Contacts of the helix formed by residues 272 - 282 (chain C) in PDB entry 4PEI
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 ASP 272 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C CYS* 3.2 37.0 + - + +
120C ASN* 3.0 27.5 + - - +
125C ARG* 2.7 46.3 + - - -
168C LEU* 4.1 0.2 - - - +
270C GLU 3.6 2.8 + - - -
271C TYR* 1.3 72.4 - - - +
273C LYS* 1.3 60.6 + - - +
274C ASP* 3.4 5.4 + - - +
275C TRP* 3.0 27.0 + - + +
276C VAL* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ASN* 4.5 14.5 - - - +
270C GLU* 5.1 8.1 + - - +
271C TYR 3.5 3.1 + - - +
272C ASP* 1.3 74.1 + - - +
274C ASP* 1.3 64.4 + - - +
276C VAL* 3.1 4.6 + - - +
277C CYS* 2.8 29.4 + - - -
315C ILE* 3.8 38.4 - - + -
324C LEU* 3.6 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 3.9 9.3 + - - +
167C ASN* 5.5 2.0 - - - +
168C LEU* 3.8 18.8 - - + +
171C SER* 2.5 35.3 + - - -
272C ASP* 3.4 10.0 + - - +
273C LYS* 1.3 79.1 - - - +
275C TRP* 1.3 62.5 + - - +
277C CYS* 3.3 0.9 + - - -
278C ASN* 3.1 19.6 + - - +
306C ARG* 2.8 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASN* 5.4 3.7 + - - -
116C CYS* 3.2 30.7 - - - -
117C SER* 3.3 26.5 - - - -
118C CYS* 3.6 27.8 - - + +
164C MET* 3.6 55.2 - - + -
165C LEU* 4.0 8.3 - - + -
168C LEU* 3.6 14.9 - - + +
271C TYR* 5.6 7.6 - + - -
272C ASP* 3.0 21.4 + - - +
274C ASP* 1.3 74.2 - - - +
276C VAL* 1.3 73.6 + - + +
278C ASN* 3.0 7.0 + - + +
279C LEU* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C TYR* 3.7 17.7 - - + -
272C ASP 2.9 17.4 + - - +
273C LYS* 3.1 7.6 + - - +
275C TRP* 1.3 80.4 - - + +
277C CYS* 1.3 65.6 + - - +
279C LEU* 3.1 7.6 + - - +
280C ILE* 2.9 22.2 + - - +
314C ILE* 3.8 12.3 - - + -
315C ILE* 3.8 20.0 - - + -
318C TRP* 3.5 55.9 - - + +
324C LEU* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LYS 2.8 22.1 + - - -
274C ASP 3.6 5.8 - - - +
276C VAL* 1.3 72.4 - - - +
278C ASN* 1.3 58.4 + - - +
280C ILE* 3.2 1.6 + - - +
281C MET* 2.8 36.3 + - - +
306C ARG* 3.5 16.4 - - - +
311C ASP* 3.4 50.0 - - - +
314C ILE* 4.1 13.9 - - + -
315C ILE* 3.9 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C MET* 2.9 30.4 + - + +
167C ASN* 2.8 33.2 + - - +
168C LEU* 3.9 10.7 - - - +
274C ASP 3.1 8.1 + - - +
275C TRP* 3.0 15.9 + - + +
277C CYS* 1.3 75.4 - - - +
279C LEU* 1.3 62.1 + - - +
281C MET 3.3 0.2 + - - -
282C THR* 2.8 32.8 + - - +
303C LEU* 3.7 17.5 - - + +
306C ARG* 2.8 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 5.9 0.4 - - + -
102C ASN* 3.3 32.8 - - + +
164C MET* 4.7 7.6 - - + +
275C TRP* 2.9 46.2 + - + +
276C VAL* 3.5 8.5 - - - +
278C ASN* 1.3 78.2 - - - +
280C ILE* 1.3 63.2 + - + +
282C THR* 3.3 14.4 + - - +
283C TRP* 3.5 6.9 + - - -
286C PHE* 5.7 5.8 - - + -
318C TRP* 3.8 27.1 - - + -
340C ARG* 5.4 1.1 - - - +
344C ILE* 3.8 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 2.9 20.7 + - + +
277C CYS 3.8 3.4 - - - +
279C LEU* 1.3 78.5 - - - +
281C MET* 1.3 58.1 + - - +
283C TRP* 3.0 18.2 + - - +
314C ILE* 3.5 23.6 - - + -
318C TRP* 3.8 30.1 - - + -
344C ILE* 3.9 31.4 - - + +
347C ILE* 4.0 14.8 - - + -
348C TYR* 3.3 40.7 - - + +
351C LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C CYS 2.8 22.5 + - - +
278C ASN 3.3 2.4 + - - +
280C ILE* 1.3 75.2 - - - +
282C THR* 1.3 60.9 + - - +
283C TRP 3.3 0.2 - - - -
284C PRO* 3.5 11.0 - - - +
302C LEU* 3.7 22.2 - - - +
303C LEU* 4.2 13.2 - - + -
305C LYS* 3.7 44.6 - - + +
306C ARG* 3.7 17.7 - - + +
310C LEU* 4.0 15.3 - - + -
314C ILE* 3.7 22.4 - - + -
348C TYR* 4.2 7.8 - - + -
351C LEU* 3.9 17.9 - - - -
353C ILE* 4.7 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C MET* 3.4 19.5 - - - +
278C ASN 2.8 23.4 + - - +
279C LEU* 3.3 7.3 + - - +
280C ILE 3.2 0.2 - - - -
281C MET* 1.3 77.4 - - - +
283C TRP* 1.3 65.8 + - - +
284C PRO* 3.2 4.5 - - - -
285C ALA* 2.8 15.3 + - - +
286C PHE* 3.3 23.5 - - - -
299C ILE* 3.9 25.1 - - + -
302C LEU* 4.0 15.3 - - + -
303C LEU* 3.7 20.4 - - + -
----------------------------------------------------------
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