Contacts of the helix formed by residues 265 - 280 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A PHE* 4.0 23.2 - - + -
258A LEU* 5.1 0.2 - - - +
263A LYS 3.5 2.9 + - - +
264A PRO* 1.3 68.0 - - - +
266A TYR* 1.3 62.3 + - - +
267A SER* 3.5 10.2 + - - -
268A TYR* 3.1 40.1 + - + +
269A LEU* 3.4 11.0 + - - +
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Residues in contact with TYR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.2 12.2 - - + +
117A GLU* 3.3 66.0 - - + +
120A HIS* 2.6 39.2 + - + +
192A ARG* 3.7 2.9 - - - -
196A LEU* 4.0 28.7 - - + -
263A LYS* 5.0 14.8 - - + -
264A PRO* 2.9 38.6 + - + +
265A ASP* 1.3 70.3 - - - +
267A SER* 1.3 62.0 + - - +
269A LEU* 3.0 11.6 + - - +
270A ARG* 3.0 31.7 + - - +
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP* 3.2 9.1 + - - -
266A TYR* 1.3 78.4 - - - +
268A TYR* 1.3 56.7 + - - +
270A ARG* 3.5 5.2 + - - +
271A GLN* 2.9 31.9 + - - +
297A SO4 2.8 39.6 + - - -
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A THR* 3.8 19.6 - - - +
254A PHE* 3.8 35.8 - + + -
265A ASP* 3.1 31.8 + - - +
267A SER* 1.3 74.2 - - - +
269A LEU* 1.3 77.4 + - + +
271A GLN* 4.0 5.7 - - + +
272A LEU* 3.1 42.1 + - + +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.1 11.2 - - + -
196A LEU* 3.8 30.5 - - + -
251A TYR* 3.8 40.4 - - + +
254A PHE* 3.3 41.5 - - + -
255A CYS* 4.8 1.1 - - - -
265A ASP 3.7 13.2 - - - +
266A TYR* 3.0 13.3 + - - +
268A TYR* 1.3 83.1 - - + +
270A ARG* 1.3 61.5 + - - +
272A LEU* 2.9 28.9 - - + +
273A PHE* 3.3 12.1 + - - -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 3.3 34.4 - - - +
113A ILE* 3.9 22.8 - - + +
114A SER* 3.0 39.8 + - - +
117A GLU* 2.9 31.9 + - - -
266A TYR* 3.0 14.2 + - - +
267A SER* 3.9 12.3 + - - +
269A LEU* 1.3 76.8 - - - +
271A GLN* 1.3 57.3 + - - +
273A PHE* 3.3 5.7 + - - +
274A ARG* 2.9 44.7 + - - +
297A SO4 2.3 36.7 + - - -
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A SER 2.9 20.0 + - - +
268A TYR* 4.0 6.3 - - + +
270A ARG* 1.3 73.8 - - - +
272A LEU* 1.3 65.1 + - - +
274A ARG* 2.4 45.9 + - - +
275A ASN* 2.7 63.1 + - - +
278A HIS* 5.8 2.6 + - - -
297A SO4 5.3 1.1 - - - +
274C ARG* 5.1 5.5 - - - +
278C HIS* 4.8 14.5 + - - -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 3.3 61.9 - - + +
250A THR* 3.7 29.4 - - + -
251A TYR* 4.1 15.7 - - + +
268A TYR* 3.1 34.9 + - + +
269A LEU* 2.9 20.0 - - + +
271A GLN* 1.3 79.4 - - - +
273A PHE* 1.3 61.6 + - + +
275A ASN* 3.7 5.9 + - - +
276A LEU 3.5 8.1 + - - -
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.8 31.4 - - + +
109A ALA* 4.0 11.0 - - + -
110A ASP* 5.8 2.7 - - + +
113A ILE* 3.9 18.4 - - + -
203A LEU* 3.8 24.5 - - + -
247A GLU* 3.9 27.1 - - + -
248A PHE* 3.8 25.8 - + - -
251A TYR* 3.5 41.7 - + + -
269A LEU 3.3 14.3 + - - -
270A ARG* 3.3 5.6 + - - +
272A LEU* 1.3 77.7 - - + +
274A ARG* 1.3 54.3 + - - +
275A ASN 3.1 2.0 - - - -
