Contacts of the helix formed by residues 279 - 286 (chain A) in PDB entry 3KQ4
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 THR 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.5 12.2 - - - +
178A LEU* 4.4 5.6 - - + -
231A GLN* 3.0 44.0 - - + +
234A SER* 4.5 5.4 - - - +
235A VAL* 3.9 16.1 - - + +
278A LYS* 1.3 77.4 - - - +
280A TYR* 1.3 58.1 + - - +
281A LEU* 2.7 33.2 + - - +
282A ASP* 2.8 32.8 + - - +
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Residues in contact with TYR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.8 22.2 + - - -
59A ILE* 4.0 30.3 - - + -
63A LEU* 4.7 3.8 - - + -
94A LEU* 5.0 9.2 - - + -
97A MET* 4.6 12.1 - - + +
137A LEU* 4.8 6.1 - - + -
140A LEU* 4.0 22.4 - - + -
144A GLN* 3.2 17.4 + - - +
175A MET* 3.4 36.6 - - + -
178A LEU* 4.4 9.6 - - + +
228A LEU* 4.7 3.3 - - + +
231A GLN* 2.9 29.5 + - - +
269A ALA 4.0 13.3 + - - -
270A GLN* 4.0 12.3 + - - +
273A PRO* 4.3 11.9 - - + -
279A THR* 1.3 71.8 - - - +
281A LEU* 1.3 58.4 + - - +
282A ASP 3.2 1.7 + - - -
283A VAL* 3.4 18.3 - - + +
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Residues in contact with LEU 281 (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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140A LEU* 4.0 13.5 - - + -
144A GLN* 3.7 13.2 + - + +
178A LEU* 4.0 21.8 - - + +
181A THR* 4.4 9.4 - - + -
182A CYS* 3.7 31.2 - - + +
185A ASN* 6.1 0.2 - - - +
235A VAL* 3.6 39.3 - - + -
279A THR* 2.7 14.6 + - - +
280A TYR* 1.3 78.4 - - - +
282A ASP* 1.3 59.0 + - - +
283A VAL 3.2 1.9 + - - -
284A PRO* 3.8 3.3 - - - +
285A GLN* 3.7 10.4 + - - -
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Residues in contact with ASP 282 (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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63A LEU* 4.1 11.1 - - + +
277A GLY 4.8 0.5 - - - +
278A LYS* 3.4 24.2 - - + +
279A THR* 2.8 39.6 + - - +
281A LEU* 1.3 78.9 - - - +
283A VAL* 1.3 65.1 + - - +
284A PRO 3.3 2.7 - - - -
285A GLN* 3.0 29.7 + - + +
286A VAL* 3.5 10.4 + - - +
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Residues in contact with VAL 283 (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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59A ILE* 3.7 31.2 - - + -
63A LEU* 4.1 9.0 - - + -
97A MET* 3.7 30.5 - - + +
100A THR* 3.9 17.9 - - + +
101A SER* 4.4 11.9 - - - -
144A GLN* 3.9 9.9 - - - +
279A THR 4.2 0.2 + - - -
280A TYR* 3.4 17.9 - - - +
281A LEU 3.2 0.2 - - - -
282A ASP* 1.3 78.3 - - - +
284A PRO* 1.3 77.8 - - + +
286A VAL* 3.0 26.7 + - - +
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Residues in contact with PRO 284 (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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100A THR* 4.6 10.5 - - + -
144A GLN* 2.9 54.7 - - + +
145A LYS* 5.9 1.3 - - - +
281A LEU 3.8 4.3 - - - +
282A ASP 3.7 2.0 - - - -
283A VAL* 1.3 90.3 - - + +
285A GLN* 1.3 73.1 + - - +
286A VAL 3.8 3.5 + - - +
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Residues in contact with GLN 285 (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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281A LEU 3.7 7.7 + - - -
282A ASP* 3.0 36.3 + - + +
284A PRO* 1.3 91.9 - - - +
286A VAL* 1.3 67.9 + - - +
287A THR* 3.3 8.5 + - - -
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Residues in contact with VAL 286 (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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62A ASN* 3.7 22.2 - - + +
63A LEU* 3.8 23.3 - - + -
100A THR 5.2 0.9 - - - +
101A SER* 3.2 42.8 - - - +
103A CYS* 4.4 10.4 - - - -
282A ASP 3.5 2.1 + - - +
283A VAL* 3.0 22.7 + - - +
284A PRO 3.4 3.1 - - - +
285A GLN* 1.3 79.2 - - - +
287A THR* 1.3 73.0 + - - +
288A CYS* 4.6 2.2 - - - -
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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