Contacts of the helix formed by residues 170 - 176 (chain A) in PDB entry 6N8P
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 SER 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLY 4.7 0.2 - - - -
152A ASN* 3.5 16.4 + - - -
168A THR* 3.6 10.1 + - - -
169A ILE* 1.3 78.9 - - - +
171A SER* 1.3 69.2 + - - +
172A ASP* 2.7 24.0 + - - -
173A ALA* 3.7 20.1 - - - +
174A VAL* 3.4 20.4 + - - +
185A ARG* 5.8 0.2 + - - -
208A TYR* 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER 4.2 4.6 + - - -
151A GLY* 4.0 19.8 + - - -
152A ASN* 2.7 16.1 + - - -
170A SER* 1.3 72.8 + - - +
172A ASP* 1.3 59.8 + - - -
173A ALA 3.1 1.1 - - - -
174A VAL* 3.0 18.9 + - - +
175A LEU* 3.2 18.0 + - - +
185A ARG* 3.1 37.5 + - - -
189A GLU* 3.3 16.5 + - - -
208A TYR* 4.7 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 2.7 21.3 + - - -
171A SER* 1.3 75.6 - - - +
173A ALA* 1.3 61.8 + - - -
175A LEU* 3.7 12.1 - - + +
176A GLN* 3.1 41.5 + - + +
185A ARG* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR 5.9 0.2 - - - +
169A ILE* 5.4 0.9 - - - -
170A SER* 3.7 29.8 - - - +
171A SER 3.1 0.6 - - - -
172A ASP* 1.3 84.3 + - - +
174A VAL* 1.3 57.9 + - + +
176A GLN* 3.9 6.4 + - - +
177A ARG* 2.6 44.0 + - - +
216A TRP* 4.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.7 16.4 - - + -
170A SER 3.4 15.3 - - - +
171A SER 3.0 8.9 + - - +
173A ALA* 1.3 78.3 - - - +
175A LEU* 1.3 65.9 + - + +
176A GLN 3.2 0.4 - - - -
177A ARG* 3.2 16.1 + - - +
178A LEU* 3.5 14.6 - - + +
206A ILE* 4.6 3.6 - - + -
208A TYR* 3.7 24.2 - - + +
212A LEU* 5.0 0.2 - - + -
214A VAL* 4.1 33.9 - - + -
216A TRP* 3.7 22.4 - - + -
223A VAL* 4.0 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER* 3.2 22.2 + - - +
172A ASP* 3.3 11.8 + - + +
174A VAL* 1.3 80.5 - - + +
176A GLN* 1.3 60.8 + - + +
177A ARG 3.2 0.2 - - - -
178A LEU* 3.2 21.6 + - + -
182A ALA 4.8 0.4 - - - +
183A ARG* 2.8 63.8 + - + +
185A ARG* 3.5 26.9 - - + -
189A GLU* 3.9 18.6 - - - +
208A TYR* 5.6 1.6 - - + -
210A ARG* 5.0 2.0 - - - +
212A LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.1 33.7 + - + +
173A ALA* 4.2 10.4 - - - +
174A VAL 3.2 0.6 - - - -
175A LEU* 1.3 77.5 - - + +
177A ARG* 1.3 73.3 + - - +
178A LEU 3.3 3.7 + - - +
183A ARG* 3.3 22.8 + - - +
----------------------------------------------------------
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