Contacts of the helix formed by residues 292 - 301 (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 ASN 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211C LEU 4.1 3.8 + - - +
212C SER 4.0 5.6 - - - +
239C GLU 4.7 11.1 + - - -
240C PHE* 4.8 12.9 + - - +
243C HIS* 3.9 30.2 + - + +
290C VAL 4.2 0.6 + - - -
291C VAL* 1.3 74.5 - - - +
293C LEU* 1.3 66.1 + - - +
294C GLU* 3.2 20.7 + - - +
295C ASN* 3.3 22.2 + - + +
296C PHE* 3.2 18.4 + - - +
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Residues in contact with LEU 293 (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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105C LEU* 4.2 15.3 - - + +
106C ALA* 5.8 1.1 - - - -
108C LYS* 3.4 28.7 - - + +
109C GLU 3.7 4.9 - - - +
110C SER* 3.5 26.9 - - - -
111C LEU* 3.6 28.7 - - + +
291C VAL* 3.0 31.7 + - + +
292C ASN* 1.3 71.7 + - - +
294C GLU* 1.3 53.1 + - - +
296C PHE* 3.5 11.5 - - + +
297C ARG* 2.6 55.6 + - - +
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Residues in contact with GLU 294 (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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292C ASN* 3.1 13.1 + - - +
293C LEU* 1.3 77.3 - - - +
295C ASN* 1.3 57.8 + - - +
297C ARG* 3.1 29.4 + - - +
298C LYS* 2.9 31.1 + - - +
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Residues in contact with ASN 295 (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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212C SER 2.6 29.2 + - - +
213C GLY* 3.6 6.9 - - - -
214C ALA 3.7 4.2 - - - +
239C GLU 5.7 0.7 - - - +
240C PHE* 3.2 41.6 - - + +
292C ASN* 3.3 21.7 + - + +
294C GLU* 1.3 73.9 - - - +
296C PHE* 1.3 61.3 + - - +
298C LYS* 4.5 7.8 - - - +
299C GLN* 3.0 49.5 + - - +
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Residues in contact with PHE 296 (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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102C PHE* 3.3 60.3 - + + -
105C LEU* 3.7 20.2 - - + -
106C ALA* 3.9 16.6 - - + -
111C LEU* 6.5 0.2 - - + -
209C ILE* 3.6 26.9 - - + -
210C LEU* 3.7 24.0 - - - +
212C SER 3.6 4.3 + - - +
213C GLY* 4.0 10.0 - - - -
291C VAL* 5.0 3.1 - - + -
292C ASN 3.2 13.3 + - - +
293C LEU* 3.5 15.9 - - + +
295C ASN* 1.3 76.9 - - - +
297C ARG* 1.3 57.7 + - - +
299C GLN* 4.0 0.7 - - - +
300C TYR* 3.0 36.6 + - + +
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Residues in contact with ARG 297 (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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106C ALA* 3.3 32.4 + - + +
107C GLN* 4.7 1.0 - - - +
108C LYS 2.8 28.7 + - - -
109C GLU* 4.6 3.2 + - - +
293C LEU* 2.6 59.6 + - - +
294C GLU* 3.1 33.2 + - - +
296C PHE* 1.3 77.2 - - - +
298C LYS* 1.3 58.4 + - - +
300C TYR* 3.9 5.2 - - + -
301C VAL* 3.2 33.7 + - + +
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Residues in contact with LYS 298 (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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294C GLU* 2.9 17.8 + - - +
295C ASN* 4.0 9.6 - - - +
297C ARG* 1.3 76.5 - - - +
299C GLN* 1.3 68.0 + - + +
301C VAL* 3.3 21.7 - - - +
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Residues in contact with GLN 299 (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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213C GLY* 3.1 31.6 + - - +
214C ALA* 4.5 10.3 - - - +
240C PHE* 4.7 9.7 - - - -
295C ASN* 3.0 38.8 + - - +
296C PHE 4.3 0.4 - - - +
298C LYS* 1.3 77.2 - - + +
300C TYR* 1.3 65.9 + - - +
301C VAL 4.1 2.8 - - - +
50D ARG* 6.1 1.9 - - - +
51D ALA* 4.9 12.5 - - - +
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Residues in contact with TYR 300 (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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102C PHE* 4.5 13.5 - - + -
103C ASP* 2.7 50.1 + - - +
106C ALA* 3.9 23.3 - - + -
296C PHE* 3.0 28.0 + - + +
297C ARG* 3.9 4.9 - - + -
299C GLN* 1.3 78.5 - - - +
301C VAL* 1.3 98.9 + - + +
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Residues in contact with VAL 301 (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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297C ARG* 3.2 18.7 + - + +
298C LYS* 3.3 16.7 - - - +
299C GLN 4.1 2.9 - - - +
300C TYR* 1.3 113.8 - - + +
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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