Contacts of the helix formed by residues 179 - 185 (chain A) in PDB entry 5HNK
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 ASP 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU 5.4 0.5 - - - +
176A HIS* 3.2 24.5 + - - +
177A LEU 3.2 1.4 - - - -
178A ARG* 1.3 100.5 + - - +
180A MET* 1.3 62.9 + - - +
181A TYR 3.3 3.3 + - - -
182A GLU* 3.4 22.4 + - - +
183A HIS* 3.0 44.3 + - + +
222B ARG* 4.3 12.3 + - - -
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Residues in contact with MET 180 (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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157A ASP* 3.7 14.6 - - + +
160A LEU* 4.2 20.0 - - - -
176A HIS 3.9 1.1 + - - +
177A LEU* 3.2 18.5 + - + +
178A ARG 3.3 2.8 + - - -
179A ASP* 1.3 76.6 - - - +
181A TYR* 1.3 57.0 + - - +
183A HIS* 3.8 3.0 - - - +
184A HIS* 2.9 46.8 + - + -
186A VAL* 3.2 23.9 - - + +
187A ASP 3.7 11.2 - - - +
188A ASP* 4.1 11.4 - - - -
189A VAL* 4.0 15.5 - - + -
192A PHE* 3.5 44.2 - - + -
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Residues in contact with TYR 181 (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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178A ARG 5.1 0.6 + - - -
179A ASP 3.3 0.4 - - - -
180A MET* 1.3 73.4 - - - +
182A GLU* 1.3 63.9 + - - +
185A ASN* 2.9 58.2 + - + +
186A VAL 3.1 22.5 + - - +
187A ASP* 3.6 18.3 + - - +
215A LYS* 4.5 7.3 + - - +
218A TYR* 3.5 36.2 - + - -
181B TYR* 3.7 24.0 - + + -
182B GLU* 2.2 45.5 + - + -
183B HIS 5.1 0.2 - - - -
185B ASN* 3.4 21.9 - - - +
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Residues in contact with GLU 182 (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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173A ARG* 2.8 33.5 + - - -
179A ASP* 3.4 25.7 + - + +
181A TYR* 1.3 78.7 - - - +
183A HIS* 1.3 60.8 + - - +
185A ASN* 4.6 0.9 - - - +
181B TYR* 3.4 24.9 + - - +
185B ASN* 4.6 7.8 - - + +
215B LYS* 2.7 36.8 + - + +
218B TYR* 3.7 27.0 - - + -
219B ASN* 4.8 1.2 - - - +
222B ARG* 3.2 26.4 + - - -
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Residues in contact with HIS 183 (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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160A LEU* 6.2 0.9 - - + -
173A ARG* 3.6 32.8 + - - -
174A GLU 3.9 13.0 + - - -
175A TYR* 3.4 45.1 - + + -
176A HIS 4.4 3.8 + - - -
179A ASP* 3.0 40.4 + - + +
180A MET* 4.1 1.6 - - - +
181A TYR 3.2 0.6 - - - -
182A GLU* 1.3 89.9 + - - +
184A HIS* 1.3 85.3 + - + +
215B LYS* 3.0 22.2 + - - +
4X A 4.6 8.1 + - - -
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Residues in contact with HIS 184 (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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154A GLY* 4.0 15.9 - - - -
157A ASP* 2.5 32.7 + - + +
160A LEU* 5.8 0.2 - - + -
166A ARG* 4.8 2.5 - - - -
175A TYR* 5.4 1.3 - + - -
180A MET* 2.9 37.8 + - + +
183A HIS* 1.3 93.6 + + + +
185A ASN* 1.3 73.0 + - - +
186A VAL* 3.2 12.8 + - + +
192A PHE* 3.5 38.8 - + + -
195A LEU* 4.4 8.3 - - - +
214A ALA* 5.7 0.9 - - - +
215B LYS* 4.8 0.7 - - - +
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Residues in contact with ASN 185 (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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180A MET 3.7 0.2 + - - -
181A TYR* 2.9 46.3 + - + +
184A HIS* 1.3 79.0 - - - +
186A VAL* 1.3 65.1 + - - +
195A LEU* 4.8 1.6 - - + +
214A ALA* 5.0 19.4 - - + +
215A LYS* 4.9 16.0 - - + +
218A TYR* 3.6 14.4 - - + +
185B ASN* 3.0 35.1 - - - +
215B LYS* 4.6 10.8 + - - +
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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