Contacts of the helix formed by residues 276 - 287 (chain C) in PDB entry 5DO7
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 THR 276 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE 5.0 0.2 - - - +
261C ASP* 3.5 11.9 + - - +
262C LYS* 4.8 1.1 - - - +
263C ILE* 4.6 0.4 - - - -
275C GLY* 1.3 73.2 - - - -
277C PRO* 1.3 81.9 - - + +
278C ALA* 4.0 14.6 - - + +
279C GLU* 2.8 29.7 + - - +
280C MET* 2.8 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PHE* 3.4 55.8 - - + +
258C GLN* 4.7 13.0 - - - +
260C PHE* 2.9 33.9 - - + +
263C ILE* 4.4 10.3 - - + -
275C GLY 3.9 4.5 - - - +
276C THR* 1.3 86.9 - - + +
278C ALA* 1.3 64.5 + - - +
280C MET* 2.8 14.7 + - + +
281C LEU* 2.8 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C GLN* 5.6 1.0 + - - -
276C THR* 3.2 11.1 - - + +
277C PRO* 1.3 77.3 - - - +
279C GLU* 1.3 54.1 + - - +
281C LEU* 3.0 13.4 + - - +
282C ASP* 2.8 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LYS* 5.5 2.3 - - - -
273C PHE* 3.7 4.5 - - + -
275C GLY* 3.4 7.0 - - - -
276C THR* 2.8 49.4 + - - +
278C ALA* 1.3 75.2 - - - +
280C MET* 1.3 54.5 + - - -
282C ASP* 3.5 6.7 + - - +
283C PHE* 2.8 29.8 + - - +
334C ILE* 3.1 47.2 - - + +
337C LYS* 5.6 4.2 - - - +
338C THR* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 6.4 0.2 - - + -
257C PHE* 3.5 29.4 - - + -
263C ILE* 4.0 21.3 - - + -
265C ILE* 4.7 14.1 - - + -
273C PHE* 3.4 31.4 - - + -
276C THR 2.8 6.4 + - - +
277C PRO* 2.8 16.2 + - + +
279C GLU* 1.3 67.8 - - - +
281C LEU* 1.3 61.2 + - - +
282C ASP 3.0 1.5 + - - -
283C PHE* 4.2 0.9 - - - -
284C PHE* 2.8 67.9 + - + +
297C PRO 5.2 0.9 - - - +
298C PHE* 5.3 2.0 - - - -
301C TYR* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PHE* 4.1 20.9 - - + -
258C GLN* 6.3 0.4 - - - +
277C PRO 2.8 13.9 + - - +
278C ALA* 3.4 13.7 - - - +
280C MET* 1.3 72.9 - - - +
282C ASP* 1.3 56.9 + - - +
285C ASN* 3.1 30.3 + - - +
291C CYS* 4.2 5.2 - - - -
293C GLU* 5.7 4.3 - - - +
297C PRO* 4.2 9.6 - - + -
301C TYR* 3.4 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ALA* 2.8 12.7 + - - +
279C GLU* 3.6 10.3 - - - +
281C LEU* 1.3 76.2 - - - +
283C PHE* 1.3 54.9 + - - +
285C ASN* 2.8 12.5 + - - +
286C ASP* 2.7 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 5.5 0.4 - - + -
273C PHE* 3.1 39.7 - + + -
279C GLU 2.8 22.1 + - - +
280C MET 3.8 1.6 - - - +
282C ASP* 1.3 73.2 - - - +
284C PHE* 1.3 72.0 + + - +
286C ASP* 2.8 20.7 + - - +
287C CYS* 2.8 51.6 + - - -
325C ILE* 4.4 4.7 - - + -
328C ALA* 4.5 1.6 - - + -
329C TYR* 3.4 46.0 - + + -
332C SER* 4.0 17.0 - - - -
334C ILE* 3.9 20.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
265C ILE* 5.1 0.9 - - + -
272C ILE* 5.1 1.6 - - + -
273C PHE* 4.0 18.6 - - + -
280C MET* 2.8 53.3 + - + +
283C PHE* 1.3 82.5 - + - +
285C ASN* 1.3 60.8 + - - +
287C CYS* 3.2 9.0 + - + +
288C GLY 2.8 8.7 + - - -
289C TYR* 2.8 23.5 + - - +
301C TYR* 3.4 42.2 - + + -
304C LEU* 3.8 24.9 - - + -
305C THR* 3.7 30.5 - - + -
325C ILE* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU* 3.1 21.8 + - - +
282C ASP* 2.8 9.7 + - - +
284C PHE* 1.3 75.7 - - - +
286C ASP* 1.3 63.0 + - - +
287C CYS 3.3 0.7 - - - -
288C GLY* 3.3 12.6 + - - +
289C TYR 2.5 36.1 + - - +
290C PRO* 3.2 25.3 - - + +
301C TYR* 3.8 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASP 2.7 7.7 + - - +
283C PHE* 2.8 31.4 + - + +
285C ASN* 1.3 78.8 - - - +
287C CYS* 1.3 57.2 + - - +
288C GLY* 3.6 0.3 + - - -
332C SER* 4.2 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 2.8 52.9 + - - -
284C PHE* 3.2 11.0 + - + +
286C ASP* 1.3 76.2 - - - +
288C GLY* 1.3 59.5 + - - +
289C TYR* 3.7 8.4 - - - -
325C ILE* 3.5 32.4 - - + +
328C ALA* 3.8 21.3 - - + -
----------------------------------------------------------
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