Contacts of the helix formed by residues 272 - 287 (chain C) in PDB entry 3OFN
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LYS* 5.5 1.7 - - - -
208C VAL* 3.7 22.7 + - - +
210C GLN* 5.5 0.2 - - - +
270C TYR* 3.2 7.2 - - - -
271C ASP* 1.3 78.0 + - - +
273C LEU* 1.3 61.8 + - - +
274C SER* 3.3 9.9 + - - +
275C LYS* 2.8 67.9 + - - +
276C GLN 3.7 1.0 + - - -
328C VAL* 3.2 29.0 - - + +
329C ILE* 4.4 1.8 - - - +
330C GLU* 4.4 9.9 - - + +
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Residues in contact with LEU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 6.1 0.2 - - + -
249C PRO* 4.5 6.1 - - + -
270C TYR* 3.6 22.0 + - + -
272C ASP* 1.3 70.1 - - - +
274C SER* 1.3 62.6 + - - +
275C LYS 3.3 0.4 - - - -
276C GLN* 3.2 29.8 + - - +
277C ALA* 3.0 19.8 + - - +
304C HIS* 3.5 28.4 + - + +
307C LEU* 3.7 19.7 - - + -
308C LEU* 3.9 16.6 - - + -
327C PRO* 3.6 26.7 - - + -
328C VAL 2.6 15.5 + - - +
329C ILE* 3.9 9.9 - - + -
344C VAL* 4.5 7.4 - - + -
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Residues in contact with SER 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASP* 3.3 9.6 - - - -
273C LEU* 1.3 78.1 - - - +
275C LYS* 1.3 64.1 + - - +
277C ALA* 3.2 9.1 + - - +
278C VAL* 3.1 27.2 + - - +
296C TYR* 5.3 0.5 + - - -
329C ILE* 3.1 17.2 - - - +
330C GLU* 2.9 42.3 + - - -
340C ILE* 5.1 3.0 - - - +
341C PRO* 6.0 0.3 - - - +
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 3.3 31.4 - - - +
209C GLY* 3.9 25.1 - - - +
210C GLN* 4.5 6.7 - - + +
245C GLN* 4.6 3.2 - - - +
272C ASP* 2.8 36.3 + - - +
274C SER* 1.3 71.6 - - - +
276C GLN* 1.3 65.7 + - - +
278C VAL* 3.2 11.6 + - + +
279C ALA* 3.1 20.8 + - - +
330C GLU* 3.9 23.2 + - - -
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Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 3.5 18.0 - - + +
245C GLN 3.5 18.6 - - - +
246C TYR* 3.1 22.1 + - - +
249C PRO* 3.5 15.2 - - + +
250C PHE* 3.4 23.0 - - - -
272C ASP 3.7 0.8 + - - +
273C LEU* 3.2 37.2 + - - +
274C SER 3.3 0.2 - - - -
275C LYS* 1.3 78.3 - - - +
277C ALA* 1.3 61.1 + - - +
279C ALA* 3.0 17.1 + - - +
280C TYR* 3.0 13.2 + - - +
303C LEU* 3.4 22.6 - - - +
304C HIS* 3.5 10.4 + - - -
307C LEU* 4.5 1.6 - - - +
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Residues in contact with ALA 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LEU 3.0 13.4 + - - +
274C SER 3.2 9.6 + - - +
276C GLN* 1.3 76.1 - - - +
278C VAL* 1.3 62.5 + - - +
280C TYR* 3.8 3.0 - - - +
281C ARG* 3.1 23.2 + - - +
296C TYR* 3.7 16.0 - - + +
300C VAL* 4.1 16.0 - - + +
303C LEU* 4.4 9.9 - - - -
304C HIS* 4.1 16.4 - - + -
340C ILE* 4.3 10.3 - - + -
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C SER* 3.1 18.8 + - - +
275C LYS* 3.5 11.2 - - + +
276C GLN 3.1 0.4 - - - -
277C ALA* 1.3 77.3 - - - +
279C ALA* 1.3 61.7 + - - +
281C ARG* 3.4 28.5 + - - +
282C GLN* 3.1 23.2 + - + +
296C TYR* 4.3 16.2 - - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ALA* 3.6 30.6 - - + +
245C GLN* 3.7 23.6 - - + +
246C TYR* 3.9 4.7 - - - +
275C LYS 3.1 9.5 + - - +
276C GLN 3.0 10.0 + - - +
