Contacts of the helix formed by residues 265 - 281 (chain C) in PDB entry 3UYS
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 265 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PHE* 4.0 24.2 - - + -
263C LYS 5.2 0.4 - - - +
264C PRO* 1.3 71.0 - - - +
266C TYR* 1.3 65.9 + - - +
267C SER* 3.1 10.9 + - - -
268C TYR* 2.7 39.6 + - + +
269C LEU* 3.1 13.7 + - - +
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Residues in contact with TYR 266 (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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113C ILE* 4.2 15.9 - - + +
117C GLU* 2.9 66.0 - - + +
120C HIS* 2.6 36.3 + - + +
192C ARG* 3.6 3.1 + - - -
196C LEU* 3.8 26.9 - - + -
263C LYS* 4.6 17.9 - - - -
264C PRO* 3.5 34.3 - - + +
265C ASP* 1.3 72.0 - - - +
267C SER* 1.3 58.7 + - - +
269C LEU* 3.1 8.2 + - - +
270C ARG* 2.8 41.6 + - - +
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 5.3 0.2 + - - -
265C ASP* 3.1 8.7 - - - -
266C TYR* 1.3 77.5 - - - +
268C TYR* 1.3 58.2 + - - +
270C ARG* 3.4 4.7 + - - +
271C GLN* 2.9 30.5 + - - +
295C SO4 2.6 41.7 + - - -
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Residues in contact with TYR 268 (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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250C THR* 3.7 20.7 - - + +
254C PHE* 3.4 46.7 - + + -
265C ASP* 2.7 31.0 + - + +
267C SER* 1.3 75.8 - - - +
269C LEU* 1.3 73.1 + - + +
271C GLN* 3.0 9.1 + - + +
272C LEU* 3.0 44.4 + - + +
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Residues in contact with LEU 269 (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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113C ILE* 4.1 13.7 - - + -
196C LEU* 4.2 28.7 - - + -
251C TYR* 3.9 34.5 - - + +
254C PHE* 3.9 37.5 - - + -
255C CYS* 4.6 3.1 - - - -
264C PRO* 5.0 0.9 - - + -
265C ASP 3.1 11.4 + - - +
266C TYR* 3.1 13.5 + - - +
268C TYR* 1.3 82.5 - - + +
270C ARG* 1.3 63.1 + - - +
272C LEU* 3.4 29.7 - - + +
273C PHE* 3.4 15.2 - - - -
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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
----------------------------------------------------------
279A ARG* 6.4 1.3 - - - -
110C ASP* 3.5 27.9 - - - +
113C ILE* 3.6 34.1 - - + +
114C SER* 3.4 40.6 + - - +
117C GLU* 2.7 32.9 + - - -
266C TYR* 2.8 21.1 + - - +
267C SER* 3.9 7.2 + - - +
269C LEU* 1.3 73.8 - - - +
271C GLN* 1.3 59.8 + - - +
273C PHE* 3.4 5.5 + - - +
274C ARG* 3.0 38.7 + - - +
295C SO4 3.1 40.5 + - - +
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Residues in contact with GLN 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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275A ASN* 5.2 1.0 - - - +
267C SER 2.9 19.0 + - - +
268C TYR* 3.0 10.9 + - + +
270C ARG* 1.3 74.3 - - - +
272C LEU* 1.3 67.1 + - - +
274C ARG* 2.4 40.3 + - - +
275C ASN* 2.6 64.5 + - - +
295C SO4 5.1 1.0 + - - -
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Residues in contact with LEU 272 (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 GLU* 3.6 31.4 - - + +
250C THR* 3.9 26.5 - - + -
251C TYR* 4.1 22.7 - - + +
268C TYR* 3.0 43.4 + - + +
269C LEU* 3.4 24.0 - - + +
271C GLN* 1.3 78.4 - - - +
273C PHE* 1.3 64.6 + - + +
275C ASN* 3.4 8.0 + - - +
276C LEU 3.2 14.9 + - - -
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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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106C LEU* 3.6 33.2 - - + +
109C ALA* 4.0 17.3 - - + -
110C ASP* 5.7 4.0 - - + +
113C ILE* 4.0 15.5 - - + -
203C LEU* 4.2 7.2 - - + -
247C GLU* 3.9 23.6 - - + -
248C PHE* 3.5 33.2 - + - -
251C TYR* 3.5 46.7 - + + -
