Contacts of the helix formed by residues 277 - 291 (chain C) in PDB entry 1OHV
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 SER 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C LEU* 4.9 1.7 - - - +
238C GLU* 2.5 40.0 + - - -
276C ALA* 1.3 77.5 - - - +
278C ASP* 1.3 65.8 + - - +
279C ASP* 3.6 11.2 + - - +
280C PHE* 3.0 24.6 + - - +
281C PHE* 3.3 9.9 - - - -
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Residues in contact with ASP 278 (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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276C ALA 4.9 0.9 - - - +
277C SER* 1.3 73.9 - - - +
279C ASP* 1.3 62.9 + - - +
281C PHE* 3.1 5.3 + - - +
282C ARG* 3.0 48.3 + - - +
315C HIS 3.3 16.1 - - - +
316C TRP* 3.5 23.9 + - + -
408C ARG* 2.8 45.4 + - - -
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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
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238C GLU* 4.7 4.2 - - - +
242C LEU* 5.7 0.2 - - - +
277C SER* 3.6 11.4 + - - +
278C ASP* 1.3 78.0 - - - +
280C PHE* 1.3 64.3 + - - +
282C ARG* 3.3 26.4 + - - +
283C LYS* 2.8 63.6 + - - +
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Residues in contact with PHE 280 (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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185C PHE* 4.3 18.2 - + - -
220C PHE* 4.2 5.4 - + - -
221C PRO* 3.4 37.2 - - + -
238C GLU* 3.6 32.8 - - + +
241C CYS* 4.2 5.6 - - + -
242C LEU* 3.5 33.5 - - + +
245C VAL* 6.0 0.2 - - + -
276C ALA* 3.5 19.5 - - + -
277C SER* 3.0 13.0 + - - +
279C ASP* 1.3 82.5 + - - +
281C PHE* 1.3 80.0 + + - +
283C LYS* 3.4 6.1 + - - +
284C LEU* 2.9 41.3 + - + +
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Residues in contact with PHE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C PHE* 3.9 16.4 - + - -
264C VAL* 3.8 23.6 - - + -
265C GLU 3.5 19.3 - - - -
266C PRO* 3.2 31.9 - - + -
276C ALA* 3.7 25.4 - - + -
277C SER 3.3 19.0 + - - -
278C ASP* 3.1 5.2 + - - +
280C PHE* 1.3 87.6 - + - +
282C ARG* 1.3 60.4 - - - +
284C LEU* 3.7 6.4 - - + +
285C ARG* 2.9 30.0 + - - +
295C PHE* 4.5 4.1 - + - -
316C TRP* 3.3 51.9 - + + +
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Residues in contact with ARG 282 (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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278C ASP* 3.0 30.2 + - - +
279C ASP* 3.6 37.9 + - - +
281C PHE* 1.3 75.6 - - - +
283C LYS* 1.3 58.9 + - + +
285C ARG* 3.4 4.2 + - - +
286C ASP* 3.0 33.0 + - - +
315C HIS 4.5 1.4 + - - -
316C TRP* 2.8 40.8 + - + +
318C LEU* 3.6 37.3 - - + +
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Residues in contact with LYS 283 (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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242C LEU* 3.7 33.8 - - + +
279C ASP* 2.8 50.2 + - - +
280C PHE 3.7 0.4 - - - +
282C ARG* 1.3 75.7 - - + +
284C LEU* 1.3 60.4 + - - +
286C ASP* 3.2 12.8 + - - +
287C ILE* 3.0 32.2 + - + +
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Residues in contact with LEU 284 (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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185C PHE* 3.6 33.2 - - + -
242C LEU* 3.8 14.1 - - + +
245C VAL* 3.9 31.0 - - + -
262C ILE* 4.7 8.5 - - + -
264C VAL* 4.1 9.4 - - + -
280C PHE* 2.9 32.5 + - + +
281C PHE* 3.3 9.2 + - + +
283C LYS* 1.3 75.8 - - - +
285C ARG* 1.3 58.5 + - - +
287C ILE* 3.2 7.2 + - + +
288C SER* 2.9 26.5 + - - -
295C PHE* 3.8 25.8 - - + -
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Residues in contact with ARG 285 (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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281C PHE 2.9 17.5 + - - +
282C ARG 3.5 5.4 - - - +
284C LEU* 1.3 77.6 - - - +
286C ASP* 1.3 63.0 + - - +
288C SER* 3.3 2.8 + - - -
289C ARG* 3.1 52.8 + - - +
295C PHE* 3.4 44.3 - - + +
318C LEU* 4.4 12.6 - - + -
320C ASP* 2.7 52.3 + - - +
321C PRO 3.5 9.3 - - - +
322C ALA* 3.7 5.5 - - - -
323C ASP* 3.1 31.7 + - - -
339C LYS* 3.4 0.8 - - - +
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Residues in contact with ASP 286 (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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282C ARG* 3.0 18.5 + - - +
283C LYS* 3.2 16.2 + - + +
285C ARG* 1.3 75.3 - - - +
287C ILE* 1.3 61.2 + - + +
289C ARG* 2.9 29.4 + - - +
290C LYS* 2.9 29.3 + - - +
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Residues in contact with ILE 287 (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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242C LEU* 3.7 46.0 - - + +
245C VAL* 4.2 11.2 - - + -
246C GLU* 3.9 22.2 - - + +
249C ILE* 3.9 24.0 - - + -
262C ILE* 4.9 0.7 - - + -
283C LYS* 3.0 19.6 + - + +
284C LEU* 3.2 10.3 + - + +
286C ASP* 1.3 72.3 - - + +
288C SER* 1.3 68.4 + - - +
290C LYS* 3.1 9.2 + - + -
291C HIS* 3.1 33.0 + - + +
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ILE* 3.8 16.2 - - - +
284C LEU 2.9 12.3 + - - -
285C ARG* 3.4 10.1 - - - -
286C ASP 3.2 0.2 - - - -
287C ILE* 1.3 77.5 - - - +
289C ARG* 1.3 60.8 + - - +
291C HIS 3.4 0.5 + - - -
292C GLY 3.2 2.8 + - - -
293C CYS* 2.7 59.0 + - - +
294C ALA 3.4 10.6 + - - -
295C PHE* 3.5 24.7 - - - +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 3.1 33.7 + - - +
286C ASP* 2.9 36.3 + - - +
288C SER* 1.3 78.3 - - - +
290C LYS* 1.3 65.7 + - - +
292C GLY* 3.2 12.9 + - - +
293C CYS 4.6 2.5 - - - +
320C ASP* 3.2 32.9 + - - +
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Residues in contact with LYS 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C GLU* 2.7 34.3 + - - +
286C ASP 2.9 18.7 + - - +
287C ILE* 3.1 9.6 + - + +
289C ARG* 1.3 78.6 - - - +
291C HIS* 1.3 68.2 + - + +
292C GLY 3.7 0.5 + - - -
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Residues in contact with HIS 291 (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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151C TYR* 4.5 9.4 + - - -
246C GLU* 2.6 40.3 + - + +
249C ILE* 3.8 30.3 - - + +
250C VAL* 4.1 19.0 - - + +
259C VAL 5.2 0.5 - - - +
287C ILE* 3.1 37.1 + - + +
290C LYS* 1.3 89.8 - - + +
292C GLY* 1.3 62.5 + - - +
293C CYS* 3.2 13.0 + - - -
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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