Contacts of the helix formed by residues 274 - 292 (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 TRP 274 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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Residues in contact with GLY 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271R SER* 2.7 28.9 + - - +
274R TRP* 1.3 76.6 - - - +
276R VAL* 1.3 61.9 + - - +
278R LEU* 3.2 13.9 - - - +
279R LEU* 2.9 30.8 + - - +
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Residues in contact with VAL 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242R TYR* 3.4 34.8 - - + +
245R LEU* 5.9 2.2 - - + -
271R SER 3.8 0.8 + - - -
272R ILE* 3.0 41.9 + - + +
275R GLY* 1.3 75.4 - - - +
277R PRO* 1.3 58.1 - - + +
279R LEU* 4.7 2.5 - - - -
280R PHE* 2.8 45.1 + - + +
312R PRO* 6.3 0.2 - - + -
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Residues in contact with PRO 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235R TYR* 3.2 28.1 - - + +
238R ALA* 4.0 18.2 - - + +
239R ALA* 4.1 6.7 - - - -
242R TYR* 3.3 23.3 - - + -
273R GLY 3.1 21.1 - - - +
274R TRP* 2.9 16.6 - - - +
276R VAL* 1.3 88.8 - - + +
278R LEU* 1.3 55.4 + - - +
281R VAL* 2.6 43.7 + - + +
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Residues in contact with LEU 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235R TYR* 3.3 19.3 - - + +
274R TRP* 3.0 31.0 - - + +
275R GLY* 3.2 21.1 - - - +
277R PRO* 1.3 74.9 - - - +
279R LEU* 1.3 71.8 + - + +
282R ILE* 2.9 45.8 + - + +
283R PRO* 3.7 0.2 - - - +
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Residues in contact with LEU 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275R GLY* 2.9 20.5 + - - +
276R VAL* 4.4 2.2 - - - +
278R LEU* 1.3 81.6 - - + +
280R PHE* 1.3 57.1 + - - +
283R PRO* 3.1 23.4 - - + +
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Residues in contact with PHE 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242R TYR* 4.2 13.2 - + - -
276R VAL* 2.8 28.3 + - + +
279R LEU* 1.3 77.9 - - - +
281R VAL* 1.3 82.5 + - + +
283R PRO* 3.1 13.2 - - - +
284R TRP* 3.6 12.8 + - + +
308R ILE* 4.6 3.1 - - + -
309R ILE* 3.7 41.1 - - + -
312R PRO* 3.2 38.6 - - + -
313R ILE* 4.9 2.0 - - + -
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Residues in contact with VAL 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231R LEU* 4.8 4.0 - - + +
234R GLN* 3.8 30.5 - - + +
235R TYR* 4.6 3.6 - - + +
238R ALA* 4.0 23.6 - - + -
277R PRO* 2.6 33.2 + - + +
280R PHE* 1.3 97.3 - - + +
282R ILE* 1.3 62.9 + - + +
284R TRP* 2.8 15.4 + - + +
285R GLY* 2.6 35.9 + - - +
309R ILE* 4.8 6.7 - - + -
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Residues in contact with ILE 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231R LEU* 5.5 18.4 - - + +
235R TYR* 5.4 6.7 - - + -
278R LEU* 2.9 39.3 + - + +
281R VAL* 1.3 87.5 - - + +
283R PRO* 1.3 66.0 - - + +
285R GLY* 4.4 0.9 - - - +
286R ILE* 2.9 38.6 + - + +
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Residues in contact with PRO 283 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278R LEU 3.7 0.2 - - - +
279R LEU* 3.1 26.9 - - - +
280R PHE 3.1 9.2 - - - +
282R ILE* 1.3 93.0 - - + +
284R TRP* 1.3 56.2 + - - +
286R ILE* 4.3 5.4 - - + -
287R VAL* 2.9 41.0 + - + +
