Contacts of the helix formed by residues 180 - 185 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36Y ILE* 3.9 8.5 - - - +
175Y MET* 3.6 17.7 + - + -
176Y TRP 3.4 22.0 - - - -
177Y GLU* 3.0 25.5 + - + +
178Y HIS 3.2 1.4 + - - -
179Y ALA* 1.3 82.4 - - - +
181Y TYR* 1.3 71.0 + + - +
182Y LEU 3.3 3.1 - - - -
183Y GLN* 3.0 4.8 + - - -
184Y TYR* 2.8 39.6 + - + +
185Y LEU 3.2 23.6 - - - -
186Y ASN* 4.8 3.1 + - - -
188Y LYS* 3.7 38.9 - - + +
191Y TYR* 3.5 44.0 - + + -
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Residues in contact with TYR 181 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X LEU* 3.8 16.5 - - - +
44X HIS* 2.7 39.5 + + - -
178X HIS* 3.6 32.9 + - + +
181X TYR* 4.9 18.2 - - + -
182X LEU* 3.7 35.2 - - + -
177Y GLU* 2.8 37.3 + - + +
178Y HIS 4.6 0.8 - - - -
180Y TYR* 1.3 77.7 - + - +
182Y LEU* 1.3 60.6 + - - +
185Y LEU* 2.8 64.4 + - + +
186Y ASN* 3.6 3.8 + - - +
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Residues in contact with LEU 182 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X TYR* 3.7 28.2 - - + +
182X LEU* 4.1 24.6 - - + +
185X LEU* 4.0 18.2 - - + -
33Y SER* 5.2 0.4 - - - +
35Y GLN* 3.6 32.8 + - + +
36Y ILE* 3.9 20.6 - - + +
39Y LEU* 3.5 32.8 - - + -
178Y HIS 5.7 1.0 + - - +
180Y TYR 3.2 1.4 + - - -
181Y TYR* 1.3 77.0 - - - +
183Y GLN* 1.3 59.7 + - - +
185Y LEU* 4.6 6.8 - - - +
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Residues in contact with GLN 183 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y PRO 2.8 25.9 + - - +
31Y TYR 3.5 0.4 + - - +
32Y ILE* 3.4 6.8 + - - -
33Y SER* 2.8 41.0 + - - +
36Y ILE* 3.7 15.8 - - + +
180Y TYR 3.0 2.6 + - - +
182Y LEU* 1.3 81.5 - - - +
184Y TYR* 1.3 94.7 + - + +
185Y LEU* 3.5 5.3 + - - +
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Residues in contact with TYR 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y PRO 4.0 0.3 + - - -
31Y TYR* 2.6 39.3 + - - +
32Y ILE* 5.3 0.7 - - + -
36Y ILE* 5.6 1.3 - - + -
180Y TYR* 2.8 28.7 + - + +
183Y GLN* 1.3 102.2 + - + +
185Y LEU* 1.3 72.4 + - - +
187Y ASP* 2.9 37.6 + - + +
190Y SER* 3.7 30.7 + - - -
191Y TYR* 3.6 40.3 + + + -
194Y GLY* 4.5 7.7 - - - -
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Residues in contact with LEU 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X GLN* 4.4 10.5 - - - +
39X LEU* 3.9 20.2 - - + -
182X LEU* 3.6 36.1 - - + -
180Y TYR* 3.2 24.8 - - - -
181Y TYR* 2.8 44.6 + - + +
182Y LEU 4.6 4.7 - - - +
183Y GLN 4.7 5.4 - - - +
184Y TYR* 1.3 82.1 - - - +
186Y ASN* 1.3 67.1 + - - +
187Y ASP 3.3 0.2 + - - -
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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