Contacts of the helix formed by residues 172 - 180 (chain C) in PDB entry 1JKR
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 172 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A G 3.3 33.4 + - - -
10A A 4.4 7.4 - - - -
166C ALA* 4.3 0.2 - - - -
171C ILE* 1.3 77.0 - - - +
173C VAL* 1.3 67.1 + - - -
174C SER 3.1 2.9 - - - -
175C THR* 3.0 24.2 + - - -
176C LEU* 3.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A A 5.2 1.2 + - - -
19B T 5.8 2.0 - - + -
20B T 5.8 0.7 - - + -
162C ARG* 4.7 9.6 - - + -
163C GLN* 3.6 37.5 - - - +
166C ALA* 3.7 23.1 - - + -
167C ILE* 6.2 0.4 - - + -
172C GLY* 1.3 73.4 - - - -
174C SER* 1.3 63.3 + - - +
176C LEU* 3.0 14.0 + - - +
177C TYR* 3.1 40.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A G 3.9 13.5 - - - +
10A A 2.9 48.1 + - - -
11A C 4.2 5.1 + - - -
20B T 5.0 5.3 - - - +
21B G 3.9 10.8 - - - -
173C VAL* 1.3 77.9 + - - +
175C THR* 1.3 63.7 + - - +
177C TYR* 3.4 8.7 + - - +
178C ARG* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A T 3.8 4.0 - - - +
9A G 2.7 43.9 + - - +
143C ALA* 3.9 20.2 - - + -
144C ILE* 4.6 0.7 - - + -
171C ILE* 4.1 10.8 - - + -
172C GLY 3.0 15.6 + - - -
174C SER* 1.3 78.9 - - - +
176C LEU* 1.3 55.6 + - - +
178C ARG* 2.9 43.1 + - - +
179C TYR* 3.1 20.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 5.6 2.2 - - + -
152C ILE* 4.8 13.2 - - + -
156C LEU* 6.3 0.9 - - + -
162C ARG* 3.9 25.1 + - + +
165C LEU* 4.2 9.6 - - + -
166C ALA* 3.4 45.5 - - + +
171C ILE* 3.3 28.0 - - + -
172C GLY 3.9 3.6 - - - +
173C VAL* 3.0 6.7 + - - +
175C THR* 1.3 74.0 - - + +
177C TYR* 1.3 61.5 + - - +
178C ARG 2.8 5.2 - - - -
179C TYR* 4.5 2.5 - - + +
180C PHE* 2.9 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B C 3.6 12.5 - - - +
19B T 2.8 57.4 + - + +
20B T 3.6 51.7 + - + +
162C ARG* 3.4 38.1 - - + +
163C GLN* 6.0 0.2 - - - -
173C VAL* 3.1 42.8 + - + -
174C SER 4.0 5.2 - - - +
175C THR 3.4 0.2 - - - -
176C LEU* 1.3 79.7 - - - +
178C ARG* 1.3 58.1 + - - +
180C PHE 3.6 4.5 - - - -
181C PRO* 3.4 25.3 - - - +
182C ALA* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A T 2.7 60.9 + - - +
9A G 2.6 47.3 + - - -
22B T 5.1 3.6 + - - +
174C SER* 3.2 11.5 + - - +
175C THR* 3.0 31.3 - - - +
176C LEU 2.8 2.4 - - - -
177C TYR* 1.3 80.2 - - - +
179C TYR* 1.3 66.4 + - + +
180C PHE 3.3 0.2 - - - -
181C PRO* 4.1 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A T 2.6 36.8 + - - -
142C ARG* 2.8 38.2 + - - +
144C ILE* 2.8 43.2 + - + +
149C GLN* 3.5 31.6 - - - +
175C THR* 3.1 24.7 + - + +
176C LEU* 4.2 1.8 - - + +
178C ARG* 1.3 83.8 - - + +
180C PHE* 1.3 89.4 + + + +
181C PRO* 3.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 5.6 1.6 - - + -
149C GLN* 2.9 45.5 - - + -
152C ILE* 3.2 31.0 - - + -
153C SER* 3.6 20.0 - - - -
156C LEU* 3.8 23.8 - - + -
162C ARG* 3.2 12.6 + - - +
176C LEU* 2.9 32.3 + - + +
177C TYR* 3.5 6.2 - - - +
179C TYR* 1.3 106.5 - + + +
181C PRO* 1.3 67.4 - - - +
184C SER* 4.1 10.1 - - - +
----------------------------------------------------------
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