Contacts of the helix formed by residues 278 - 282 (chain E) in PDB entry 1QK1
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 CYS 278 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E VAL* 4.1 15.3 - - - -
69E MET 4.9 3.4 - - - -
70E VAL* 5.1 6.3 - - + -
77E TYR* 4.0 2.7 + - - -
227E GLU* 6.1 1.1 - - - +
228E ASP* 5.3 1.0 + - - -
276E LEU* 4.3 3.6 - - - +
277E THR* 1.3 80.2 + - - +
279E PRO* 1.3 74.6 - - - +
280E SER* 3.1 29.8 - - - +
281E ASN* 2.9 32.8 + - - +
282E LEU* 4.1 2.8 + - - +
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Residues in contact with PRO 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E VAL* 4.1 16.2 - - + -
69E MET* 3.3 24.7 - - + +
70E VAL* 4.5 0.4 - - - -
77E TYR* 3.7 5.4 - - - +
84E PHE* 3.7 31.2 - - + -
87E VAL* 4.8 5.8 - - + -
88E ILE* 4.4 14.4 - - + -
91E ARG* 5.2 2.2 - - + -
92E HIS* 2.9 19.8 + - - -
277E THR 3.8 5.2 - - - +
278E CYS* 1.3 87.3 - - - +
280E SER* 1.3 58.1 + - - +
281E ASN 3.2 0.9 + - - -
282E LEU* 3.3 30.9 + - + +
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Residues in contact with SER 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E VAL* 4.0 7.6 - - - +
91E ARG* 3.6 38.4 + - - -
92E HIS* 3.3 22.5 - - - -
278E CYS* 3.0 23.0 - - - +
279E PRO* 1.3 78.1 - - - +
281E ASN* 1.3 67.2 + - - +
282E LEU 3.4 0.4 - - - -
336E ARG* 3.5 16.9 + - - -
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Residues in contact with ASN 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ARG* 2.8 28.5 + - - +
227E GLU* 5.0 3.6 + - - -
228E ASP* 4.8 1.2 + - - -
231E ARG* 4.0 24.5 - - - +
274E TYR* 4.4 1.2 - - - +
276E LEU* 3.4 28.0 - - + +
278E CYS* 2.9 24.0 + - - +
280E SER* 1.3 88.6 + - - +
282E LEU* 1.3 63.1 + - - +
285E GLY* 3.0 24.7 + - - -
336E ARG* 4.0 11.5 + - - +
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Residues in contact with LEU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E TYR* 3.6 30.1 - - + +
88E ILE* 3.6 35.7 - - + -
92E HIS* 4.5 1.0 - - - +
272E LEU* 4.0 20.0 - - + +
274E TYR 3.8 6.7 - - - +
275E ILE* 4.4 3.8 - - + -
276E LEU 3.9 20.9 - - - +
278E CYS 4.3 2.7 - - - +
279E PRO* 3.3 24.9 - - + +
280E SER 3.4 3.4 + - - -
281E ASN* 1.3 84.2 - - - +
283E GLY* 1.3 60.5 + - - +
284E THR 3.0 7.6 + - - -
285E GLY 3.3 2.6 + - - -
336E ARG* 3.5 14.4 - - - +
337E LEU* 4.1 15.1 - - + +
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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