Contacts of the helix formed by residues 167 - 181 (chain C) in PDB entry 2NS8
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 PRO 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C SER 3.7 3.1 - - - +
166C MET* 1.3 91.5 - - + +
168C PRO* 1.3 79.6 - - + +
169C LEU 3.5 0.7 - - - -
170C LEU* 3.3 10.5 + - + -
171C ARG* 3.1 17.2 + - - +
110D TYR* 3.8 31.4 - - + +
111D GLU* 5.0 1.3 - - - +
114D GLU* 3.4 31.0 - - + -
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Residues in contact with PRO 168 (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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166C MET 4.7 0.2 - - - +
167C PRO* 1.3 90.6 - - + +
169C LEU* 1.3 66.6 + - + +
171C ARG* 3.4 9.1 + - + +
172C GLN* 3.2 31.7 + - - +
114D GLU* 3.6 8.7 - - - +
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Residues in contact with LEU 169 (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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168C PRO* 1.3 81.7 - - + +
170C LEU* 1.3 61.1 + - - +
172C GLN* 3.4 23.3 + - - +
173C ALA* 2.9 26.2 + - - +
114D GLU* 3.2 21.4 + - - +
117D LEU* 3.7 16.9 - - + +
118D ALA* 3.7 37.9 - - + +
121D THR* 4.2 11.0 - - + +
127D LEU* 4.4 17.1 - - + +
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Residues in contact with LEU 170 (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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166C MET* 3.8 22.2 - - + -
167C PRO* 3.3 12.8 + - + +
169C LEU* 1.3 73.6 - - - +
171C ARG* 1.3 57.3 + - - +
173C ALA* 3.0 4.1 + - + +
174C ILE* 2.7 50.7 + - + +
110D TYR* 4.0 38.1 - - + +
113D LEU* 4.5 14.8 - - + -
114D GLU* 2.9 18.4 + - + +
117D LEU* 3.9 7.4 - - + +
1G TRP* 5.0 2.5 - - + -
3G TRP* 4.0 28.3 - - + -
8G PHE* 5.5 2.9 - - + -
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Residues in contact with ARG 171 (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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163C THR* 3.4 27.9 + - - +
164C ASP* 3.7 32.9 + - - +
166C MET* 4.2 21.9 + - + +
167C PRO 3.1 11.1 + - - +
168C PRO* 3.6 12.5 - - - +
170C LEU* 1.3 79.6 - - - +
172C GLN* 1.3 52.6 + - - +
174C ILE* 3.2 7.6 + - + +
175C GLU* 2.8 55.6 + - + +
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Residues in contact with GLN 172 (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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168C PRO* 3.2 17.8 + - - +
169C LEU* 3.5 26.2 - - - +
171C ARG* 1.3 79.4 - - + +
173C ALA* 1.3 61.4 + - - +
175C GLU* 3.5 15.6 + - - +
176C LEU* 3.1 23.4 + - - +
127D LEU* 4.4 17.7 - - + +
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Residues in contact with ALA 173 (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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169C LEU 2.9 15.3 + - - +
170C LEU* 3.0 18.6 + - + +
172C GLN* 1.3 73.2 - - - +
174C ILE* 1.3 69.0 + - + +
176C LEU* 3.1 7.2 + - - +
177C PHE* 3.0 24.5 + - + -
117D LEU* 4.2 8.7 - - + -
127D LEU* 4.2 2.2 - - + +
131D LEU* 3.7 39.6 - - + +
3G TRP* 4.6 0.4 - - + -
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Residues in contact with ILE 174 (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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163C THR* 5.1 12.1 - - - +
166C MET* 4.6 9.0 - - + -
170C LEU* 2.7 43.0 + - + +
171C ARG* 3.7 8.5 - - + +
173C ALA* 1.3 74.7 - - + +
175C GLU* 1.3 71.3 + - + +
177C PHE* 2.9 29.1 + - + +
178C ASP* 2.8 21.5 + - + +
1G TRP* 4.8 4.3 - - + -
8G PHE* 3.7 48.9 - - + +
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Residues in contact with GLU 175 (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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163C THR* 5.9 1.3 - - - +
171C ARG* 2.8 41.8 + - + +
172C GLN* 3.8 16.8 + - - +
174C ILE* 1.3 76.1 - - + +
176C LEU* 1.3 65.8 + - - +
178C ASP* 3.0 17.6 - - - +
179C HIS* 3.1 15.1 + - - +
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Residues in contact with LEU 176 (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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172C GLN 3.1 13.5 + - - +
173C ALA* 3.2 11.2 - - - +
175C GLU* 1.3 74.4 - - - +
177C PHE* 1.3 61.3 + - + +
179C HIS* 3.0 22.0 + - + +
180C GLN* 2.8 69.5 + - - +
127D LEU* 5.3 4.0 - - + -
128D GLU* 3.7 33.4 - - + +
131D LEU* 4.0 20.9 - - + -
132D TYR* 4.3 1.3 - - + +
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Residues in contact with PHE 177 (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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173C ALA* 3.0 14.8 + - + -
174C ILE* 2.9 21.6 + - + +
176C LEU* 1.3 80.7 - - + +
178C ASP* 1.3 54.6 + - - +
180C GLN* 3.1 13.2 + - - -
181C GLY* 2.5 41.6 + - - -
185C ALA* 5.1 8.1 - - + -
131D LEU* 3.4 42.2 - - + -
132D TYR* 4.9 7.9 - + - -
135D SER* 5.3 2.5 - - - -
1G TRP* 4.9 5.2 - + - -
3G TRP* 3.1 40.2 - + + -
4G ASN 4.5 2.7 - - - -
5G ALA* 3.4 38.8 - - + +
8G PHE* 6.3 0.2 - + - -
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Residues in contact with ASP 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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174C ILE* 2.8 23.2 + - - +
175C GLU* 3.0 14.6 - - - +
177C PHE* 1.3 72.1 - - - +
179C HIS* 1.3 62.3 + - - +
181C GLY* 4.6 1.8 - - - +
5G ALA 4.6 4.7 + - - +
8G PHE 6.0 1.3 - - - +
9G ALA* 5.9 10.1 - - + -
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Residues in contact with HIS 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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175C GLU 3.1 14.5 + - - +
176C LEU* 3.0 29.6 + - + +
178C ASP* 1.3 78.0 - - - +
180C GLN* 1.3 61.6 + - + +
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Residues in contact with GLN 180 (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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176C LEU* 2.8 52.4 + - - +
177C PHE* 4.1 6.7 - - - +
179C HIS* 1.3 85.8 + - + +
181C GLY* 1.3 71.2 + - - +
182C ALA 3.9 0.3 + - - -
183C GLU* 4.5 1.0 + - - +
184C PRO* 3.5 28.1 - - + +
185C ALA* 5.8 0.2 - - - +
128D GLU* 4.0 3.8 - - - +
132D TYR* 2.5 41.0 + - - -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PHE* 2.5 27.8 + - - +
178C ASP* 4.6 1.9 - - - +
179C HIS 3.9 0.8 - - - -
180C GLN* 1.3 83.5 + - - +
182C ALA* 1.3 61.5 + - - -
183C GLU 3.8 0.2 + - - -
184C PRO* 3.8 1.4 - - - +
185C ALA* 5.0 2.3 + - - +
5G ALA* 3.5 17.7 - - - +
6G TYR* 4.2 14.8 - - - -
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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