Contacts of the helix formed by residues 271 - 280 (chain A) in PDB entry 3VAH
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 ASN 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TYR 3.9 2.3 + - - +
270A LEU* 1.3 75.6 - - - +
272A ASP* 1.3 70.3 + - - +
273A ASP* 3.1 11.8 + - - +
274A GLN* 3.0 46.6 + - - +
275A VAL* 3.0 21.7 + - - +
290A LEU* 3.9 4.3 - - - -
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Residues in contact with ASP 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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271A ASN* 1.3 77.2 - - - +
273A ASP* 1.3 62.5 + - - +
275A VAL* 3.2 3.8 + - - +
276A LYS* 2.8 32.7 + - + +
288A PHE* 4.1 16.6 - - + -
290A LEU* 3.2 21.9 + - - +
292A LYS* 3.1 36.2 + - - +
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Residues in contact with ASP 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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271A ASN* 3.1 8.5 + - - +
272A ASP* 1.3 78.7 - - - +
274A GLN* 1.3 63.1 + - + +
276A LYS* 3.6 28.2 + - - +
277A GLU* 3.0 24.3 + - - +
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Residues in contact with GLN 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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269A TYR 4.5 2.1 - - - +
270A LEU* 3.4 30.9 - - + +
271A ASN* 3.0 48.4 + - - +
273A ASP* 1.3 78.7 - - + +
275A VAL* 1.3 62.5 + - - +
277A GLU* 3.4 26.3 - - - +
278A LEU* 3.9 4.0 + - - +
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Residues in contact with VAL 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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263A ILE* 5.9 1.3 - - + -
266A LEU* 3.9 39.9 - - + -
267A PRO 5.7 0.2 - - - +
270A LEU* 4.0 26.9 - - + +
271A ASN 3.0 16.7 + - - +
272A ASP* 3.7 3.8 - - - +
274A GLN* 1.3 73.7 - - - +
276A LYS* 1.3 67.0 + - - +
277A GLU 3.2 1.0 + - - -
278A LEU* 3.3 17.0 + - + +
279A LEU* 3.6 16.7 + - + +
288A PHE* 4.0 22.7 - - + -
290A LEU* 4.4 10.5 - - + -
303A ALA* 4.7 2.7 - - + -
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Residues in contact with LYS 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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272A ASP* 2.8 20.4 + - + +
273A ASP* 3.3 28.2 + - - +
275A VAL* 1.3 73.7 - - - +
277A GLU* 1.3 56.5 + - - +
279A LEU* 3.3 4.7 + - - +
280A THR* 3.0 40.1 + - + +
285A LEU* 3.8 22.0 - - + -
288A PHE* 3.6 37.4 - - + -
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Residues in contact with GLU 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 ASP 3.0 11.5 + - - +
274A GLN* 3.4 20.7 - - - +
275A VAL 3.1 0.4 - - - -
276A LYS* 1.3 74.7 - - - +
278A LEU* 1.3 65.3 + - - +
279A LEU 3.5 0.3 + - - -
280A THR* 3.7 7.9 + - - +
281A SER* 3.6 17.8 + - - -
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Residues in contact with LEU 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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263A ILE* 6.1 2.0 - - + -
266A LEU* 5.2 8.3 - - + -
274A GLN 3.9 3.8 + - - +
275A VAL* 3.3 13.2 + - + +
277A GLU* 1.3 80.7 - - - +
279A LEU* 1.3 58.6 - - + +
281A SER* 2.8 29.9 + - - +
282A PHE* 4.0 4.9 - - + -
320A LEU* 4.0 34.1 - - + -
325A LEU* 4.7 20.0 - - + -
330A LEU* 4.3 17.3 - - + -
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Residues in contact with LEU 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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261A LEU* 6.2 1.1 - - + -
263A ILE* 4.2 28.7 - - + -
275A VAL* 3.6 15.9 + - + +
276A LYS* 3.3 6.4 + - - +
278A LEU* 1.3 78.2 - - + +
280A THR* 1.3 58.2 + - - +
281A SER 3.1 9.0 + - - -
282A PHE* 3.3 10.3 + - - +
285A LEU* 4.4 12.1 - - + -
288A PHE* 3.8 35.7 - - + -
305A CYS* 4.0 17.9 - - + -
307A TYR* 2.8 36.8 + - - +
316A ALA* 5.8 0.4 - - + -
320A LEU* 4.0 21.1 - - + -
332A VAL* 6.0 1.3 - - + -
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Residues in contact with THR 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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276A LYS* 3.0 26.7 + - + +
277A GLU* 3.7 10.2 + - - -
278A LEU 3.5 0.2 - - - -
279A LEU* 1.3 71.4 - - - +
281A SER* 1.3 63.2 + - - +
282A PHE 3.1 1.8 - - - -
283A GLY* 3.3 22.4 + - - +
284A PRO* 4.8 2.5 - - + -
285A LEU* 3.7 33.0 - - + +
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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