Contacts of the helix formed by residues 292 - 299 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU 4.1 4.4 + - - +
212A SER 4.3 3.5 - - - +
239A GLU 5.0 1.7 - - - +
240A PHE 4.9 8.0 - - - +
243A HIS* 3.9 34.1 + - + +
290A VAL 4.2 1.0 + - - -
291A VAL* 1.3 74.8 - - - +
293A LEU* 1.3 62.2 + - - +
294A GLU* 3.1 29.4 + - - +
295A ASN* 3.1 34.5 + - + +
296A PHE* 3.2 19.1 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.4 9.2 - - + +
106A ALA* 5.9 0.2 - - - -
108A LYS* 3.2 34.1 - - + +
109A GLU 3.9 3.6 - - - +
110A SER* 3.6 29.8 - - - +
111A LEU* 3.7 24.9 - - + +
291A VAL* 3.1 30.7 + - + +
292A ASN* 1.3 71.4 - - - +
294A GLU* 1.3 55.0 + - - +
296A PHE* 3.4 12.3 + - + +
297A ARG* 2.7 54.4 + - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ASN* 3.1 22.9 - - - +
293A LEU* 1.3 75.1 - - - +
295A ASN* 1.3 68.4 + - - +
296A PHE 3.1 1.6 - - - -
297A ARG* 3.8 15.4 - - - +
298A LYS* 2.8 33.9 + - - +
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Residues in contact with ASN 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A SER 3.2 19.3 - - - +
213A GLY* 3.9 2.8 - - - -
239A GLU* 3.3 23.2 + - - +
240A PHE* 3.9 20.9 - - + +
292A ASN* 3.1 32.4 + - + +
294A GLU* 1.3 87.0 + - - +
296A PHE* 1.3 60.5 + - - +
298A LYS* 3.7 7.2 + - - +
299A GLN* 3.3 30.5 + - - +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.6 63.5 - + + -
105A LEU* 4.1 13.0 - - + -
106A ALA* 3.9 23.8 - - + -
209A ILE* 3.7 26.7 - - + -
210A LEU* 3.9 17.5 - - + +
212A SER 4.0 0.8 + - - -
213A GLY* 3.9 12.1 - - - +
291A VAL* 5.3 1.8 - - + -
292A ASN 3.2 11.6 + - - +
293A LEU* 3.5 19.1 - - + +
294A GLU 3.1 0.4 - - - -
295A ASN* 1.3 77.5 - - - +
297A ARG* 1.3 66.1 + - - +
298A LYS 3.3 0.2 + - - -
299A GLN* 3.4 4.3 + - - +
300A TYR* 3.2 32.6 + + - +
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ALA* 3.2 44.8 + - + +
107A GLN 4.5 1.4 - - - -
108A LYS 3.2 25.7 + - - +
109A GLU* 5.2 3.8 + - - +
293A LEU* 2.7 47.4 + - - +
294A GLU* 3.2 13.0 + - - +
296A PHE* 1.3 74.0 - - - +
298A LYS* 1.3 58.0 + - - +
300A TYR* 3.8 4.9 - - - -
301A VAL* 3.0 34.4 + - - +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU 2.8 21.4 + - - +
295A ASN* 3.8 9.4 - - - +
297A ARG* 1.3 72.2 - - - +
299A GLN* 1.3 73.9 + - - +
300A TYR 3.1 9.8 + - - +
301A VAL* 3.5 12.9 - - - +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLY* 3.0 32.0 - - - +
214A ALA* 4.8 4.7 - - + -
240A PHE* 5.5 9.5 - - - -
295A ASN* 3.3 16.8 + - - +
296A PHE 3.4 3.1 + - - +
298A LYS* 1.3 97.4 - - - +
300A TYR* 1.3 64.1 + - - +
49B SER* 5.5 3.1 + - - -
51B ALA* 5.7 5.0 - - - +
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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