Contacts of the helix formed by residues 165 - 171 (chain P) in PDB entry 3Q2K
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 165 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163P THR* 4.4 4.6 - - + -
164P ARG* 1.3 85.0 - - - +
166P GLN* 1.3 65.2 + - - +
167P GLU* 3.2 38.8 - - + +
168P TYR* 3.2 24.9 + - + +
169P TYR* 3.4 5.4 - - - -
215P ARG* 3.7 11.9 - - - +
550P HP7 3.0 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P PRO* 1.3 71.5 - - - +
167P GLU* 1.3 59.1 + - - +
169P TYR* 2.6 34.2 + - - +
170P ASP* 3.0 39.2 + - - +
215P ARG* 3.4 25.0 - - - +
216P ARG* 2.8 74.9 + - - +
217P ILE* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165P PRO* 3.2 32.8 - - + +
166P GLN* 1.3 77.3 + - - +
168P TYR* 1.3 68.8 + - - +
169P TYR 3.0 1.0 + - - -
170P ASP* 3.1 10.7 + - - +
171P ALA* 3.0 22.7 + - - +
550P HP7 5.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ARG* 5.0 11.7 - - - +
164P ARG* 3.8 17.5 - - + -
165P PRO* 3.2 18.9 + - + +
166P GLN 3.1 0.4 - - - -
167P GLU* 1.3 86.1 - - - +
169P TYR* 1.3 84.8 + + - +
171P ALA* 3.5 10.4 - - - +
175P ARG* 3.4 40.7 + - + -
181P ASP* 5.5 1.3 + - - -
187P ASN* 3.9 3.8 + - - -
188P GLN* 3.2 25.2 + - - -
550P HP7 2.5 78.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164P ARG* 3.5 37.1 - - + +
165P PRO 3.4 13.2 - - - -
166P GLN* 2.6 25.8 + - - +
168P TYR* 1.3 88.3 - + - +
170P ASP* 1.3 63.1 + - - +
171P ALA 3.2 2.8 + - - -
172P ALA 3.3 17.5 - - - +
175P ARG* 3.4 17.7 - - + +
176P GLY* 4.3 16.4 - - - -
181P ASP* 5.5 0.9 - - - -
183P GLY* 6.3 2.0 - - - -
184P ALA 5.7 0.6 + - - -
188P GLN* 4.1 11.9 + - - -
215P ARG* 4.0 17.1 - - + +
217P ILE* 3.4 49.4 - - + +
220P GLU 5.4 0.5 + - - -
221P ASP* 4.7 2.8 - - - +
241P MET* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P GLN* 3.0 43.2 + - - +
167P GLU* 3.1 9.9 + - - +
169P TYR* 1.3 75.8 - - - +
171P ALA* 1.3 63.9 + - - +
172P ALA* 3.0 8.3 + - - -
216P ARG* 4.2 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ARG* 4.6 16.6 - - - +
167P GLU 3.0 11.7 + - - +
168P TYR* 3.5 17.3 - - - +
169P TYR 3.2 1.0 - - - -
170P ASP* 1.3 75.6 - - - +
172P ALA* 1.3 61.9 + - - +
175P ARG* 4.4 8.7 - - - +
----------------------------------------------------------
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