Contacts of the helix formed by residues 273 - 281 (chain A) in PDB entry 3HS0
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 LYS 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASN* 3.5 21.0 - - - +
271A THR* 3.9 13.3 + - + +
272A LEU* 1.3 76.4 - - - +
274A ARG* 1.3 65.3 + - - +
275A ASP* 4.1 20.0 + - + +
276A THR* 3.1 31.7 + - - +
277A PHE* 3.1 11.8 + - - +
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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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213A PHE* 3.2 38.1 - - - -
214A TYR 2.9 29.1 + - - -
215A ILE 3.9 11.9 + - - -
216A ASP 4.4 0.6 - - - -
217A GLY 3.5 23.6 + - - -
218A ASN* 3.6 12.3 - - - +
219A GLU* 2.9 39.6 + - - +
220A ASN* 2.8 14.5 + - - +
272A LEU 3.6 1.4 + - - -
273A LYS* 1.3 71.4 - - - +
275A ASP* 1.3 60.4 + - - +
277A PHE* 3.3 17.9 + - - +
278A ARG* 3.0 63.4 + - - +
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Residues in contact with ASP 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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273A LYS* 4.4 19.7 + - + +
274A ARG* 1.3 79.7 - - - +
276A THR* 1.3 65.7 + - - +
277A PHE 3.2 0.2 + - - -
278A ARG* 3.3 21.0 + - - +
279A SER* 3.0 26.8 + - - -
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Residues in contact with THR 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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254A ILE* 4.0 13.3 - - + +
256A ASP* 3.7 42.4 + - + +
257A SER* 4.3 3.1 - - - +
272A LEU* 4.7 6.7 - - - -
273A LYS* 3.1 24.5 + - - +
275A ASP* 1.3 78.0 - - - +
277A PHE* 1.3 61.3 + - - +
279A SER* 3.5 9.0 + - - -
280A ARG* 3.3 21.3 + - - +
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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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213A PHE* 3.8 31.0 - + + -
214A TYR 5.8 0.2 - - - -
215A ILE 4.9 3.8 - - - -
245A VAL* 4.0 14.4 - - + -
254A ILE* 3.8 22.7 - - + -
272A LEU* 4.2 12.5 - - + +
273A LYS 3.1 10.0 + - - +
274A ARG* 3.4 33.0 - - - +
275A ASP 3.1 0.4 - - - -
276A THR* 1.3 75.3 - - - +
278A ARG* 1.3 67.4 + - + +
280A ARG* 3.0 4.9 + - - +
281A PHE* 2.8 36.4 + + + +
284A LEU* 6.1 1.1 - - + -
287A LEU* 3.3 37.9 - - + -
292A LEU* 3.9 14.6 - - + -
316A ILE* 4.5 4.5 - - + -
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Residues in contact with ARG 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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216A ASP 5.6 0.6 + - - -
217A GLY 3.6 13.1 + - - -
218A ASN* 2.9 28.9 + - - +
274A ARG* 3.0 46.3 + - - +
275A ASP* 3.8 20.2 + - - +
277A PHE* 1.3 80.0 - - + +
279A SER* 1.3 63.0 + - - +
281A PHE 3.4 23.3 - - - +
282A PRO* 3.5 11.8 - - + +
284A LEU* 6.5 0.9 - - + -
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Residues in contact with SER 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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275A ASP 3.0 14.7 + - - -
276A THR* 3.5 14.2 - - - -
277A PHE 3.1 0.2 - - - -
278A ARG* 1.3 78.7 - - - +
280A ARG* 1.3 59.9 + - - +
282A PRO* 4.2 9.1 - - - +
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Residues in contact with ARG 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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252A LYS* 3.9 29.3 - - - +
253A SER 3.5 15.3 + - - +
254A ILE* 4.0 21.1 - - + -
255A PRO* 4.5 8.2 - - + +
276A THR 3.3 8.7 + - - +
277A PHE 3.0 6.9 + - - +
279A SER* 1.3 82.4 - - - +
281A PHE* 1.3 92.5 + - + +
282A PRO* 3.6 7.3 - - - +
286A GLU* 5.3 1.6 + - - -
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Residues in contact with PHE 281 (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 VAL* 3.5 35.7 - - + -
252A LYS* 4.0 25.4 - - + -
254A ILE* 3.9 13.2 - - + -
277A PHE* 2.8 26.3 + + + +
278A ARG* 3.4 15.5 - - - +
280A ARG* 1.3 117.2 - - + +
282A PRO* 1.3 63.9 - - + +
283A ASN 3.6 3.7 - - - +
284A LEU* 5.2 4.2 + - - +
286A GLU* 3.8 25.1 - - + -
287A LEU* 3.9 35.4 - - + +
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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