Contacts of the strand formed by residues 243 - 246 (chain C) in PDB entry 3OQN
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 ALA 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C LEU* 3.8 11.4 - - + -
178C HIS* 3.2 39.7 - - + +
180C ASP 3.6 1.1 + - - +
181C ILE* 3.1 11.8 - - + -
182C ALA 2.8 23.0 + - - -
241C PRO* 3.9 0.3 - - - +
242C THR* 1.3 77.7 + - - +
244C ILE* 1.3 65.3 + - - +
270C LEU* 4.9 1.1 - - - -
271C ASP* 3.2 20.4 - - + +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 5.3 1.9 - - - +
181C ILE* 4.9 1.6 - - - -
182C ALA* 3.3 29.6 - - + -
184C VAL* 5.1 2.0 - - + -
231C LEU* 3.7 18.2 - - + -
234C LEU* 3.6 19.1 - - + -
235C MET* 5.3 1.6 - - + -
241C PRO* 4.1 7.9 - - + -
243C ALA* 1.3 75.5 - - - +
245C LEU* 1.3 61.7 + - - +
255C ILE* 3.2 40.2 - - + -
270C LEU* 3.8 17.5 - - + -
271C ASP 2.9 4.9 + - - +
272C ILE* 3.2 43.3 - - + +
273C ILE* 3.3 4.2 + - - +
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 3.6 36.1 - - + -
169C ALA* 4.0 21.5 - - + -
170C VAL* 4.1 12.8 - - + +
173C LEU* 4.3 12.6 - - + -
181C ILE* 4.8 1.5 - - + +
182C ALA 2.6 14.6 + - - +
183C PHE* 3.2 19.6 - - + -
184C VAL* 2.8 31.4 + - - -
201C TYR* 5.3 1.3 - - + -
244C ILE* 1.3 73.0 - - - +
246C SER* 1.3 58.9 + - - +
255C ILE* 5.4 0.2 - - - -
273C ILE* 2.9 47.8 - - + +
274C GLY 4.7 1.8 - - - +
275C PHE* 5.7 0.7 - - + -
291C VAL* 5.2 2.9 - - + -
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Residues in contact with SER 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 5.6 0.2 - - - +
183C PHE* 4.6 0.2 - - - -
184C VAL* 3.6 7.2 - - - -
244C ILE 4.1 1.6 + - - -
245C LEU* 1.3 78.3 - - - +
247C ALA* 1.3 65.7 + - - +
248C THR 2.7 23.3 + - - -
251C MET* 3.0 21.2 - - - +
252C ALA* 3.6 22.9 - - - -
255C ILE* 4.0 13.4 - - - +
272C ILE* 5.2 1.1 - - - -
273C ILE 3.0 14.9 + - - +
274C GLY 3.8 9.0 - - - -
275C PHE* 3.8 3.1 - - - +
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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