Contacts of the helix formed by residues 179 - 187 (chain A) in PDB entry 1NVP
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 ASP 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 1.3 70.2 - - - +
180A LEU* 1.3 62.2 + - - +
181A LYS* 3.3 18.4 + - - +
182A THR* 2.7 26.8 + - - -
183A ILE* 3.4 21.7 + - - +
246A PHE* 3.5 24.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 3.3 6.5 + - + -
179A ASP* 1.3 70.8 + - - +
181A LYS* 1.3 65.3 + - - +
183A ILE* 3.4 17.6 + - + +
184A ALA* 2.9 24.8 + - - +
192A TYR* 3.6 30.7 - - + +
198A ALA 3.3 27.1 - - - +
199A ALA* 4.1 1.8 - - - -
200A VAL* 3.7 17.4 - - + +
213A ILE* 3.7 24.7 - - + +
214A PHE 4.1 2.9 - - - -
215A SER* 3.8 37.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.3 9.4 + - - +
180A LEU* 1.3 78.3 - - - +
182A THR* 1.3 65.0 + - - +
184A ALA* 3.2 2.6 + - - +
185A LEU* 3.0 48.4 + - + +
192A TYR* 3.9 17.7 + - + -
68D CYS* 4.6 7.4 - - - -
69D ASP* 4.1 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 2.7 37.3 + - - -
180A LEU 3.3 0.2 - - - -
181A LYS* 1.3 77.8 - - - +
183A ILE* 1.3 61.9 + - - +
185A LEU* 3.2 6.9 + - - -
186A ARG* 3.0 57.7 + - - +
244A LEU* 5.1 1.1 - - + +
246A PHE* 4.2 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.0 35.0 - - + -
179A ASP 3.4 14.3 + - - +
180A LEU* 3.7 16.6 - - + +
181A LYS 3.3 0.4 - - - -
182A THR* 1.3 75.7 - - - +
184A ALA* 1.3 57.5 + - - +
187A ALA* 2.9 38.4 + - + +
200A VAL* 4.5 12.6 - - + -
202A MET* 3.7 28.0 - - + -
213A ILE* 5.0 3.1 - - + -
241A VAL* 4.3 15.3 - - + -
244A LEU* 3.9 16.6 - - + -
246A PHE* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU 2.9 14.9 + - - +
181A LYS 3.7 1.1 - - - +
183A ILE* 1.3 77.5 - - - +
185A LEU* 1.3 59.1 + - - +
187A ALA 4.0 3.8 - - - +
190A ALA* 4.3 14.4 - - + +
192A TYR* 3.4 35.7 - - + +
200A VAL* 4.4 3.4 - - + -
66D ARG* 3.0 29.0 + - - +
67D PHE 4.8 0.9 - - - +
68D CYS* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS* 3.0 46.1 + - + +
182A THR* 3.8 5.6 - - - +
184A ALA* 1.3 78.8 - - - +
186A ARG* 1.3 63.1 + - + +
66D ARG* 2.9 27.1 + - - +
68D CYS* 3.8 26.9 - - + -
69D ASP* 4.7 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 3.0 36.3 + - + +
185A LEU* 1.3 84.1 - - + +
187A ALA* 1.3 63.4 + - - +
188A ARG* 3.9 3.8 + - - +
243A LYS 4.7 3.2 + - - -
244A LEU* 2.8 63.4 + - + +
66D ARG* 3.7 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE 2.9 23.1 + - - +
184A ALA 4.0 4.3 - - - +
186A ARG* 1.3 74.9 - - - +
188A ARG* 1.3 64.7 + - - +
189A ASN 4.0 0.2 + - - -
190A ALA* 4.1 6.9 + - + +
202A MET* 3.9 25.4 - - + -
240A VAL* 4.2 9.9 - - + -
244A LEU* 3.9 18.5 - - + +
66D ARG* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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