Contacts of the helix formed by residues 167 - 181 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C TYR* 4.2 19.1 - - + +
111C GLU* 5.2 1.8 - - - +
114C GLU* 3.3 35.0 - - + +
166D MET* 1.3 97.1 - - + +
168D PRO* 1.3 77.9 - - + +
169D LEU 3.6 0.9 - - - -
170D LEU* 3.8 12.1 + - + -
171D ARG* 3.1 22.3 + - - +
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Residues in contact with PRO 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU* 3.2 11.4 - - + +
167D PRO* 1.3 92.2 - - + +
169D LEU* 1.3 65.7 + - + +
171D ARG* 3.3 6.5 + - + +
172D GLN* 3.0 28.7 + - - +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLU* 2.7 25.3 + - - +
117C LEU* 3.6 19.4 - - + +
118C ALA* 3.5 40.6 - - + +
121C THR* 4.4 10.3 - - + +
127C LEU* 4.0 16.3 - - + +
168D PRO* 1.3 79.2 - - + +
170D LEU* 1.3 53.8 + - - +
172D GLN* 3.3 20.2 + - - +
173D ALA* 2.8 33.8 + - - +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 3.8 35.2 - - + +
113C LEU* 4.0 21.5 - - + -
114C GLU* 2.9 19.3 + - - +
117C LEU* 3.6 9.1 - - + +
166D MET* 3.7 24.9 - - + -
167D PRO* 4.1 8.7 - - + -
169D LEU* 1.3 75.6 - - - +
171D ARG* 1.3 66.0 + - - +
173D ALA* 3.4 2.8 + - + +
174D ILE* 3.2 34.6 + - + +
1F TRP* 4.8 5.6 - - + -
3F TRP* 4.2 22.4 - - + -
8F PHE* 5.2 1.3 - - + -
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Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 3.7 34.5 + - - -
165D SER* 5.5 3.0 - - - +
166D MET* 4.0 24.1 - - + +
167D PRO 3.1 20.2 + - - +
168D PRO* 3.4 6.7 - - + +
170D LEU* 1.3 74.7 - - - +
172D GLN* 1.3 65.0 + - - +
174D ILE* 2.9 16.2 + - - +
175D GLU* 3.0 35.9 + - + +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU* 4.1 30.1 - - + +
168D PRO 3.0 13.4 + - - +
169D LEU* 3.4 24.6 - - - +
171D ARG* 1.3 75.6 - - - +
173D ALA* 1.3 63.0 + - - +
175D GLU* 3.3 15.1 + - - +
176D LEU* 3.0 24.2 + - + +
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 4.2 7.6 - - + -
127C LEU* 4.1 5.5 - - + +
131C LEU* 3.8 35.2 - - + +
169D LEU 2.8 20.2 + - - +
170D LEU* 3.4 16.4 - - + +
171D ARG 3.1 0.2 + - - -
172D GLN* 1.3 74.2 - - - +
174D ILE* 1.3 57.8 + - + +
176D LEU* 3.3 4.3 + - - +
177D PHE* 3.0 34.2 + - + -
3F TRP* 4.8 1.1 - - + -
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 6.2 0.2 - - - +
166D MET* 3.3 42.2 - - + -
170D LEU* 3.2 15.4 + - + +
171D ARG* 2.9 8.2 + - - +
173D ALA* 1.3 75.2 - - + +
175D GLU* 1.3 61.1 + - + +
177D PHE* 3.7 13.1 - - + +
178D ASP* 2.8 31.0 + - + +
1F TRP* 5.6 2.2 - - + -
8F PHE* 3.5 48.2 - - + +
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ARG* 3.0 47.6 + - + +
172D GLN* 3.6 16.5 - - + +
174D ILE* 1.3 76.1 - - + +
176D LEU* 1.3 66.1 + - - +
178D ASP* 3.2 8.3 + - + +
179D HIS* 2.9 25.2 + - - +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU* 4.3 9.4 - - + -
128C GLU* 4.0 34.5 - - + +
131C LEU* 4.1 17.9 - - + -
132C TYR* 4.4 6.7 - - + +
172D GLN* 3.0 13.7 + - + +
173D ALA* 3.4 9.6 - - - +
175D GLU* 1.3 76.7 - - - +
177D PHE* 1.3 67.7 + - + +
179D HIS* 3.3 6.6 + - - +
180D GLN* 3.0 71.0 + - + +
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LEU* 3.5 37.0 - - + -
132C TYR* 5.3 2.9 - + - -
135C SER* 4.9 5.2 - - - -
173D ALA* 3.0 24.3 + - + +
174D ILE* 3.7 14.4 - - + +
176D LEU* 1.3 80.5 - - + +
178D ASP* 1.3 64.1 + - - +
180D GLN* 4.6 0.9 - - + -
181D GLY* 2.8 39.0 + - - +
185D ALA* 4.5 17.0 - - + -
1F TRP* 5.2 4.3 - + - -
3F TRP* 3.1 34.5 - + + -
4F ASN 4.4 3.6 - - - -
5F ALA* 3.5 44.5 - - + +
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ILE* 2.8 26.3 + - + +
175D GLU* 3.5 8.4 - - + +
177D PHE* 1.3 73.2 - - - +
179D HIS* 1.3 60.6 + - - +
181D GLY 4.9 0.2 + - - -
5F ALA 5.1 1.1 + - - -
9F ALA* 5.9 4.0 - - - +
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Residues in contact with HIS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D GLU 2.9 16.0 + - - +
176D LEU* 3.5 6.3 - - - +
177D PHE 3.1 0.2 - - - -
178D ASP* 1.3 79.7 - - - +
180D GLN* 1.3 75.4 + - + +
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Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLU* 5.1 3.8 - - - +
132C TYR* 2.3 39.0 + - - -
176D LEU* 3.0 45.3 + - + +
177D PHE* 4.6 2.1 - - - -
179D HIS* 1.3 90.2 - - + +
181D GLY* 1.3 72.8 + - - +
182D ALA 4.0 0.2 + - - -
183D GLU* 4.5 1.7 + - - +
184D PRO* 3.4 33.5 - - + +
185D ALA* 4.5 1.4 - - - +
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D PHE* 2.8 30.2 + - - -
178D ASP 4.8 0.6 + - - -
179D HIS 3.9 0.2 - - - -
180D GLN* 1.3 87.6 + - - +
182D ALA* 1.3 63.9 + - - -
183D GLU 3.7 0.2 + - - -
184D PRO* 4.0 1.0 - - - +
185D ALA* 4.8 1.4 + - - +
5F ALA* 3.3 16.6 - - - +
6F TYR* 4.3 13.2 - - - -
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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