Contacts of the helix formed by residues 271 - 281 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.8 27.2 + - + +
236B TYR 5.4 2.8 + - - -
269B ILE 3.8 0.4 + - - -
270B ASP* 1.3 87.6 + - + +
272B VAL* 1.3 66.7 + - - +
273B GLU 3.1 3.6 - - - +
274B GLU* 2.9 28.0 + - + -
275B ILE* 2.9 32.3 + - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 4.9 7.4 - - + -
258B ILE* 3.6 38.4 - - + -
259B PHE* 3.9 18.2 - - + -
262B LEU* 4.0 17.9 - - + -
268B ASN* 5.3 0.9 - - + +
269B ILE* 2.8 38.4 - - + +
270B ASP 3.3 1.4 + - - -
271B HIS* 1.3 72.9 - - - +
273B GLU* 1.3 63.8 + - - +
275B ILE* 3.7 5.9 - - - +
276B ARG* 2.8 29.8 + - + +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PHE* 3.9 24.0 - - + -
271B HIS* 3.1 1.2 - - - +
272B VAL* 1.3 78.4 - - - +
274B GLU* 1.3 68.6 + - + +
276B ARG* 3.9 6.0 - - - +
277B ASN* 3.2 26.4 + - - +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.6 35.6 - - + +
271B HIS* 2.9 32.1 + - + +
273B GLU* 1.3 82.5 - - + +
275B ILE* 1.3 55.9 + - - +
277B ASN* 3.8 3.2 - - - +
278B PHE* 3.0 29.3 + - - +
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.3 35.7 - - + -
230B ILE* 3.9 14.4 - - + -
236B TYR* 3.4 26.2 - - + +
237B ASN* 4.1 20.0 - - + +
269B ILE* 6.2 0.7 - - + -
270B ASP 4.9 1.6 - - - +
271B HIS* 2.9 26.8 + - + +
272B VAL* 3.7 4.9 - - - +
274B GLU* 1.3 72.6 - - - +
276B ARG* 1.3 69.2 + - - +
278B PHE* 3.0 16.9 + - + +
279B PHE* 3.0 37.2 + - + -
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B GLU* 4.2 22.9 + - - +
226B ILE* 3.9 19.3 - - + +
227B ASP* 2.7 48.1 + - - +
230B ILE* 3.8 11.8 - - + +
257B ASP* 4.3 9.1 - - - +
258B ILE* 3.7 22.2 - - - +
259B PHE* 4.0 25.4 - - - -
272B VAL* 2.8 18.8 - - - +
273B GLU* 3.9 4.2 - - - +
275B ILE* 1.3 75.2 - - - +
277B ASN* 1.3 57.2 + - - +
279B PHE* 3.2 2.9 + - - +
280B LEU* 2.8 33.5 + - - +
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLU 3.2 18.9 + - - +
274B GLU* 3.9 4.0 - - - +
276B ARG* 1.3 77.7 - - - +
278B PHE* 1.3 57.6 + - - +
280B LEU* 4.3 11.2 - - - +
281B ASN* 2.9 40.2 + - - +
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PRO* 3.9 20.0 - - + -
86B PHE* 3.7 23.3 - + + -
150B SER* 3.5 22.4 - - - -
151B GLU* 3.6 25.1 - - + -
154B ALA* 5.7 0.2 - - + -
178B PHE* 4.0 16.2 - + - -
236B TYR* 3.8 17.7 - + - -
274B GLU 3.0 13.8 + - - +
275B ILE* 3.0 10.3 + - - +
277B ASN* 1.3 76.9 + - - +
279B PHE* 1.3 65.9 + + - +
281B ASN 4.7 2.0 - - - -
282B PRO* 3.0 32.5 - - + +
283B PRO* 3.2 35.7 - - + -
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Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ASP* 4.8 6.7 - - - -
177B LEU* 3.7 32.3 - - + +
178B PHE* 3.5 42.1 - + - -
222B ARG* 3.2 13.0 + - - -
226B ILE* 3.6 36.3 - - + -
229B ALA* 5.9 0.2 - - + -
230B ILE* 4.6 4.3 - - + -
234B THR* 4.0 23.1 - - + -
236B TYR* 3.4 26.9 - + - -
275B ILE* 3.0 44.0 + - + -
276B ARG 3.7 2.9 - - - +
278B PHE* 1.3 79.1 - + + +
280B LEU* 1.3 64.9 + - - +
282B PRO* 3.5 8.5 - - - +
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 2.9 49.8 + - + +
223B GLU* 3.7 44.4 - - + +
226B ILE* 3.7 8.0 - - + +
276B ARG* 2.8 19.5 + - - +
277B ASN* 4.0 12.3 - - - +
279B PHE* 1.3 78.1 - - - +
281B ASN* 1.3 59.7 + - + +
282B PRO* 3.6 3.5 - - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ASN* 2.9 28.9 + - - +
278B PHE* 3.5 4.9 - - - +
280B LEU* 1.3 82.4 + - + +
282B PRO* 1.3 69.8 + - - +
283B PRO* 4.0 2.3 - - - +
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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