278C VAL* 1.3 76.5 - - - +
280C TYR* 1.3 61.4 + - - +
282C GLN* 3.1 16.0 + - - +
283C LEU* 3.2 21.1 + - - +
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Residues in contact with TYR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C TYR* 3.8 36.0 - + + +
276C GLN 3.0 11.0 + - - +
277C ALA* 3.8 8.5 - - - +
279C ALA* 1.3 77.0 - - - +
281C ARG* 1.3 54.5 + - - +
283C LEU* 3.5 15.9 - - + +
284C SER* 2.4 38.2 + - - -
289C ARG* 3.1 29.5 + - - -
297C PRO* 3.4 32.5 - - + +
299C ASP* 2.9 32.5 + - - -
300C VAL* 4.3 17.0 - - + -
303C LEU* 3.8 27.6 - - + -
306C ARG* 5.7 3.3 + - - -
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Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA 3.1 17.2 + - - +
278C VAL* 3.6 26.5 + - - +
279C ALA 3.3 0.2 - - - -
280C TYR* 1.3 76.1 - - - +
282C GLN* 1.3 57.2 + - - +
284C SER* 3.5 1.2 + - - -
285C LEU* 3.0 45.6 + - + +
294C GLU* 3.2 18.4 + - - +
295C ALA* 3.1 39.0 - - - +
296C TYR* 3.3 32.1 + - + -
297C PRO* 3.6 19.9 - - + +
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Residues in contact with GLN 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP 5.5 0.8 + - - -
242C ALA* 3.9 22.2 - - + +
278C VAL* 3.1 13.1 + - + +
279C ALA* 3.1 13.4 + - - +
281C ARG* 1.3 73.8 - - - +
283C LEU* 1.3 67.4 + - - +
285C LEU* 3.3 6.9 + - - +
286C LEU* 3.0 49.9 + - + +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 4.1 3.0 - - - +
66C LEU* 3.8 22.2 - - + -
76C VAL* 4.0 17.7 - - + -
242C ALA* 3.5 9.3 - - + +
243C PRO* 3.4 34.5 - - + -
246C TYR* 3.7 34.1 - - + -
279C ALA 3.2 21.5 + - - +
280C TYR* 3.5 18.2 - - + +
282C GLN* 1.3 77.6 - - - +
284C SER* 1.3 53.8 + - - +
286C LEU* 3.1 5.9 + - - +
287C LEU* 2.7 43.7 + - + +
289C ARG* 6.4 0.2 - - - +
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Residues in contact with SER 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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280C TYR* 2.4 38.1 + - - -
281C ARG 3.9 2.0 - - - -
282C GLN 3.2 1.2 - - - -
283C LEU* 1.3 72.7 - - - +
285C LEU* 1.3 62.3 + - - +
287C LEU* 3.4 9.7 + - - -
288C ARG 3.0 6.1 + - - -
289C ARG* 2.9 53.8 + - - +
297C PRO* 3.3 25.7 - - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ARG* 3.0 46.0 + - + +
282C GLN* 3.8 5.8 - - - +
284C SER* 1.3 77.3 - - - +
286C LEU* 1.3 61.4 + - + +
288C ARG* 3.2 24.3 + - - +
289C ARG 4.5 4.7 - - - +
291C PRO* 3.6 36.8 - - + -
295C ALA* 3.9 15.3 - - + +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 3.4 45.8 - - + +
40C ILE* 3.5 28.7 - - + +
282C GLN* 3.0 47.7 + - + +
283C LEU* 3.5 4.3 - - - +
285C LEU* 1.3 77.2 - - + +
287C LEU* 1.3 58.1 + - - +
288C ARG* 3.0 14.8 + - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 3.8 28.3 - - + -
66C LEU* 4.2 20.6 - - + -
67C ILE* 4.1 34.7 - - + +
74C GLY* 4.4 21.5 - - - +
76C VAL* 3.9 18.2 - - + -
283C LEU* 2.7 32.5 + - + +
284C SER* 3.4 9.8 + - - +
286C LEU* 1.3 70.7 - - - +
288C ARG* 1.3 63.7 + - - +
289C ARG* 3.1 19.0 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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