Contacts of the helix formed by residues 292 - 299 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B LEU 4.3 4.8 + - - +
212B SER* 4.4 2.0 - - - +
240B PHE 4.9 4.0 - - - +
243B HIS* 3.6 34.8 + - + +
290B VAL 3.9 3.0 + - - -
291B VAL* 1.3 72.3 - - - +
293B LEU* 1.3 61.9 + - - +
294B GLU* 3.2 22.6 + - - +
295B ASN* 3.3 36.2 + - + +
296B PHE* 3.2 19.9 + - - +
74C HIS* 3.6 22.2 - - - -
156C HIS* 3.8 20.4 + - - -
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Residues in contact with LEU 293 (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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105B LEU* 3.8 22.4 - - + +
106B ALA* 5.5 0.4 - - - -
108B LYS* 3.5 10.1 - - + +
109B GLU 3.1 37.9 - - - +
110B SER* 3.3 18.2 - - - +
111B LEU* 3.7 25.8 - - + +
291B VAL* 3.0 18.6 + - + +
292B ASN* 1.3 70.0 + - - +
294B GLU* 1.3 60.2 + - - +
296B PHE* 3.8 12.8 - - + -
297B ARG* 2.9 50.7 + - - +
74C HIS* 4.1 8.9 - - + -
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Residues in contact with GLU 294 (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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292B ASN* 3.1 15.0 - - - +
293B LEU* 1.3 74.5 - - - +
295B ASN* 1.3 70.2 + - - +
296B PHE 3.1 0.3 + - - -
297B ARG* 3.2 24.3 + - - +
298B LYS* 2.9 29.0 + - - +
74C HIS* 3.7 16.7 + - + +
75C ASN* 5.4 0.7 - - - +
121C LYS* 3.0 22.1 + - - +
122C GLN* 6.3 2.5 - - + -
125C ASP* 2.9 32.6 - - - +
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Residues in contact with ASN 295 (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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212B SER 3.1 20.0 - - - +
213B GLY* 4.4 0.9 - - - -
239B GLU* 3.6 22.7 + - - +
240B PHE* 3.7 26.4 - - + +
292B ASN* 3.3 37.3 + - + +
294B GLU* 1.3 81.5 - - - +
296B PHE* 1.3 63.0 + - - +
298B LYS* 3.9 4.7 - - - +
299B GLN* 3.1 27.7 + - - +
156C HIS* 4.6 4.6 + - - -
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Residues in contact with PHE 296 (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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102B PHE* 3.5 61.2 - + + -
105B LEU* 4.1 13.2 - - + -
106B ALA* 3.9 23.3 - - + -
209B ILE* 3.6 27.4 - - + -
210B LEU* 3.9 19.5 - - - -
212B SER 3.6 2.4 + - - +
213B GLY* 3.9 12.6 - - - -
291B VAL* 5.1 3.4 - - + -
292B ASN 3.2 12.4 + - - +
293B LEU* 3.9 15.5 - - + +
294B GLU 3.1 0.6 - - - -
295B ASN* 1.3 83.7 - - - +
297B ARG* 1.3 65.9 + - - +
298B LYS 3.2 0.2 + - - -
299B GLN 3.3 4.7 - - - +
300B TYR* 3.1 29.6 - + + +
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Residues in contact with ARG 297 (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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106B ALA* 3.2 35.5 + - + +
108B LYS 3.4 18.8 + - - -
109B GLU* 5.1 3.0 + - - +
293B LEU* 2.9 48.0 + - + +
294B GLU* 3.2 39.6 + - - +
296B PHE* 1.3 75.4 - - + +
298B LYS* 1.3 65.0 + - - +
300B TYR* 3.2 26.9 - - + -
301B VAL* 3.6 8.2 + - - +
74C HIS* 5.2 3.8 - - - -
121C LYS* 5.6 0.2 - - - +
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Residues in contact with LYS 298 (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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294B GLU 2.9 22.2 + - - +
295B ASN* 3.9 4.9 - - - +
297B ARG* 1.3 76.1 - - - +
299B GLN* 1.3 68.9 + - + +
300B TYR 2.9 8.5 + - - -
301B VAL* 3.5 17.3 + - - +
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Residues in contact with GLN 299 (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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49A SER* 4.8 11.3 - - - -
50A ARG* 4.4 22.2 - - - +
51A ALA* 4.9 15.2 - - - +
213B GLY* 3.2 30.9 + - - +
214B ALA* 5.5 4.5 - - + -
218B LEU* 6.3 0.2 - - - +
240B PHE* 5.9 7.9 - - + -
295B ASN 3.1 12.0 + - - +
296B PHE 3.3 3.8 - - - +
298B LYS* 1.3 84.6 - - + +
300B TYR* 1.3 66.2 + - - +
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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