Contacts of the helix formed by residues 176 - 183 (chain F) in PDB entry 2NYM
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 THR 176 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174F ILE* 3.7 8.9 - - - +
175F ASP* 1.3 84.6 - - + +
177F LEU* 1.3 65.1 + - - +
178F ASP* 3.2 14.3 + - - +
179F HIS* 3.0 48.7 + - + +
180F ILE 3.6 2.4 + - - -
228F PHE* 4.8 1.3 - - - -
231F ALA* 6.1 2.5 - - + -
232F ASN* 3.1 12.3 - - - +
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Residues in contact with LEU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 4.2 11.1 - - + +
158F LEU* 3.9 31.0 - - + -
164F PHE* 3.7 35.4 - - + -
176F THR* 1.3 70.6 - - - +
178F ASP* 1.3 66.3 + - - +
180F ILE* 3.0 11.9 + - + +
181F ARG* 3.0 44.3 + - - +
228F PHE* 4.3 12.6 - - + -
232F ASN* 2.7 34.9 + - + +
234F LEU* 4.7 6.1 - - + -
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Residues in contact with ASP 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F THR* 3.1 11.3 + - - +
177F LEU* 1.3 75.2 + - - +
179F HIS* 1.3 67.6 + - - +
180F ILE 2.9 1.8 - - - -
181F ARG* 2.8 38.6 + - + +
182F ALA* 3.0 14.5 + - - +
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Residues in contact with HIS 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F SER 4.5 10.3 + - - +
174F ILE* 4.2 10.8 - - + +
175F ASP* 3.4 31.3 + - + +
176F THR* 3.0 52.8 + - + +
178F ASP* 1.3 76.1 - - - +
180F ILE* 1.3 59.0 + - - +
182F ALA* 3.5 16.7 - - - +
183F LEU* 3.7 11.4 + - - +
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Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASN* 3.9 17.6 - - + +
45F VAL* 3.8 18.6 - - + -
155F LEU* 4.8 4.0 - - + -
156F THR* 4.4 4.3 - - - +
164F PHE* 4.0 23.3 - - + -
174F ILE* 3.4 38.1 - - + -
176F THR 4.0 4.5 - - - +
177F LEU* 3.0 12.7 + - + +
178F ASP 2.8 1.0 + - - -
179F HIS* 1.3 74.1 - - - +
181F ARG* 1.3 58.1 + - - +
182F ALA 2.8 11.5 + - - -
183F LEU* 3.0 23.6 + - + +
198F LEU* 3.9 33.9 - - + -
228F PHE* 4.9 2.2 - - + -
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Residues in contact with ARG 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F SER* 5.4 8.4 + - - -
44F ASN* 4.3 16.9 - - - +
45F VAL* 4.2 36.6 + - + +
47F GLU* 5.9 4.2 + - - +
158F LEU* 5.4 4.2 - - - +
177F LEU* 3.0 41.9 + - - +
178F ASP* 2.8 38.2 + - + +
180F ILE* 1.3 71.3 - - - +
182F ALA* 1.3 58.6 + - - +
183F LEU 3.5 4.5 - - - +
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F ASP 3.0 8.5 + - - +
179F HIS* 3.5 14.4 - - - +
180F ILE 2.8 0.6 - - - -
181F ARG* 1.3 77.8 - - - +
183F LEU* 1.3 68.8 + - - +
184F ASP* 5.1 0.9 - - - +
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Residues in contact with LEU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASN* 3.8 16.9 + - - +
155F LEU* 4.6 7.0 - - + -
174F ILE* 3.7 18.4 - - + -
179F HIS 3.9 9.4 - - - +
180F ILE* 3.0 18.4 + - + +
181F ARG 4.0 4.7 - - - +
182F ALA* 1.3 84.6 - - - +
184F ASP* 1.3 64.0 + - - +
185F ARG 3.8 0.9 - - - +
194F PRO* 3.1 44.6 - - + -
195F MET* 3.8 16.8 - - + +
198F LEU* 4.4 5.4 - - + -
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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