Contacts of the helix formed by residues 164 - 178 (chain D) in PDB entry 2OV2
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 GLY 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D LEU* 5.8 0.4 - - - -
155D LEU* 5.6 0.5 - - - +
156D GLU 3.9 12.4 - - - +
157D CYS* 3.7 4.7 - - - +
162D GLN 3.2 1.8 + - - -
163D ARG* 1.3 74.6 - - - +
165D LEU* 1.3 60.9 + - - +
166D LYS 3.6 1.8 - - - -
167D THR* 3.5 15.9 + - - -
168D VAL* 3.3 25.3 + - - +
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Residues in contact with LEU 165 (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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19D LEU* 3.8 37.9 - - + +
22D SER* 3.2 33.4 - - - +
23D TYR* 3.8 16.6 - - + +
157D CYS* 4.0 8.7 - - + -
158D SER 4.0 2.9 - - - +
159D ALA* 4.2 7.2 - - - +
162D GLN* 3.2 39.8 + - + +
163D ARG 3.1 1.8 - - - -
164D GLY* 1.3 73.8 - - - +
166D LYS* 1.3 66.1 + - - +
168D VAL* 3.2 12.7 + - - +
169D PHE* 3.3 30.7 - - + -
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Residues in contact with LYS 166 (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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23D TYR* 4.3 19.7 - - + -
162D GLN 4.5 2.2 + - - -
165D LEU* 1.3 78.6 - - - +
167D THR* 1.3 58.3 + - - +
169D PHE* 3.2 4.3 + - - +
170D ASP* 2.6 59.5 + - - +
11L ILE* 3.0 27.3 + - - +
12L SER* 4.0 16.4 - - - +
13L ALA* 4.2 9.4 - - + +
14L PRO* 6.0 0.2 - - + -
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Residues in contact with THR 167 (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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155D LEU* 4.2 15.7 - - + -
164D GLY* 3.5 17.0 + - - -
165D LEU 3.2 0.6 - - - -
166D LYS* 1.3 75.9 - - - +
168D VAL* 1.3 67.3 + - - +
170D ASP* 3.6 10.4 + - + +
171D GLU* 2.8 42.7 + - + +
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Residues in contact with VAL 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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19D LEU* 5.1 2.0 - - + -
79D LEU* 3.9 24.0 - - + -
111D LEU* 3.9 3.6 - - - +
113D VAL* 4.0 32.3 - - + -
155D LEU* 3.6 24.7 - - + -
157D CYS* 4.0 14.8 - - + -
164D GLY 3.3 14.1 + - - +
165D LEU* 3.2 9.8 + - - +
166D LYS 3.2 0.2 - - - -
167D THR* 1.3 78.8 - - - +
169D PHE* 1.3 74.6 + - + +
171D GLU* 3.5 3.1 + - - +
172D ALA* 3.0 24.8 + - - +
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Residues in contact with PHE 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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6D CYS* 5.1 2.5 - - - -
19D LEU* 4.1 15.3 - - + -
20D LEU* 3.8 31.0 - - + -
23D TYR* 3.4 67.8 - + + +
53D LEU* 4.9 4.0 - - + -
55D LEU* 4.1 12.8 - - + -
79D LEU* 4.0 18.2 - - + -
165D LEU* 3.3 28.9 - - + -
166D LYS 3.2 2.0 + - - +
168D VAL* 1.3 83.7 - - + +
170D ASP* 1.3 61.8 + - - +
171D GLU 3.2 0.4 - - - -
172D ALA* 3.2 8.7 + - + +
173D ILE* 2.9 39.6 + - + +
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Residues in contact with ASP 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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23D TYR* 4.8 4.2 + - - -
166D LYS* 2.6 60.4 + - - +
167D THR* 3.6 10.5 + - + +
169D PHE* 1.3 76.2 - - - +
171D GLU* 1.3 59.5 + - + +
173D ILE* 3.4 0.8 + - - -
174D ARG* 3.0 30.1 + - - +
11L ILE* 3.6 41.7 - - + +
12L SER 4.8 0.7 - - - +
