Contacts of the helix formed by residues 271 - 280 (chain B) in PDB entry 3VAG
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B TYR 3.6 1.1 + - - +
270B LEU* 1.3 72.4 - - - +
272B ASP* 1.3 67.0 + - - +
273B ASP* 4.0 14.5 + - - +
274B GLN* 3.1 37.2 + - - +
275B VAL* 3.1 23.6 + - - +
290B LEU* 3.9 7.9 - - - -
403B DIO 4.1 24.7 - - - +
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Residues in contact with ASP 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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271B ASN* 1.3 78.8 - - - +
273B ASP* 1.3 61.6 + - - +
275B VAL* 3.3 2.6 + - - +
276B LYS* 3.0 39.2 + - + +
288B PHE* 3.8 24.3 - - + -
289B ASN* 5.1 1.0 - - - -
290B LEU* 3.9 14.4 + - - +
292B LYS* 2.9 34.1 + - - +
403B DIO 5.1 2.4 - - - +
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Residues in contact with ASP 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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271B ASN* 3.5 12.9 + - - +
272B ASP* 1.3 81.0 - - - +
274B GLN* 1.3 61.3 + - + +
276B LYS* 3.3 29.6 + - - +
277B GLU* 3.2 25.4 + - - +
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Residues in contact with GLN 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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269B TYR* 4.1 3.8 - - - +
270B LEU* 3.4 19.5 - - + +
271B ASN* 3.1 42.2 + - - +
272B ASP 3.2 0.2 - - - -
273B ASP* 1.3 75.3 - - + +
275B VAL* 1.3 64.4 + - - +
277B GLU* 3.3 19.3 + - - +
278B LEU 3.4 8.8 + - - -
404B CPQ 3.8 40.8 - - + +
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Residues in contact with VAL 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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263B ILE* 5.4 3.4 - - + -
266B LEU* 4.0 39.0 - - + -
270B LEU* 4.0 23.8 - - + -
271B ASN 3.1 19.0 + - - +
272B ASP 3.9 3.4 - - - +
274B GLN* 1.3 76.8 - - - +
276B LYS* 1.3 60.9 + - - +
278B LEU* 3.3 13.3 + - + +
279B LEU* 3.3 24.9 + - + +
288B PHE* 3.8 24.7 - - + -
290B LEU* 4.5 9.9 - - + -
303B ALA* 4.5 3.6 - - + -
404B CPQ 5.4 0.9 - - - -
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Residues in contact with LYS 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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272B ASP* 3.0 24.7 + - + +
273B ASP* 3.3 26.8 + - - +
275B VAL* 1.3 75.9 - - - +
277B GLU* 1.3 53.0 + - - +
279B LEU* 3.1 7.3 + - - +
280B THR* 2.8 46.0 + - + +
285B LEU* 4.0 11.0 - - + -
288B PHE* 3.5 41.0 - - + -
401B DIO 4.0 22.3 + - - -
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Residues in contact with GLU 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 ASP 3.2 16.2 + - - +
274B GLN* 3.5 14.9 - - - +
275B VAL 3.3 0.4 - - - -
276B LYS* 1.3 73.2 - - - +
278B LEU* 1.3 64.5 + - - +
279B LEU 3.6 0.2 + - - -
280B THR* 3.8 16.3 + - - +
281B SER* 3.9 9.9 + - - -
404B CPQ 4.1 33.9 + - - +
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Residues in contact with LEU 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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263B ILE* 5.9 1.6 - - + -
266B LEU* 4.7 9.4 - - + -
270B LEU* 5.8 1.1 - - + -
274B GLN 3.4 7.1 + - - +
275B VAL* 3.3 15.7 + - + +
277B GLU* 1.3 79.4 - - - +
279B LEU* 1.3 59.7 + - + +
281B SER* 3.2 20.7 + - - -
282B PHE* 4.2 7.1 - - - -
320B LEU* 4.1 20.8 - - + +
323B MET* 4.5 7.4 - - + -
325B LEU* 3.8 41.7 - - + -
330B LEU* 4.0 17.5 - - + -
404B CPQ 4.2 28.5 - - + +
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Residues in contact with LEU 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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261B LEU* 5.7 2.5 - - + -
263B ILE* 4.1 27.6 - - + -
275B VAL* 3.3 15.2 + - + +
276B LYS* 3.1 7.8 + - - +
278B LEU* 1.3 77.7 - - + +
280B THR* 1.3 58.1 + - - +
281B SER 3.2 9.2 + - - -
282B PHE* 3.4 11.1 + - - -
285B LEU* 4.2 12.8 - - + -
288B PHE* 3.7 36.1 - - + -
305B CYS* 3.8 20.4 - - + -
307B TYR* 2.8 33.5 + - + +
320B LEU* 3.6 26.0 - - + -
332B VAL* 6.0 0.2 - - + -
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Residues in contact with THR 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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276B LYS* 2.8 31.0 + - + +
277B GLU* 3.8 11.6 + - - +
278B LEU 3.6 0.4 - - - -
279B LEU* 1.3 69.5 - - - +
281B SER* 1.3 62.6 + - - +
282B PHE 3.1 2.0 + - - -
283B GLY* 3.4 23.2 + - - +
284B PRO* 5.1 2.0 - - + -
285B LEU* 4.0 30.3 - - + +
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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