Contacts of the helix formed by residues 179 - 187 (chain R) in PDB entry 3SN6
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 GLN 179 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180R GLU* 1.3 70.0 + - - +
181R ALA* 3.0 9.2 + - - +
182R ILE* 3.5 17.7 + - - +
183R ASN* 2.9 43.2 + - - +
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Residues in contact with GLU 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R GLN* 1.3 79.5 - - - +
181R ALA* 1.3 57.0 + - - +
183R ASN* 3.5 9.5 - - - +
184R CYS* 3.0 32.8 + - + +
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Residues in contact with ALA 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R ARG 5.9 2.9 - - - +
179R GLN 3.0 7.3 - - - +
180R GLU* 1.3 75.9 - - - +
182R ILE* 1.3 72.1 + - + +
183R ASN 3.0 1.6 + - - -
184R CYS* 3.2 3.8 + - - +
185R TYR* 2.9 48.0 + - + -
194R PHE* 4.5 15.7 - - + -
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Residues in contact with ILE 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175R ARG* 6.0 6.1 - - + +
179R GLN* 3.5 20.6 + - - +
181R ALA* 1.3 79.5 - - + +
183R ASN* 1.3 57.8 - - - +
185R TYR* 3.7 12.2 - - + +
186R ALA* 2.9 40.6 + - + +
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Residues in contact with ASN 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179R GLN* 2.9 50.2 + - - +
180R GLU* 3.5 8.4 - - - +
181R ALA 3.0 1.0 - - - -
182R ILE* 1.3 79.2 - - - +
184R CYS* 1.3 58.1 + - - +
186R ALA* 4.0 1.7 - - - +
187R GLU* 3.0 30.4 + - - +
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Residues in contact with CYS 184 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R ASN* 4.6 0.3 - - - +
180R GLU* 3.0 20.1 + - + +
181R ALA* 4.1 2.0 - - - +
183R ASN* 1.3 73.6 - - - +
185R TYR* 1.3 67.4 + - + +
187R GLU* 2.9 21.4 + - - +
190R CYS* 2.0 79.3 - - - +
192R ASP* 3.5 27.4 - - + +
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Residues in contact with TYR 185 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R ASN* 2.9 25.5 + - - +
174R TYR* 3.9 27.4 + + - -
175R ARG* 4.2 25.3 - - + -
181R ALA* 2.9 40.8 + - + +
182R ILE* 3.7 12.8 - - + +
184R CYS* 1.3 79.0 - - + +
186R ALA* 1.3 64.1 + - - +
187R GLU 3.0 0.9 + - - -
192R ASP 4.4 16.8 - - - -
194R PHE* 2.5 41.7 + - + +
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Residues in contact with ALA 186 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R ASN* 3.1 13.4 + - - +
182R ILE* 2.9 25.2 + - + +
183R ASN* 4.3 2.0 - - - +
185R TYR* 1.3 77.7 - - - +
187R GLU* 1.3 56.7 + - - +
188R GLU* 3.4 5.4 + - - +
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Residues in contact with GLU 187 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R ASN* 3.0 10.4 + - - +
183R ASN 3.0 21.5 + - - +
184R CYS* 2.9 23.4 - - - +
185R TYR 3.0 1.3 - - - +
186R ALA* 1.3 76.2 - - - +
188R GLU* 1.3 74.8 + - - +
189R THR* 3.4 8.8 + - - +
190R CYS* 3.8 21.9 + - + +
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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