Contacts of the helix formed by residues 271 - 281 (chain A) in PDB entry 1RXV
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 HIS 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A PHE* 3.9 22.4 + - + +
236A TYR 5.7 1.6 + - - -
270A ASP* 1.3 89.0 + - + +
272A VAL* 1.3 59.1 + - - +
273A GLU* 3.2 3.6 - - - +
274A GLU* 3.1 35.6 + - + +
275A ILE* 2.7 43.4 + - + +
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Residues in contact with VAL 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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230A ILE* 4.8 7.0 - - + -
258A ILE* 3.6 37.7 - - + -
259A PHE* 4.1 15.5 - - + -
262A LEU* 3.9 18.2 - - + -
268A ASN* 6.0 0.2 - - + -
269A ILE* 2.9 42.6 - - + +
270A ASP 3.2 0.8 - - - -
271A HIS* 1.3 76.3 - - - +
273A GLU* 1.3 63.1 + - - +
275A ILE* 3.6 7.1 - - - +
276A ARG* 3.0 29.8 + - - +
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Residues in contact with GLU 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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259A PHE* 4.3 20.0 - - + -
271A HIS* 3.2 1.0 - - - +
272A VAL* 1.3 79.7 - - - +
274A GLU* 1.3 61.0 + - + +
276A ARG* 3.7 6.8 - - - +
277A ASN* 2.6 53.9 + - - +
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Residues in contact with GLU 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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86A PHE* 3.9 28.7 - - + +
271A HIS* 3.1 41.8 + - + +
273A GLU* 1.3 79.6 - - + +
275A ILE* 1.3 59.7 + - - +
277A ASN* 3.3 5.5 + - - +
278A PHE* 2.9 31.5 + - - +
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Residues in contact with ILE 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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86A PHE* 3.4 26.2 - - + -
230A ILE* 3.6 26.5 - - + -
236A TYR* 3.4 38.6 - - + +
237A ASN* 4.1 14.4 - - + +
269A ILE* 5.9 0.4 - - + -
270A ASP 4.5 3.6 - - - +
271A HIS* 2.7 33.4 - - + +
272A VAL* 3.6 6.7 - - - +
274A GLU* 1.3 75.1 - - - +
276A ARG* 1.3 63.5 + - - +
278A PHE* 3.2 4.7 + - - +
279A PHE* 3.1 37.9 + - + -
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Residues in contact with ARG 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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223A GLU* 4.3 23.4 + - - +
226A ILE* 3.9 20.9 - - + +
227A ASP* 2.7 42.4 + - - +
230A ILE* 3.9 10.7 - - + +
257A ASP* 4.1 8.7 - - - +
258A ILE* 3.1 27.1 - - - +
259A PHE* 3.8 26.1 - - - -
272A VAL* 3.0 17.7 - - - +
273A GLU* 3.7 6.3 - - - +
275A ILE* 1.3 78.1 - - - +
277A ASN* 1.3 60.1 + - - +
279A PHE* 3.3 2.3 + - - +
280A LEU* 2.8 32.5 + - - +
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Residues in contact with ASN 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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273A GLU* 2.6 52.1 + - - +
274A GLU* 3.7 6.3 - - - +
276A ARG* 1.3 78.6 + - - +
278A PHE* 1.3 57.9 + - - +
280A LEU* 3.8 11.4 - - - +
281A ASN* 2.8 36.6 + - + +
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Residues in contact with PHE 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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84A PRO* 3.7 17.5 - - + -
86A PHE* 3.6 24.2 - + + -
150A SER* 3.6 22.0 - - - -
151A GLU* 3.6 15.9 - - + -
178A PHE* 3.8 16.2 - + - -
236A TYR* 3.5 33.0 - + - -
274A GLU 2.9 17.7 + - - +
275A ILE 3.4 5.2 - - - +
277A ASN* 1.3 77.4 - - - +
279A PHE* 1.3 59.0 + + - +
281A ASN 4.6 2.9 - - - -
282A PRO* 3.0 37.6 - - + +
283A PRO* 3.3 33.9 - - + -
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Residues in contact with PHE 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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174A ASP* 4.4 8.1 - - + -
177A LEU* 3.6 41.6 - - + +
178A PHE* 3.5 46.0 - + - -
222A ARG* 3.1 16.6 + - - -
226A ILE* 3.7 30.3 - - + -
229A ALA* 5.7 0.2 - - + -
230A ILE* 4.8 2.9 - - + -
234A THR* 4.3 19.1 - - + -
236A TYR* 3.5 35.2 - + - -
275A ILE* 3.1 32.7 + - + -
276A ARG 3.7 6.1 - - - +
278A PHE* 1.3 77.9 - + - +
280A LEU* 1.3 62.4 + - - +
282A PRO* 3.5 2.8 - - - +
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Residues in contact with LEU 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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222A ARG* 3.0 45.3 + - + +
223A GLU* 3.5 43.3 - - + +
226A ILE* 3.8 8.5 - - + +
276A ARG 2.8 17.8 + - - +
277A ASN* 3.8 13.2 - - - +
279A PHE* 1.3 78.4 - - - +
281A ASN* 1.3 60.5 + - + +
282A PRO* 3.6 3.3 - - - +
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Residues in contact with ASN 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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277A ASN* 2.8 18.0 + - + +
278A PHE* 3.4 5.0 - - - +
280A LEU* 1.3 79.5 + - + +
282A PRO* 1.3 69.5 + - - +
283A PRO* 3.9 2.4 - - - +
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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