Contacts of the helix formed by residues 261 - 274 (chain R) in PDB entry 5VAI
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 SER 261 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLN* 3.2 33.6 + - - +
259R VAL 4.1 1.0 + - - -
260R PHE* 1.3 103.1 - - - +
262R GLU* 1.3 59.7 + - - +
264R ARG* 3.1 12.3 + - - -
265R ILE* 2.4 44.8 + - - +
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Residues in contact with GLU 262 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.6 6.5 - - - -
35A GLN* 3.0 16.8 - - + +
38A ARG* 4.9 23.9 + - - +
175R THR* 3.9 27.5 - - + +
259R VAL* 3.4 43.8 - - + +
261R SER* 1.3 75.8 - - - +
263R GLN* 1.3 49.5 + - - +
265R ILE* 3.8 7.4 - - - -
266R PHE* 2.4 41.4 + - - +
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Residues in contact with GLN 263 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 5.6 5.0 - - - +
31A GLN* 2.7 44.5 + - - +
34A LYS* 6.2 1.1 - - - +
35A GLN* 3.1 13.0 - - - +
262R GLU* 1.3 77.9 - - - +
264R ARG* 1.3 65.8 + - - +
266R PHE* 3.2 7.7 + - + +
267R LYS* 3.0 22.7 + - - +
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Residues in contact with ARG 264 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN* 4.0 3.6 - - - +
261R SER* 3.1 16.8 + - - +
263R GLN* 1.3 79.3 - - - +
265R ILE* 1.3 63.3 + - - +
267R LYS* 3.3 14.8 + - - +
268R LEU* 3.5 9.4 + - - +
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Residues in contact with ILE 265 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259R VAL* 4.5 6.1 - - + -
260R PHE* 3.0 40.6 - - + +
261R SER* 2.4 35.6 + - - +
262R GLU* 3.8 7.9 - - - +
264R ARG* 1.3 68.6 - - - +
266R PHE* 1.3 59.1 + - - +
268R LEU* 3.1 20.8 + - + +
269R TYR* 2.9 58.2 + - + +
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Residues in contact with PHE 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R THR* 4.5 20.0 - - + -
178R TYR* 3.3 42.6 - + + -
179R ILE* 3.4 40.6 - - + -
182R ASN* 4.9 2.2 - - - -
250R TYR* 5.8 2.2 - + - -
262R GLU 2.4 29.9 + - - +
263R GLN* 3.4 8.5 - - + +
265R ILE* 1.3 77.0 - - + +
267R LYS* 1.3 69.2 + - - +
269R TYR* 2.9 16.3 + + + +
270R LEU* 2.9 34.5 + - + +
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Residues in contact with LYS 267 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263R GLN 3.0 13.2 + - - +
264R ARG* 3.3 9.8 + - - +
265R ILE 3.2 0.8 - - - -
266R PHE* 1.3 81.8 - - + +
268R LEU* 1.3 56.8 + - - +
270R LEU* 3.3 11.6 + - + +
271R SER* 2.9 38.6 + - - +
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Residues in contact with LEU 268 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264R ARG 3.5 5.9 + - - +
265R ILE* 3.1 23.1 + - + +
267R LYS* 1.3 77.3 - - - +
269R TYR* 1.3 65.2 + - + +
271R SER* 3.1 10.2 + - - -
272R ILE* 2.8 34.1 + - + +
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Residues in contact with TYR 269 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R ILE* 5.1 3.6 - - + -
246R VAL* 4.0 29.4 - - + +
249R ALA* 4.4 22.9 - - + -
250R TYR* 5.4 7.4 - + - -
253R THR* 3.6 27.4 + - - +
259R VAL* 5.0 8.3 - - + +
265R ILE* 2.9 61.5 + - + +
266R PHE* 2.9 25.1 + + + +
268R LEU* 1.3 79.4 - - + +
270R LEU* 1.3 61.0 + - - +
272R ILE* 2.9 29.4 - - + +
273R GLY* 2.9 6.4 + - - -
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Residues in contact with LEU 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R TYR* 5.0 11.0 - - + +
179R ILE* 6.0 0.4 - - - -
182R ASN* 3.8 17.0 - - - +
243R TRP* 3.4 22.4 - - + -
266R PHE* 2.9 21.6 + - + +
267R LYS* 3.6 15.3 - - + +
269R TYR* 1.3 77.3 - - - +
271R SER* 1.3 57.9 + - - +
273R GLY* 3.1 1.3 + - - +
274R TRP* 2.9 65.0 + - + +
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Residues in contact with SER 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267R LYS* 2.9 31.0 + - - +
268R LEU* 3.1 13.3 + - - -
270R LEU* 1.3 78.2 - - - +
272R ILE* 1.3 53.2 + - - +
274R TRP* 5.6 0.2 - - - -
275R GLY* 2.7 33.7 - - - +
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Residues in contact with ILE 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242R TYR* 5.0 1.4 - - - +
245R LEU* 5.5 13.5 - - + -
246R VAL* 4.6 11.7 - - + -
268R LEU* 2.8 23.3 + - + +
269R TYR* 2.9 33.0 - - + +
271R SER* 1.3 75.5 - - - +
273R GLY* 1.3 67.8 + - - +
276R VAL* 3.0 44.4 + - + +
277R PRO* 3.8 0.2 - - - +
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Residues in contact with GLY 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239R ALA* 4.7 0.7 - - - +
242R TYR* 3.9 12.3 - - - +
243R TRP* 4.2 18.7 + - - -
246R VAL* 3.6 24.7 - - - -
269R TYR 2.9 12.0 + - - -
270R LEU 3.1 3.1 + - - -
272R ILE* 1.3 77.4 - - - +
274R TRP* 1.3 59.3 + - - +
277R PRO* 3.1 21.8 - - - +
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Residues in contact with TRP 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R ASN* 4.5 6.1 - - + +
185R ALA* 4.3 30.5 - - + -
186R SER* 4.8 2.9 - - - -
189R LEU* 3.5 32.8 - - + -
235R TYR* 3.0 39.5 + + - +
239R ALA* 4.6 7.4 - - + -
243R TRP* 3.0 32.7 - + - -
270R LEU* 2.9 37.5 + - + +
271R SER* 5.6 0.4 - - - -
273R GLY* 1.3 74.4 - - - +
275R GLY* 1.3 62.4 + - - +
277R PRO* 2.9 17.9 - - - +
278R LEU* 3.0 16.0 + - + +
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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