Contacts of the helix formed by residues 224 - 229 (chain V) in PDB entry 4ADV
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 THR 224 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223V LYS* 1.3 76.6 - - - +
225V ILE* 1.3 61.1 + - - +
226V ARG* 3.6 11.9 - - - +
227V ASN* 3.0 22.2 + - - +
228V SER* 2.9 22.5 + - - -
245V PRO 3.3 16.2 - - - +
246V ALA* 3.6 21.1 - - + +
247V MET 3.1 7.9 - - - -
248V ARG* 4.0 6.1 - - + -
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Residues in contact with ILE 225 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217V ALA* 4.9 2.2 - - + -
224V THR* 1.3 73.2 - - - +
226V ARG* 1.3 59.7 + - - +
228V SER* 3.4 11.9 - - - +
229V LEU* 2.7 53.1 + - + +
230V GLY 3.7 0.3 + - - -
238V LEU* 3.9 21.9 - - + +
243V ILE* 3.4 33.0 - - + -
244V ASP 3.8 11.4 - - - +
245V PRO* 4.1 2.9 - - + +
247V MET 2.8 20.0 + - - +
248V ARG 3.8 4.0 - - - -
249V ALA* 3.7 28.0 - - + +
252V ILE* 3.7 20.4 - - + -
260V MET* 5.3 1.3 - - - -
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Residues in contact with ARG 226 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224V THR* 3.1 9.0 + - - +
225V ILE* 1.3 83.3 - - - +
227V ASN* 1.3 59.2 + - + +
230V GLY* 3.3 22.7 - - - -
233V PHE 5.2 0.8 - - - +
235V VAL* 3.7 29.5 - - + +
238V LEU* 4.4 11.0 - - + -
245V PRO* 3.4 50.2 + - + +
246V ALA* 4.1 6.1 - - - +
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Residues in contact with ASN 227 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220V GLN* 3.9 18.5 + - - +
223V LYS* 3.6 33.4 - - + +
224V THR* 3.0 16.4 + - - +
226V ARG* 1.3 82.0 - - + +
228V SER* 1.3 65.7 + - - +
229V LEU 3.3 0.6 + - - -
230V GLY* 3.5 7.7 + - - -
231V ASN* 4.4 4.3 + - - +
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Residues in contact with SER 228 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216V GLU* 3.9 23.0 - - - +
217V ALA* 3.7 15.0 + - - -
220V GLN* 3.7 44.7 + - - +
223V LYS* 4.5 1.5 + - - -
224V THR 2.9 14.7 + - - -
225V ILE* 3.4 19.8 - - - +
227V ASN* 1.3 73.8 - - - +
229V LEU* 1.3 65.8 + - - +
231V ASN* 3.3 13.0 - - - +
249V ALA* 5.2 0.2 - - - +
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Residues in contact with LEU 229 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213V ILE* 3.6 36.8 - - + +
216V GLU* 3.8 11.9 - - + -
217V ALA* 3.7 18.6 - - + +
225V ILE* 2.7 34.9 + - + +
228V SER* 1.3 78.0 - - - +
230V GLY* 1.3 54.3 + - - +
231V ASN* 3.2 4.3 - - - -
232V LEU* 2.9 17.0 + - + +
233V PHE* 2.8 46.9 + - + +
238V LEU* 5.4 3.8 - - + -
257V TYR* 4.9 0.4 - - + -
260V MET* 3.7 32.3 - - + -
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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