276A LEU* 3.0 7.1 + - - +
277A PHE* 2.8 34.9 + - - +
284A TYR* 4.7 0.4 - - - -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 3.7 13.1 + - - +
270A ARG* 2.9 43.7 + - - +
271A GLN* 2.4 38.4 + - - +
272A LEU 3.4 0.2 - - - -
273A PHE* 1.3 77.1 - - - +
275A ASN* 1.3 58.2 + - - +
277A PHE* 3.1 2.5 - - - +
278A HIS* 3.0 45.7 + - + -
284A TYR* 3.2 37.6 + - + +
297A SO4 2.9 36.8 + - - -
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Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 5.8 1.1 - - - +
271A GLN* 2.7 55.3 + - - +
272A LEU* 3.9 5.7 - - - +
274A ARG* 1.3 75.0 - - - +
276A LEU* 1.3 61.3 + - - +
278A HIS* 4.0 8.6 + - - +
279A ARG* 3.0 28.8 + - - +
271C GLN* 5.2 0.4 - - - +
274C ARG* 3.5 39.2 + - - +
295C SO4 4.2 21.2 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.5 1.3 - - + -
106A LEU* 4.0 28.0 - - + -
245A PRO* 3.2 34.8 - - + -
247A GLU* 3.4 42.8 + - + +
248A PHE* 4.3 3.6 - - + -
272A LEU 3.5 2.4 + - - -
273A PHE 3.0 8.4 + - - +
275A ASN* 1.3 77.0 - - - +
277A PHE* 1.3 64.7 + - - +
279A ARG* 3.4 33.9 + - - +
280A GLN* 3.1 37.6 + - + +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.1 7.2 - - + -
106A LEU* 3.5 35.9 - - + +
107A LEU* 3.7 14.1 - - + -
273A PHE 2.8 12.5 + - - +
274A ARG 3.1 11.0 - - - +
276A LEU* 1.3 72.8 - - - +
278A HIS* 1.3 62.1 + + - +
280A GLN* 2.7 27.5 + - - +
281A GLY 3.2 6.9 + - - -
282A PHE* 3.4 38.4 + + + -
283A SER 3.4 37.0 - - - -
284A TYR* 3.3 51.1 - + - +
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Residues in contact with HIS 278 (chain A).
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* 5.8 2.0 + - - -
274A ARG* 3.0 33.4 + - + +
275A ASN* 4.1 9.1 + - - +
277A PHE* 1.3 92.8 - + - +
279A ARG* 1.3 57.2 + - - +
281A GLY* 3.0 9.7 + - - -
282A PHE 4.4 2.2 - - - -
284A TYR* 4.0 17.3 - + - -
110C ASP* 5.0 4.0 - - - +
111C GLN* 5.5 5.4 - - - +
274C ARG* 6.3 0.8 - - - -
278C HIS* 6.3 2.0 - + - -
284C TYR* 3.5 68.4 + + + +
286C TYR* 2.9 26.2 + + - -
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 5.4 3.4 - - - +
247A GLU* 5.2 0.8 + - - -
275A ASN 3.0 20.0 + - - +
276A LEU* 3.4 32.0 - - - +
277A PHE 3.0 0.4 + - - -
278A HIS* 1.3 78.0 - - - +
280A GLN* 1.3 79.7 + - - +
281A GLY* 3.2 0.8 - - - -
62C GLY* 6.2 0.4 - - - -
63C VAL* 3.7 34.0 - - - +
110C ASP* 5.8 2.5 - - - -
111C GLN* 6.1 1.2 - - - +
114C SER* 4.3 25.9 - - - +
115C ARG* 4.5 7.6 + - - +
118C TYR* 5.4 10.1 - - - -
270C ARG* 6.4 1.1 - - - -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.9 20.6 - - + +
245A PRO* 5.6 1.4 - - - +
276A LEU* 3.1 21.2 + - + +
277A PHE 2.7 9.9 + - - +
279A ARG* 1.3 113.6 - - - +
281A GLY* 1.3 58.7 + - - +
282A PHE* 3.2 44.5 + - + -
63C VAL* 3.7 26.8 - - - +
141C LYS* 5.8 2.6 - - - -
144C LEU* 4.8 7.6 - - - +
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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