (chain C) in PDB entry 5AYR
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 282 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU* 2.7 24.2 + - - +
179C THR 4.5 5.1 + - - -
180C ASP* 2.8 53.1 + - + +
280C GLY* 3.8 11.9 - - - +
281C CYS* 1.3 74.2 - - - +
283C HIS* 1.3 57.4 + - - +
284C PHE 3.2 2.7 - - - -
285C SER* 3.2 14.8 + - - +
286C LYS* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ASP* 3.7 0.4 + - - -
243C LEU* 4.0 15.8 - - + +
245C TRP* 3.2 21.9 + - + +
264C LEU* 3.6 46.9 - - + +
265C GLN 3.6 9.4 + - - -
266C THR* 3.6 21.7 - - + +
281C CYS* 3.0 53.0 + - + +
282C ARG* 1.3 75.9 - - - +
284C PHE* 1.3 63.9 + - + +
286C LYS* 3.8 10.3 + - + +
287C THR* 2.6 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ILE* 5.6 0.7 - - + -
173C ILE* 3.7 30.3 - - + -
176C GLU* 3.7 30.7 - - + -
177C LEU* 3.4 34.8 - - + -
180C ASP* 3.1 15.0 + - + +
181C ILE* 4.0 3.4 - - + -
195C TRP* 4.9 2.5 - + - -
243C LEU* 5.0 2.9 - - + -
245C TRP* 4.2 21.3 - + - -
278C PHE* 4.1 13.5 - + - -
281C CYS* 5.2 0.2 - - - -
283C HIS* 1.3 84.3 - - + +
285C SER* 1.3 65.0 + - - +
287C THR* 3.6 1.6 + - - -
288C ASN* 3.3 15.4 + - - -
301C TRP* 3.0 58.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ASP* 2.9 38.5 + - - -
181C ILE* 4.1 9.8 - - - +
282C ARG* 3.2 20.2 + - - +
284C PHE* 1.3 73.2 - - - +
286C LYS* 1.3 72.2 + - - +
288C ASN* 2.9 7.2 + - - +
289C GLU* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 3.8 29.0 - - + +
280C GLY 5.6 0.2 + - - -
281C CYS* 3.5 21.3 + - - +
282C ARG* 2.9 30.1 + - + +
283C HIS* 3.9 4.9 + - + +
285C SER* 1.3 83.9 + - - +
287C THR* 1.3 53.4 + - - +
289C GLU* 3.1 12.3 + - - +
290C LEU* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 3.7 34.1 - - + -
241C VAL* 3.5 19.3 - - + +
243C LEU* 3.5 24.8 - - - +
264C LEU* 4.1 1.3 - - - +
283C HIS 2.6 25.1 + - - -
284C PHE 3.7 6.7 - - - -
286C LYS* 1.3 76.7 - - - +
288C ASN* 1.3 56.1 + - - +
290C LEU* 3.5 2.4 + - - +
291C LEU* 2.9 40.7 + - + +
301C TRP* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 4.4 8.5 - - - +
284C PHE 3.3 7.5 + - - +
285C SER* 2.9 9.9 + - - +
287C THR* 1.3 75.6 - - - +
289C GLU* 1.3 61.4 + - + +
291C LEU* 3.6 4.2 - - - +
292C GLN* 2.9 38.6 + - + +
298C PRO* 3.7 13.9 - - + +
299C ILE* 2.8 53.7 + - - +
301C TRP* 3.3 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 2.8 27.8 + - - +
286C LYS* 3.7 10.6 - - - +
288C ASN* 1.3 76.4 - - + +
290C LEU* 1.3 57.6 + - + +
292C GLN* 3.6 6.5 - - + +
293C LYS* 2.8 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C VAL* 4.0 6.1 - - + -
262C HIS* 3.6 56.0 + - + +
264C LEU* 3.9 36.1 - - + -
286C LYS* 2.8 27.0 + - + +
287C THR 3.9 3.4 - - - +
289C GLU* 1.3 72.9 - - + +
291C LEU* 1.3 57.9 + - - +
293C LYS* 3.7 22.1 - - + +
294C SER* 3.2 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LYS* 4.0 25.6 - - + +
139C VAL* 3.9 20.9 - - + -
239C GLY 4.5 5.6 - - - +
241C VAL* 4.0 17.0 - - + -
287C THR* 2.9 27.3 + - + +
288C ASN* 3.2 6.0 + - - +
290C LEU* 1.3 73.7 - - - +
292C GLN* 1.3 58.1 + - - +
293C LYS 3.1 1.1 - - - -
294C SER* 2.7 23.9 + - - -
296C LYS* 3.1 41.2 + - + +
297C LYS 3.9 17.3 - - - +
298C PRO* 4.5 1.8 - - + -
299C ILE* 4.0 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASN* 2.9 31.7 + - + +
289C GLU* 3.6 6.5 - - + +
291C LEU* 1.3 69.6 - - - +
293C LYS* 1.3 62.6 + - - +
295C GLY* 3.2 13.5 + - - -
296C LYS 3.4 9.9 + - - -
298C PRO* 3.4 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 293 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C HIS* 5.9 1.3 - - + +
289C GLU* 2.8 33.8 + - - +
290C LEU* 3.7 26.8 - - + +
292C GLN* 1.3 72.8 - - - +
294C SER* 1.3 56.9 + - - +
295C GLY* 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLY* 3.9 17.2 - - - -
262C HIS* 3.9 14.9 + - - -
290C LEU 3.2 16.1 + - - -
291C LEU* 2.7 14.1 + - - -
293C LYS* 1.3 72.1 - - - +
295C GLY* 1.3 60.9 + - - -
296C LYS* 3.3 22.1 + - - +
----------------------------------------------------------
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