Contacts of the helix formed by residues 180 - 185 (chain X) in PDB entry 1KKC
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 TYR 180 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X ILE* 4.1 8.1 - - - -
175X MET* 3.7 18.1 + - + +
176X TRP 3.5 20.9 - - - -
177X GLU* 3.0 22.9 + - - +
178X HIS 3.3 1.0 + - - -
179X ALA* 1.3 81.6 - - - +
181X TYR* 1.3 66.8 + + - +
182X LEU 3.4 2.9 - - - -
183X GLN 3.1 4.0 + - - -
184X TYR* 2.7 44.9 + - + +
185X LEU 3.3 23.1 - - - -
186X ASN* 4.7 2.7 + - - -
188X LYS* 3.7 41.0 - - + +
191X TYR* 3.5 45.1 - + + -
44Y HIS* 6.1 0.5 - - - -
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Residues in contact with TYR 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X GLU* 2.8 39.2 + - + +
178X HIS 4.6 0.6 - - - -
180X TYR* 1.3 77.9 - + - +
182X LEU* 1.3 61.2 + - - +
185X LEU* 2.7 64.9 + - - +
186X ASN* 3.6 4.9 + - - -
39Y LEU* 3.7 16.5 - - + +
40Y HIS 5.1 0.2 + - - -
44Y HIS* 2.6 39.4 + + - -
178Y HIS* 3.7 26.6 + - + +
181Y TYR* 4.9 16.2 - - + -
182Y LEU* 3.7 39.9 - - + -
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Residues in contact with LEU 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X SER* 5.3 0.7 - - - +
35X GLN* 3.6 32.6 + - + +
36X ILE* 4.0 21.2 - - + +
39X LEU* 3.4 32.8 - - + -
178X HIS 5.7 1.2 + - - +
180X TYR 3.3 0.8 + - - -
181X TYR* 1.3 78.0 - - - +
183X GLN* 1.3 59.9 + - - +
185X LEU* 4.5 6.6 - - - +
181Y TYR* 3.7 24.8 - - + +
182Y LEU* 4.1 24.1 - - + +
185Y LEU* 3.6 21.8 - - + -
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Residues in contact with GLN 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X PRO 3.0 25.2 + - - +
32X ILE* 3.4 7.4 - - - -
33X SER* 2.9 37.7 + - - +
36X ILE* 3.6 15.7 - - + +
180X TYR 3.1 2.0 + - - -
181X TYR 3.1 0.2 - - - -
182X LEU* 1.3 81.6 - - - +
184X TYR* 1.3 92.9 + - + +
185X LEU* 3.5 5.6 - - - +
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Residues in contact with TYR 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X PRO 4.1 0.5 + - - -
31X TYR* 2.5 38.6 + - - +
32X ILE* 5.2 0.9 - - + -
36X ILE* 5.5 0.9 - - + -
180X TYR* 2.7 34.9 + - + +
183X GLN* 1.3 100.6 + - + +
185X LEU* 1.3 70.4 + - - +
187X ASP* 3.0 32.6 + - + +
190X SER* 3.6 30.5 + - - -
191X TYR* 3.6 38.8 + + + -
194X GLY* 4.6 6.9 - - - -
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Residues in contact with LEU 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X TYR* 3.3 13.5 - - - -
181X TYR* 2.7 55.1 + - - +
182X LEU 4.5 6.3 - - - +
183X GLN 4.7 4.3 - - - +
184X TYR* 1.3 78.5 - - - +
186X ASN* 1.3 70.8 + - - +
35Y GLN* 4.2 10.3 - - + +
39Y LEU* 4.2 22.0 - - + -
182Y LEU* 4.0 29.6 - - + -
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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