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Residues in contact with GLU 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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111D LEU* 3.7 9.5 - - + +
153D LYS* 3.9 22.7 - - + +
155D LEU* 3.7 29.6 - - + -
167D THR* 2.8 36.8 + - + +
170D ASP* 1.3 72.0 - - + +
172D ALA* 1.3 55.7 + - - +
174D ARG* 3.3 21.9 + - - +
175D ALA* 2.8 35.3 + - - +
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Residues in contact with ALA 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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4D ILE* 5.8 0.7 - - + -
6D CYS* 5.0 5.8 - - + -
77D VAL* 4.1 15.3 - - + +
79D LEU* 4.2 22.2 - - + -
111D LEU* 3.6 14.0 - - + +
168D VAL 3.0 17.4 + - - +
169D PHE* 3.2 12.5 + - + +
171D GLU* 1.3 75.9 - - - +
173D ILE* 1.3 63.0 + - + +
175D ALA* 3.3 10.7 + - - +
176D VAL* 3.4 17.3 + - - +
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Residues in contact with ILE 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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4D ILE* 3.8 21.5 - - + -
23D TYR* 4.6 7.9 - - - +
44D VAL* 4.1 15.7 - - + -
46D VAL* 3.8 16.4 - - + -
51D VAL* 5.9 1.1 - - + -
53D LEU* 4.3 18.8 - - + -
169D PHE* 2.9 25.2 + - + +
170D ASP 3.7 3.6 - - - +
172D ALA* 1.3 74.4 - - + +
174D ARG* 1.3 53.4 + - - +
176D VAL* 2.9 7.1 + - - +
177D LEU* 2.8 57.6 + - + +
11L ILE* 3.9 32.1 - - + -
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Residues in contact with ARG 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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170D ASP 3.0 18.0 + - - +
171D GLU* 3.5 26.9 - - - +
173D ILE* 1.3 77.4 - - - +
175D ALA* 1.3 57.3 + - - +
177D LEU* 5.1 0.9 - - - -
178D GLY* 2.7 53.4 + - - +
11L ILE* 5.0 8.1 - - + -
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Residues in contact with ALA 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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77D VAL* 4.6 1.6 - - + -
109D PRO* 4.2 25.4 - - + +
111D LEU* 4.1 19.3 - - + -
152D VAL* 4.6 17.7 - - + -
171D GLU 2.8 20.4 + - - +
172D ALA 3.5 7.4 - - - +
173D ILE 3.2 0.4 - - - -
174D ARG* 1.3 72.2 - - - +
176D VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 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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3D ALA 5.4 1.3 - - - +
4D ILE* 3.8 19.3 - - + -
76D ASP* 3.7 46.7 - - + +
77D VAL* 3.9 11.4 - - + -
109D PRO* 5.1 1.1 - - + -
172D ALA 3.4 14.3 + - - +
173D ILE 2.9 6.8 + - - +
175D ALA* 1.3 80.8 - - - +
177D LEU* 1.3 75.9 + - + +
178D GLY 3.6 0.7 - - - -
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Residues in contact with LEU 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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2D GLN* 3.9 24.5 - - + -
3D ALA 5.4 1.1 - - - +
4D ILE* 3.9 13.5 - - + -
46D VAL* 4.2 14.1 - - + -
51D VAL* 4.0 24.2 - - + -
173D ILE* 2.8 36.8 + - + +
174D ARG* 5.1 0.2 - - - -
176D VAL* 1.3 90.0 - - + +
178D GLY* 1.3 67.1 + - - +
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Residues in contact with GLY 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 ARG* 2.7 54.8 + - - +
175D ALA 4.7 0.2 - - - -
176D VAL 3.6 0.8 - - - -
177D LEU* 1.3 78.3 - - - +
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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