269C LEU 3.4 17.0 + - - -
270C ARG* 3.4 5.5 + - - +
271C GLN 3.3 0.6 - - - -
272C LEU* 1.3 80.5 - - + +
274C ARG* 1.3 60.1 + - - +
276C LEU* 3.2 4.4 + - - +
277C PHE* 2.8 30.9 + - - +
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Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLN* 5.1 5.8 - - - +
275A ASN* 3.5 30.8 - - - +
278A HIS* 6.3 0.4 - - - -
110C ASP* 4.3 21.0 + - - +
270C ARG* 3.0 35.0 + - - +
271C GLN* 2.4 49.4 + - - +
273C PHE* 1.3 75.4 - - - +
275C ASN* 1.3 63.6 + - - +
277C PHE* 3.3 7.0 - - - +
278C HIS* 3.0 41.3 + - + -
284C TYR* 6.0 4.9 - - + -
295C SO4 2.5 46.5 + - - -
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Residues in contact with ASN 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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271C GLN* 2.6 52.8 + - - +
272C LEU* 3.7 7.2 - - - +
274C ARG* 1.3 74.5 - - - +
276C LEU* 1.3 64.3 + - - +
278C HIS* 3.4 6.0 + - - +
279C ARG* 2.9 37.6 + - - +
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Residues in contact with LEU 276 (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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102C LEU* 4.5 1.8 - - + -
106C LEU* 3.8 29.4 - - + -
245C PRO* 3.6 30.5 - - + -
247C GLU* 3.8 26.0 - - + +
248C PHE* 4.3 4.5 - - + -
272C LEU 3.2 11.1 + - - +
273C PHE 3.5 7.2 - - - +
275C ASN* 1.3 78.3 - - - +
277C PHE* 1.3 65.8 + - - +
279C ARG* 3.0 31.2 + - + +
280C GLN* 2.8 51.2 + - + +
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Residues in contact with PHE 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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103C LYS* 4.1 9.9 - - + -
106C LEU* 3.7 31.4 - - + +
107C LEU* 3.9 26.9 - - + -
273C PHE 2.8 18.2 + - - +
274C ARG* 3.3 10.8 - - - +
276C LEU* 1.3 77.4 - - - +
278C HIS* 1.3 73.6 + + - +
280C GLN* 3.4 3.3 + - - +
281C GLY 3.1 5.5 + - - -
282C PHE* 3.0 63.0 + + + +
283C SER 3.2 25.4 - - - -
284C TYR* 3.8 27.4 - + + -
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Residues in contact with HIS 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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271A GLN* 4.8 14.7 + - - -
278A HIS* 6.3 2.2 - + - -
274C ARG* 3.0 36.4 + - + +
275C ASN* 4.0 4.7 - - - +
277C PHE* 1.3 94.0 - + - +
279C ARG* 1.3 62.9 + - - +
280C GLN 3.1 1.3 - - - -
281C GLY* 2.8 22.4 + - - +
282C PHE 4.3 7.0 + - - +
284C TYR* 5.7 7.1 - + + -
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Residues in contact with ARG 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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246C SER* 5.5 1.2 + - - -
247C GLU* 3.1 29.7 + - - -
275C ASN* 2.9 23.5 + - - +
276C LEU* 3.0 38.6 + - + +
278C HIS* 1.3 77.1 - - - +
280C GLN* 1.3 65.7 + - + +
281C GLY* 3.3 0.7 + - - -
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Residues in contact with GLN 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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102C LEU* 3.7 23.5 - - + +
245C PRO* 4.9 4.8 - - - +
276C LEU* 2.8 31.8 + - + +
277C PHE 3.4 5.2 - - - +
279C ARG* 1.3 78.9 - - - +
281C GLY* 1.3 60.1 + - - +
282C PHE* 3.4 41.2 + - + -
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Residues in contact with GLY 281 (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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277C PHE 3.1 1.2 + - - -
278C HIS* 2.8 20.5 + - - -
279C ARG 3.0 1.1 - - - -
280C GLN* 1.3 80.1 - - - +
282C PHE* 1.3 68.0 + - - +
283C SER* 3.6 4.5 + - - -
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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