Contacts of the helix formed by residues 268 - 279 (chain C) in PDB entry 2OX4
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 TYR 268 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C GLY* 4.0 5.4 - - - -
87C THR* 2.8 49.8 + - + -
90C PHE* 3.7 21.8 - + + -
265C GLU 3.5 19.7 - - - -
266C ARG* 3.4 24.3 - - - -
267C ILE* 1.3 83.1 - - - +
269C SER* 1.3 78.0 + - - +
272C GLY* 3.1 13.4 + - - -
291C THR* 3.5 38.6 - - + +
292C CYS* 4.2 2.7 - - - +
81G TRP* 3.6 14.0 - + - -
84G GLY* 3.6 24.5 - - - -
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 3.7 31.3 - - - -
268C TYR* 1.3 82.6 + - - +
270C ARG* 1.3 63.2 + - - +
271C TRP* 3.1 27.2 + - - +
272C GLY 3.0 4.9 + - - -
273C PHE* 3.2 15.2 + - - -
292C CYS* 3.0 25.2 + - - +
297C GLU* 3.4 14.6 - - - -
301C ILE* 3.7 10.0 - - - +
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Residues in contact with ARG 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ASP* 3.0 31.5 + - - +
304B MET* 5.1 1.1 - - - +
306B HIS* 3.7 23.4 - - - +
307B ILE* 3.4 25.8 - - + +
72C TRP* 3.8 11.7 - - - -
73C GLU* 5.4 0.4 + - - -
269C SER* 1.3 69.8 - - - +
271C TRP* 1.3 81.1 + - + +
273C PHE* 3.3 1.3 + - - +
274C LEU* 2.9 32.0 + - - +
297C GLU* 2.8 40.4 + - - +
300C LYS* 3.6 56.5 - - + +
301C ILE* 3.6 10.1 - - - +
304C MET* 3.7 17.3 - - + +
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Residues in contact with TRP 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B HIS* 4.1 15.9 + + - -
307B ILE* 3.5 43.5 + - + -
72C TRP* 4.0 11.2 - + - -
76C PHE* 3.5 37.4 - + - -
269C SER* 3.1 28.5 + - - +
270C ARG* 1.3 112.6 - - - +
272C GLY* 1.3 61.2 + - - +
274C LEU* 3.7 6.5 + - - +
275C PRO* 3.4 17.3 - - - +
297C GLU* 3.7 8.1 - - - -
243G THR* 5.0 5.0 - - + +
245G LEU* 3.5 59.1 - - + +
246G ASN* 3.7 11.7 - - + +
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Residues in contact with GLY 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ILE* 3.2 20.7 - - - +
268C TYR 3.1 21.2 + - - -
269C SER 3.0 4.9 + - - -
271C TRP* 1.3 77.1 - - - +
273C PHE* 1.3 59.8 + - - +
275C PRO* 3.4 13.4 - - - +
276C PHE* 3.4 10.7 - - - -
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Residues in contact with PHE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C SER 4.0 1.6 - - - -
264C GLY* 3.7 30.1 - - - -
267C ILE* 3.3 42.8 - - + -
268C TYR* 4.7 0.4 - - - -
269C SER 3.2 23.5 + - - +
270C ARG* 3.3 4.0 + - - +
272C GLY* 1.3 75.0 - - - +
274C LEU* 1.3 66.3 + - - +
276C PHE* 3.1 9.0 + - + +
277C LEU* 3.0 34.1 + - + +
282C ILE* 4.7 3.8 - - + -
285C ILE* 3.8 33.4 - - + -
287C PRO* 3.9 18.8 - - + -
292C CYS* 4.8 0.2 - - + -
301C ILE* 3.6 37.5 - - + -
304C MET* 5.0 0.4 - - + -
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ILE* 3.6 24.0 - - + -
308B PHE* 3.8 21.1 - - + -
270C ARG 2.9 18.3 + - - +
271C TRP* 3.9 6.3 - - - +
272C GLY 3.3 0.2 - - - -
273C PHE* 1.3 74.9 - - - +
275C PRO* 1.3 65.5 - - + +
277C LEU* 3.1 8.4 + - + +
278C GLU* 2.8 55.8 + - + +
304C MET* 4.5 21.3 - - + +
308C PHE* 6.0 4.0 - - + -
246G ASN* 3.6 27.6 - - + +
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Residues in contact with PRO 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C PRO* 3.8 32.5 - - + -
271C TRP 3.4 9.4 - - - +
272C GLY* 3.4 17.0 - - - +
274C LEU* 1.3 96.9 - - + +
276C PHE* 1.3 57.8 + - + +
278C GLU* 3.5 17.1 + - - +
279C ASP* 3.0 37.4 + - - +
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Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PRO* 3.5 30.7 - - + -
247C PRO* 3.6 37.9 - - + -
250C LEU* 3.8 17.5 - - + -
263C SER* 5.6 0.7 - - - -
267C ILE* 3.6 30.5 - - + -
272C GLY 3.4 22.4 - - - -
273C PHE* 3.1 9.3 + - + +
275C PRO* 1.3 77.8 - - + +
277C LEU* 1.3 60.8 + - + +
279C ASP* 3.7 1.3 + - - -
280C ARG* 3.0 5.9 + - - -
281C SER* 2.9 48.5 + - - +
282C ILE* 3.5 30.0 + - + -
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ARG* 3.4 11.4 + - - -
273C PHE* 3.0 23.6 + - + +
274C LEU* 3.5 8.5 - - + +
276C PHE* 1.3 77.6 - - + +
278C GLU* 1.3 64.8 + - - +
280C ARG* 3.0 12.4 + - - +
282C ILE* 5.3 2.0 - - + +
285C ILE* 4.7 9.6 - - + -
301C ILE* 4.8 2.0 - - + +
304C MET* 3.8 41.1 - - + -
305C ALA* 4.0 28.3 - - + +
308C PHE* 3.4 27.0 - - + -
310C VAL* 4.0 30.1 - - + -
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.0 29.9 + - - +
278B GLU* 5.7 13.8 - - + +
308B PHE* 4.4 9.6 - - + -
274C LEU* 2.8 50.8 + - + +
275C PRO* 3.5 18.7 - - - +
277C LEU* 1.3 71.6 - - - +
279C ASP* 1.3 63.7 + - - +
308C PHE* 4.5 7.4 - - + -
246G ASN* 5.3 0.7 - - - +
248G ARG* 4.5 13.6 + - - +
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Residues in contact with ASP 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 4.2 3.3 + - - +
252A GLU* 4.4 8.3 - - - +
247C PRO* 4.3 4.2 - - - +
248C ARG* 3.9 27.7 + - - +
251C LYS* 3.9 45.5 + - + +
254C LYS* 5.7 0.5 - - - +
275C PRO* 3.0 21.7 + - - +
276C PHE* 4.0 4.2 - - - +
278C GLU* 1.3 78.4 - - - +
280C ARG* 1.3 67.8 + - - +
281C SER* 3.3 8.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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