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Residues in contact with TRP 284 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234R GLN* 3.5 25.1 - - + -
280R PHE* 3.6 14.5 + - + +
281R VAL* 2.8 20.2 + - + +
283R PRO* 1.3 75.7 - - - +
285R GLY* 1.3 68.9 + - - +
287R VAL* 4.1 2.8 - - - +
288R LYS* 2.9 67.3 + - + +
299R ARG* 3.5 27.6 - - - -
305R TYR* 2.9 44.0 + + + +
308R ILE* 3.5 21.5 - - + -
309R ILE* 3.3 48.0 - - + -
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Residues in contact with GLY 285 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231R LEU* 3.4 19.4 - - - +
281R VAL* 2.6 18.8 + - - -
282R ILE* 4.0 1.1 - - - -
284R TRP* 1.3 74.2 - - - +
286R ILE* 1.3 59.9 + - - +
288R LYS* 2.8 39.6 + - - +
289R TYR* 2.9 15.4 + - - +
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Residues in contact with ILE 286 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231R LEU* 4.5 10.5 - - + +
282R ILE* 2.9 32.0 + - + +
283R PRO* 3.8 7.0 - - + +
285R GLY* 1.3 76.4 - - - +
287R VAL* 1.3 74.6 + - + +
289R TYR* 3.7 10.7 - - + +
290R LEU* 2.9 31.6 + - + +
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Residues in contact with VAL 287 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283R PRO* 2.9 30.7 + - + +
284R TRP* 4.1 2.5 - - - +
286R ILE* 1.3 84.7 - - + +
288R LYS* 1.3 63.1 + - - +
290R LEU* 5.3 1.1 - - - -
291R TYR* 2.9 36.0 + - + +
305R TYR* 4.5 13.9 - - + +
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Residues in contact with LYS 288 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230R PHE* 5.8 2.0 - - - +
231R LEU* 3.7 14.5 - - - +
234R GLN* 4.8 3.3 - - - +
284R TRP* 2.9 61.9 + - + +
285R GLY* 2.8 28.2 + - - +
287R VAL* 1.3 79.5 - - - +
289R TYR* 1.3 61.7 + - - +
292R GLU* 3.0 28.6 + - - +
297R TRP* 2.9 50.7 + - + +
299R ARG* 5.7 0.9 - - - -
302R ASN* 5.9 3.1 - - - +
305R TYR* 3.4 36.2 - - + -
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Residues in contact with TYR 289 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220R TYR* 5.8 0.5 - - - -
223R SER* 2.4 43.1 + - - -
224R LEU* 4.4 11.4 - - + +
227R ARG* 5.0 3.8 - - + -
231R LEU* 5.2 5.6 - - + -
285R GLY 2.9 19.3 + - - +
286R ILE* 3.2 11.0 + - + +
288R LYS* 1.3 76.8 - - - +
290R LEU* 1.3 76.3 + - + +
292R GLU 4.4 0.7 - - - -
293R ASP* 2.8 69.6 + - + +
295R GLY 4.9 0.2 - - - -
297R TRP* 3.1 43.1 - + + +
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Residues in contact with LEU 290 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286R ILE* 2.9 21.2 + - + +
287R VAL* 4.7 1.3 - - - +
289R TYR* 1.3 91.5 - - + +
291R TYR* 1.3 66.6 + - - +
292R GLU 3.4 0.2 + - - -
293R ASP* 4.4 6.0 + - + +
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Residues in contact with TYR 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287R VAL* 2.9 27.1 + - + +
290R LEU* 1.3 79.3 - - - +
292R GLU* 1.3 81.0 + - + +
293R ASP 4.0 0.2 - - - -
305R TYR* 3.1 21.8 - - - +
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Residues in contact with GLU 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288R LYS 3.0 17.6 + - - +
289R TYR* 3.2 4.6 - - - +
291R TYR* 1.3 104.0 - - + +
293R ASP* 1.3 59.8 + - - +
294R GLU* 2.9 22.8 + - + +
297R TRP* 4.8 4.2 + - - -
302R ASN* 2.8 35.8 - - - +
305R TYR* 3.5 18.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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