Contacts of the helix formed by residues 176 - 180 (chain C) in PDB entry 3HYW
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 ILE 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU 4.9 0.2 - - - +
140C TYR* 3.8 37.9 - - + +
143C PRO* 4.1 17.5 - - + -
171C LEU* 2.9 35.7 + - + +
174C ARG* 3.7 21.3 - - + +
175C GLY* 1.3 82.4 - - - +
177C ARG* 1.3 60.0 + - - +
178C TYR* 3.2 7.9 - - - -
179C LYS* 2.9 38.0 + - + +
180C VAL* 3.4 8.7 + - + +
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Residues in contact with ARG 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C HIS* 3.1 31.3 + - + +
171C LEU* 3.3 27.3 + - - +
172C LYS* 3.8 13.2 - - - +
176C ILE* 1.3 76.3 - - - +
178C TYR* 1.3 56.4 + - - +
179C LYS 3.1 0.2 - - - -
180C VAL* 2.8 40.6 + - - +
182C MET* 3.5 34.0 - - - +
213C ARG 3.0 27.5 + - - -
214C ASN* 3.5 15.0 + - - +
215C ILE* 4.4 0.6 - - - +
366E PRO* 3.5 19.2 - - - +
367E ARG 3.6 19.6 + - - +
368E GLU* 3.5 21.1 + - - +
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C GLY 3.4 21.3 - - - -
176C ILE 3.2 1.0 - - - -
177C ARG* 1.3 74.2 - - - +
179C LYS* 1.3 88.1 + - + +
180C VAL 3.5 0.4 - - - -
342E ARG* 3.5 30.5 - - - +
362E PRO* 3.8 19.1 - - + -
366E PRO* 3.3 25.6 - - - +
368E GLU* 3.0 24.8 + - - +
417E GLU* 2.8 27.1 + - - -
429E ARG* 2.7 59.5 + - + -
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.6 40.5 - - + +
144C GLY* 4.2 1.0 + - - -
176C ILE* 2.9 21.5 + - + +
178C TYR* 1.3 116.5 + - + +
180C VAL* 1.3 59.3 + - - +
181C PRO* 3.6 9.9 - - - +
366E PRO* 4.2 0.9 - - - -
417E GLU* 5.2 1.0 + - - -
429E ARG* 4.0 20.8 - - + +
430E CYS* 3.2 29.7 + - - +
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Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.5 3.6 - - + -
143C PRO* 3.6 22.9 - - + -
144C GLY 3.4 17.7 - - - +
146C VAL* 3.5 25.4 - - + -
171C LEU* 3.7 37.2 - - + -
176C ILE* 3.5 14.4 - - + +
177C ARG* 2.8 30.7 + - - +
178C TYR 3.5 0.6 - - - -
179C LYS* 1.3 85.0 - - - +
181C PRO* 1.3 64.3 - - - +
182C MET* 4.4 0.9 - - + -
366E PRO* 3.6 3.1 - - - -
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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