Contacts of the strand formed by residues 275 - 279 (chain B) in PDB entry 2C31
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 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B LEU* 3.9 24.2 - - + +
210B ILE* 4.8 3.8 - - + -
213B ALA* 3.5 34.3 - - + -
215B ARG 4.0 0.2 - - - +
216B PRO* 3.4 4.7 - - + +
217B VAL* 3.0 28.1 + - - +
273B CYS* 4.7 0.4 - - - -
274B ASP* 1.3 93.1 + - - +
276B CYS* 1.3 63.8 + - - +
277B VAL* 4.6 15.0 - - + +
301B LYS* 3.4 24.5 - - + +
303B VAL* 4.6 11.4 - - + -
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Residues in contact with CYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 3.5 15.5 - - + -
219B MET* 3.4 34.3 - - - -
270B LEU* 5.2 0.2 - - - -
273B CYS* 4.4 4.9 - - - -
274B ASP 4.2 0.8 - - - -
275B VAL* 1.3 73.0 - - - +
277B VAL* 1.3 60.5 + - - +
278B LEU* 3.7 4.8 + - - -
295B TRP* 3.9 26.9 - - + -
300B LYS* 4.8 2.9 - - + +
301B LYS 3.1 7.5 + - - -
302B TYR* 3.5 27.9 - - + -
303B VAL 3.0 24.2 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 4.1 27.8 - - + -
216B PRO* 6.1 1.1 - - + -
217B VAL 2.8 18.9 + - - +
218B ILE* 3.5 18.1 - - + +
219B MET* 2.7 33.6 + - - +
236B LEU* 5.8 0.4 - - + -
242B ILE* 5.6 4.5 - - + -
275B VAL* 4.6 7.0 - - + +
276B CYS* 1.3 74.3 - - - +
278B LEU* 1.3 58.5 + - - +
279B ILE* 3.7 24.9 + - + -
303B VAL* 3.5 29.2 - - + -
305B ILE* 5.1 4.9 - - + -
333B LEU* 5.4 4.0 - - + -
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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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219B MET* 3.9 18.8 - - + -
276B CYS* 4.5 3.1 - - - -
277B VAL* 1.3 71.4 - - - +
279B ILE* 1.3 63.4 + - - +
280B GLY 4.0 0.4 - - - -
281B ALA* 3.9 18.8 - - + +
283B LEU* 4.4 18.8 - - + +
287B MET* 3.7 31.6 - - + -
302B TYR* 3.9 27.6 - - + -
303B VAL 2.7 13.1 + - - +
304B GLN* 3.3 32.8 - - + +
305B ILE* 2.8 29.6 + - - +
318B ILE* 4.6 2.7 - - + -
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Residues in contact with ILE 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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218B ILE* 3.6 25.8 - - + -
219B MET 2.9 12.6 + - - +
220B LEU* 4.1 11.2 - - + -
221B GLY 3.1 19.4 + - - -
224B ALA* 3.6 20.6 - - + +
233B ILE* 4.9 5.8 - - + -
236B LEU* 3.9 24.0 - - + -
277B VAL* 3.9 16.6 - - + -
278B LEU* 1.3 74.6 - - - +
280B GLY* 1.3 66.6 + - - +
281B ALA* 3.2 1.2 - - - +
305B ILE* 4.1 19.7 - - + -
326B ILE* 4.1 22.7 - - + -
330B VAL* 4.7 7.6 - - + -
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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
------------------------------------------------------------
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