Contacts of the helix formed by residues 247 - 257 (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 PRO 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C PRO* 3.9 3.8 - - + +
245C LEU 3.4 10.8 - - - +
246C ASN* 1.3 84.2 - - - +
248C ARG* 1.3 62.7 + - - +
250C LEU* 3.0 22.7 + - - +
251C LYS 3.9 2.3 + - - -
275C PRO* 3.8 38.6 - - + -
276C PHE* 3.6 38.0 - - + +
279C ASP* 4.3 4.9 - - - +
281C SER* 4.7 0.3 + - - -
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Residues in contact with ARG 248 (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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246C ASN* 3.2 12.3 + - - +
247C PRO* 1.3 77.2 - - - +
249C LEU* 1.3 66.9 + - - +
251C LYS* 3.1 21.7 + - + +
252C GLU* 2.8 48.3 + - - +
279C ASP* 3.9 16.5 + - - +
277D LEU 3.2 23.6 + - - -
278D GLU* 3.0 20.6 + - - +
279D ASP* 4.1 2.4 - - - +
280D ARG* 3.8 12.6 - - - +
308D PHE* 3.4 24.4 - - - -
278G GLU* 4.5 13.5 + - - +
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Residues in contact with LEU 249 (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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220C LEU* 3.5 11.6 - - + +
242C ASN* 3.6 15.5 - - - +
243C THR 5.2 2.0 - - - +
246C ASN* 3.1 28.7 + - + +
248C ARG* 1.3 80.3 - - - +
250C LEU* 1.3 57.6 + - - +
252C GLU* 3.2 8.6 + - + +
253C ALA* 2.9 25.6 + - - +
280D ARG* 4.1 20.9 - - + +
307D ILE 3.6 18.2 - - - +
308D PHE* 3.5 27.8 - - + +
309D GLU* 3.6 36.1 - - + +
271G TRP* 6.0 0.2 - - - +
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Residues in contact with LEU 250 (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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241C ILE* 3.7 37.9 - - + +
242C ASN* 3.9 16.6 - - - +
246C ASN 4.5 0.2 + - - -
247C PRO 3.0 13.5 + - - +
249C LEU* 1.3 76.4 - - - +
251C LYS* 1.3 59.6 + - - +
253C ALA* 3.3 3.4 + - + +
254C LYS* 2.9 29.3 + - - +
261C LEU* 3.9 17.7 - - + +
262C ALA 5.8 0.7 - - - +
263C SER* 4.8 8.5 - - - -
276C PHE* 3.8 17.5 - - + -
281C SER* 3.7 15.5 - - - +
282C ILE* 3.6 32.1 - - + -
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Residues in contact with LYS 251 (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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252A GLU* 6.0 0.4 - - - -
255A LYS* 4.6 17.3 - - - +
247C PRO 3.9 1.0 + - - -
248C ARG* 3.1 19.7 + - + +
250C LEU* 1.3 78.8 - - - +
252C GLU* 1.3 64.4 + - + +
254C LYS* 3.3 6.5 + - + +
255C LYS* 3.2 40.3 + - - +
279C ASP* 3.9 51.9 + - + +
281C SER* 3.7 10.2 - - - +
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Residues in contact with GLU 252 (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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220C LEU* 3.6 17.2 - - + +
224C ILE* 4.7 1.2 - - - +
248C ARG* 2.8 49.6 + - - +
249C LEU* 3.4 10.3 - - - +
251C LYS* 1.3 74.6 - - - +
253C ALA* 1.3 66.3 + - - +
255C LYS* 2.9 53.8 + - - +
256C LYS* 4.0 6.9 + - - +
251D LYS* 5.9 0.7 + - - -
254D LYS* 6.1 0.9 - - - +
279D ASP 4.4 7.1 - - - +
280D ARG* 4.2 20.8 - - + +
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Residues in contact with ALA 253 (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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220C LEU* 3.6 21.4 - - + +
224C ILE* 4.1 5.8 - - + +
241C ILE* 3.8 29.4 - - + -
242C ASN* 5.7 1.3 - - - +
249C LEU 2.9 13.7 + - - +
250C LEU* 3.5 11.7 - - + +
252C GLU* 1.3 75.4 - - - +
254C LYS* 1.3 58.0 + - - +
256C LYS* 2.9 20.3 + - - +
257C ILE* 3.2 22.3 + - + +
261C LEU* 4.8 0.4 - - + -
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Residues in contact with LYS 254 (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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220A LEU* 6.2 0.6 - - - +
224A ILE* 6.3 0.6 - - - +
252A GLU* 6.0 1.6 - - - +
256A LYS* 2.7 48.8 + - - +
250C LEU 2.9 17.0 + - - +
251C LYS* 3.3 8.7 + - - +
253C ALA* 1.3 76.1 - - - +
255C LYS* 1.3 54.5 + - - +
257C ILE* 3.2 11.6 + - - +
258C ASP 5.9 1.0 + - - -
259C ILE 4.9 2.4 + - - -
260C PRO* 4.9 3.0 - - - +
261C LEU* 4.1 18.8 - - + +
279C ASP 5.7 0.4 - - - +
280C ARG* 3.8 17.7 - - - +
281C SER* 3.3 31.0 - - - +
283C ASP* 2.7 34.6 + - - -
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Residues in contact with LYS 255 (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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255A LYS* 6.3 1.1 - - + +
256A LYS* 3.9 8.4 + - - +
251C LYS* 3.2 31.6 + - + +
252C GLU* 2.9 44.6 + - - +
253C ALA 3.2 0.8 - - - -
254C LYS* 1.3 77.4 - - - +
256C LYS* 1.3 71.4 + - + +
251D LYS* 4.7 17.4 - - - +
255D LYS* 6.4 0.4 - - - +
279D ASP 5.7 0.2 + - - -
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Residues in contact with LYS 256 (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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256A LYS* 5.0 0.4 - - - -
224C ILE* 3.8 38.7 - - + +
227C ALA* 5.5 0.7 - - - +
228C LYS* 3.9 19.7 + - - +
252C GLU 4.5 2.7 - - - +
253C ALA 2.9 3.8 + - - -
255C LYS* 1.3 89.8 - - + +
257C ILE* 1.3 64.1 + - - +
258C ASP* 4.4 2.1 + - - -
254D LYS* 2.8 43.5 + - - +
255D LYS* 4.1 9.7 + - - +
256D LYS 4.8 0.4 - - - -
257D ILE 2.8 22.1 + - - +
258D ASP* 3.0 26.5 + - - +
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Residues in contact with ILE 257 (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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256A LYS* 3.1 16.5 + - - -
223C ALA 4.1 4.9 - - - +
224C ILE* 3.9 28.9 - - + +
227C ALA* 3.9 25.8 - - + -
238C TYR* 4.1 5.4 - - + -
241C ILE* 3.7 29.6 - - + -
253C ALA* 3.2 19.2 + - + +
254C LYS* 3.2 11.8 + - - +
256C LYS* 1.3 82.1 - - - +
258C ASP* 1.3 65.2 + - - +
259C ILE* 3.6 30.1 - - + +
261C LEU* 3.9 10.7 - - + +
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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