Contacts of the helix formed by residues 312 - 321 (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 VAL 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B PHE* 3.4 37.9 - - + +
283B GLY* 5.3 2.9 - - - -
307B TYR* 3.8 26.5 - - + -
309B ASP* 3.2 30.7 + - + +
310B ILE 3.1 0.8 - - - -
311B ASN* 1.3 76.7 - - - +
313B THR* 1.3 63.0 + - - +
314B ASP 3.3 2.0 - - - -
315B GLN* 3.1 15.8 + - + +
316B ALA* 3.1 16.5 + - - +
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B HIS* 3.8 25.1 + - + +
261B LEU* 3.6 29.0 - - + +
307B TYR* 4.4 19.1 + - + +
309B ASP 4.4 0.4 + - - -
310B ILE* 2.9 24.4 + - - -
312B VAL* 1.3 77.0 - - - +
314B ASP* 1.3 58.1 + - - +
316B ALA* 3.3 5.2 + - - +
317B ILE* 3.2 25.9 + - + +
334B ARG* 3.6 28.9 - - - +
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE 4.9 0.5 + - - +
311B ASN 4.6 5.3 + - - +
312B VAL 3.3 0.4 - - - -
313B THR* 1.3 77.0 - - - +
315B GLN* 1.3 65.0 + - + +
316B ALA 3.3 0.2 - - - -
317B ILE* 4.0 11.2 - - - +
318B ALA* 3.1 24.9 + - - +
334B ARG* 3.0 37.4 + - - -
408B GOL 4.5 2.6 + - - -
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Residues in contact with GLN 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.8 16.6 - - + -
311B ASN 3.9 17.7 + - - +
312B VAL* 3.1 19.5 + - + +
314B ASP* 1.3 79.3 - - - +
316B ALA* 1.3 57.1 + - - +
318B ALA* 3.5 5.1 + - - +
319B GLY* 3.0 25.1 + - - -
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU* 4.6 5.6 - - + -
279B LEU* 6.0 0.2 - - + -
282B PHE* 4.1 18.8 - - + -
307B TYR* 3.5 39.0 - - + +
312B VAL 3.1 8.3 + - - +
313B THR 3.3 8.7 + - - +
315B GLN* 1.3 74.7 - - - +
317B ILE* 1.3 59.2 + - - +
320B LEU* 2.8 41.0 + - + +
332B VAL* 4.8 2.2 - - + -
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Residues in contact with ILE 317 (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* 3.7 29.2 - - + -
313B THR 3.2 16.5 + - - +
314B ASP* 4.0 11.2 - - - +
315B GLN 3.4 0.2 - - - -
316B ALA* 1.3 74.4 - - - +
318B ALA* 1.3 59.4 + - - +
321B ASN* 2.9 41.9 + - + +
332B VAL* 3.6 31.4 - - + +
334B ARG* 3.8 22.0 - - - +
408B GOL 3.4 24.9 - - - +
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Residues in contact with ALA 318 (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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314B ASP 3.1 16.8 + - - +
315B GLN* 3.8 6.1 - - - +
317B ILE* 1.3 80.8 - - - +
319B GLY* 1.3 60.6 + - - +
321B ASN 4.6 5.9 + - - +
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Residues in contact with GLY 319 (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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282B PHE* 4.0 14.8 - - - -
315B GLN 3.0 15.8 + - - -
316B ALA 3.7 2.0 - - - -
317B ILE 3.3 0.2 - - - -
318B ALA* 1.3 79.1 - - - +
320B LEU* 1.3 61.4 + - - +
321B ASN 5.2 0.8 - - - +
323B MET* 4.4 16.5 - - - +
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Residues in contact with LEU 320 (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* 6.0 0.7 - - + -
278B LEU* 4.1 25.8 - - + +
279B LEU* 3.6 31.0 - - + -
282B PHE* 3.6 31.2 - - + -
307B TYR* 4.8 1.3 - - - +
316B ALA* 2.8 21.0 + - + +
319B GLY* 1.3 74.4 - - - +
321B ASN* 1.3 66.0 + - - +
322B GLY 3.2 0.5 + - - -
323B MET* 3.1 49.2 + - + +
330B LEU* 3.8 14.4 - - + +
332B VAL* 3.6 22.0 - - + -
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Residues in contact with ASN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 2.9 27.7 + - + +
318B ALA 4.7 5.7 - - - +
319B GLY 5.2 0.3 - - - +
320B LEU* 1.3 76.4 - - - +
322B GLY* 1.3 64.6 + - - +
323B MET 3.3 0.6 + - - -
330B LEU 3.7 0.6 - - - +
331B LEU* 3.5 18.6 - - - +
332B VAL* 3.0 44.0 + - - +
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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