Contacts of the helix formed by residues 311 - 321 (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 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG* 5.0 16.2 - - - +
309A ASP* 3.2 19.8 + - - +
310A ILE* 1.3 87.8 - - - +
312A VAL* 1.3 62.7 + - + +
313A THR 3.3 0.2 - - - -
314A ASP* 3.9 10.9 + - - +
315A GLN* 4.0 17.2 + - - +
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Residues in contact with VAL 312 (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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282A PHE* 3.4 38.8 - - + +
283A GLY* 5.0 4.7 - - - -
284A PRO* 5.9 1.3 - - + -
307A TYR* 3.6 29.2 - - + -
309A ASP* 3.3 35.0 - - + +
310A ILE 3.2 0.6 - - - -
311A ASN* 1.3 77.6 - - - +
313A THR* 1.3 65.3 + - - +
315A GLN* 2.8 27.5 + - - +
316A ALA* 3.0 11.8 + - - +
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Residues in contact with THR 313 (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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259A HIS* 3.9 24.9 + - + +
261A LEU* 4.0 25.0 - - + +
307A TYR* 4.2 19.7 + - - +
309A ASP 4.1 1.3 + - - -
310A ILE* 2.9 26.8 + - - +
312A VAL* 1.3 77.3 - - - +
314A ASP* 1.3 62.9 + - - +
316A ALA* 3.4 3.8 + - - +
317A ILE* 3.2 25.2 + - + +
334A ARG* 3.6 30.7 - - - +
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE 5.8 0.7 - - - -
311A ASN* 3.9 8.9 + - - +
312A VAL 3.3 0.8 - - - -
313A THR* 1.3 80.3 - - - +
315A GLN* 1.3 57.9 + - + +
317A ILE* 3.6 10.6 + - - +
318A ALA* 3.1 27.2 + - - +
334A ARG* 3.1 37.4 + - - -
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Residues in contact with GLN 315 (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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282A PHE* 3.5 22.4 - - + +
311A ASN* 4.0 14.1 + - - +
312A VAL* 2.8 29.6 + - - +
314A ASP* 1.3 70.1 - - + +
316A ALA* 1.3 65.6 + - - +
318A ALA* 3.3 6.1 + - - +
319A GLY 2.9 19.2 + - - -
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Residues in contact with ALA 316 (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* 4.4 7.2 - - + -
279A LEU* 5.8 0.9 - - + -
282A PHE* 3.8 19.5 - - + -
307A TYR* 3.5 42.8 - - + +
312A VAL 3.0 6.5 + - - +
313A THR 3.7 5.8 - - - +
315A GLN* 1.3 75.5 - - - +
317A ILE* 1.3 64.2 + - - +
319A GLY 3.2 1.0 + - - -
320A LEU* 2.9 34.7 + - + +
332A VAL* 4.8 2.9 - - + -
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Residues in contact with ILE 317 (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* 3.9 27.6 - - + -
313A THR* 3.2 17.1 + - + +
314A ASP* 3.6 13.7 - - - +
316A ALA* 1.3 75.7 - - - +
318A ALA* 1.3 59.3 + - - +
321A ASN* 2.9 43.5 + - + +
332A VAL* 3.8 29.8 - - + +
333A GLN* 4.8 1.6 - - - -
334A ARG* 3.8 32.1 - - - +
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Residues in contact with ALA 318 (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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314A ASP 3.1 14.9 + - - +
315A GLN* 3.3 6.3 + - - +
317A ILE* 1.3 80.8 - - - +
319A GLY* 1.3 59.6 + - - +
321A ASN 4.8 3.3 + - - +
323A MET* 4.9 7.6 - - - +
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Residues in contact with GLY 319 (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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282A PHE* 4.0 12.8 - - - -
315A GLN 2.9 15.6 + - - -
316A ALA 3.7 0.9 - - - -
318A ALA* 1.3 78.3 - - - +
320A LEU* 1.3 67.8 + - - +
323A MET* 3.5 23.7 - - - +
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Residues in contact with LEU 320 (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 0.9 - - + -
278A LEU* 4.0 34.1 - - + -
279A LEU* 4.0 27.4 - - + -
282A PHE* 3.7 29.2 - - + -
316A ALA* 2.9 21.7 + - + +
319A GLY* 1.3 85.1 - - - +
321A ASN* 1.3 60.5 + - - +
322A GLY 3.4 0.7 + - - -
323A MET* 3.0 26.8 + - + +
330A LEU* 3.6 21.5 - - + +
332A VAL* 3.6 21.5 - - + -
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Residues in contact with ASN 321 (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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317A ILE* 2.9 25.0 + - + +
318A ALA 5.0 2.9 - - - +
320A LEU* 1.3 76.1 - - - +
322A GLY* 1.3 67.1 + - - +
323A MET* 3.4 9.5 + - - +
330A LEU 4.0 2.2 - - - +
331A LEU* 3.7 16.1 - - - +
332A VAL* 3.3 40.0 + - - +
333A GLN* 5.7 0.4 - - - +
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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