Contacts of the helix formed by residues 279 - 289 (chain C) in PDB entry 2CKE
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 ASP 279 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C PRO* 3.4 8.1 - - - +
278C VAL* 1.3 84.4 - - + +
280C ASN* 1.3 63.2 + - - +
281C GLN* 3.5 26.7 + - - +
282C GLN* 2.8 46.3 + - - +
283C ALA* 3.3 16.1 + - - +
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Residues in contact with ASN 280 (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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279C ASP* 1.3 75.1 - - - +
281C GLN* 1.3 62.8 + - - +
282C GLN 3.3 0.4 - - - -
283C ALA* 3.0 12.5 + - + +
284C MET* 2.8 55.2 + - + +
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Residues in contact with GLN 281 (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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279C ASP* 3.4 29.5 + - - +
280C ASN* 1.3 83.8 - - - +
282C GLN* 1.3 62.8 + - + +
284C MET* 3.3 9.6 + - - +
285C VAL* 3.2 27.1 + - + +
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Residues in contact with GLN 282 (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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247C LEU* 3.9 30.5 - - + +
273C PRO* 3.6 21.4 - - - +
277C PRO* 3.5 12.9 - - + +
278C VAL* 2.9 43.2 + - - +
279C ASP* 2.8 30.5 + - - +
281C GLN* 1.3 74.3 - - + +
283C ALA* 1.3 61.8 + - - +
285C VAL* 3.6 6.7 + - - +
286C ARG* 3.2 23.7 + - - +
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Residues in contact with ALA 283 (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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114C GLU* 4.6 2.1 - - - +
277C PRO* 4.1 15.4 - - + +
279C ASP 3.3 11.9 + - - +
280C ASN* 3.0 20.6 + - + +
282C GLN* 1.3 79.4 - - - +
284C MET* 1.3 56.5 + - - +
286C ARG* 3.4 9.3 + - - +
287C ARG* 3.0 48.6 + - - +
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Residues in contact with MET 284 (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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280C ASN* 2.8 36.3 + - + +
281C GLN* 3.8 8.3 - - - +
283C ALA* 1.3 69.4 - - + +
285C VAL* 1.3 60.5 + - + +
287C ARG* 3.3 21.2 + - - +
288C GLU* 2.9 52.1 + - - +
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Residues in contact with VAL 285 (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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245C SER* 3.9 18.4 - - - -
247C LEU* 5.1 10.1 - - + -
281C GLN 3.2 19.4 + - - +
282C GLN* 3.8 8.3 - - - +
284C MET* 1.3 77.2 - - + +
286C ARG* 1.3 55.4 + - - +
288C GLU* 3.4 9.5 + - - +
289C SER* 2.7 46.8 + - - +
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Residues in contact with ARG 286 (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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113C GLU* 3.5 17.6 - - + +
114C GLU* 3.4 48.9 + - - +
117C THR* 3.3 25.2 + - - -
245C SER* 5.6 0.4 - - - -
247C LEU* 5.8 2.2 - - + -
274C TRP* 3.2 40.4 + - + +
275C ILE 3.3 18.8 + - - -
277C PRO* 3.4 26.0 - - - +
282C GLN 3.2 14.9 + - - +
283C ALA* 3.7 9.8 + - - +
285C VAL* 1.3 80.3 - - + +
287C ARG* 1.3 62.4 + - - +
289C SER 3.3 17.3 - - - +
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Residues in contact with ARG 287 (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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112C SER* 3.7 16.1 - - - +
114C GLU* 3.1 37.6 + - + +
283C ALA* 3.0 33.4 + - - +
284C MET* 3.7 33.1 - - - +
286C ARG* 1.3 77.4 - - - +
288C GLU* 1.3 62.4 + - + +
290C VAL* 5.5 1.0 - - - +
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Residues in contact with GLU 288 (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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284C MET* 2.9 39.1 + - - +
285C VAL* 3.9 7.1 - - - +
287C ARG* 1.3 80.0 - - + +
289C SER* 1.3 62.1 + - - +
290C VAL* 3.5 13.6 + - - +
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Residues in contact with SER 289 (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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112C SER* 3.6 3.8 - - - -
113C GLU* 2.9 53.7 + - - -
243C HIS 4.0 11.3 + - - -
245C SER* 3.6 15.7 - - - -
285C VAL* 2.7 25.4 + - - +
286C ARG 3.3 3.4 - - - +
287C ARG 3.6 0.4 - - - -
288C GLU* 1.3 77.1 - - - +
290C VAL* 1.3 59.2 + - - +
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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