Contacts of the helix formed by residues 160 - 178 (chain C) in PDB entry 1J0B
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 160 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 3.1 20.9 - - - +
152C TYR* 5.8 0.7 - - - -
155C PRO* 4.4 17.7 - - - +
158C GLY 2.8 6.3 + - - -
159C ALA* 1.3 75.5 - - - +
161C PRO* 1.3 73.6 - - - +
162C ILE* 3.4 9.6 - - - +
163C GLY 2.8 24.7 + - - -
164C THR* 3.0 24.3 + - - -
230C LEU* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ALA 4.4 2.9 - - - +
160C SER* 1.3 86.3 - - - +
162C ILE* 1.3 61.6 + - + +
164C THR* 3.4 9.9 + - - +
165C LEU* 3.6 9.5 + - - +
230C LEU* 4.4 7.2 - - + +
233C GLU* 3.4 38.6 - - + +
234C ALA* 3.4 38.2 - - + +
237C LEU* 3.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.8 7.9 - - + -
60C TYR* 3.1 44.6 - - + +
61C LEU* 3.3 24.0 - - + -
64C ASP* 4.2 12.8 - - - +
152C TYR* 3.6 18.6 - - - +
160C SER* 3.4 9.2 - - - +
161C PRO* 1.3 76.5 - - + +
163C GLY* 1.3 65.4 + - - +
165C LEU* 3.6 16.7 - - + +
237C LEU* 3.3 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 3.3 24.6 - - - +
61C LEU* 3.4 22.2 - - - -
158C GLY 3.7 10.8 - - - -
160C SER* 2.8 21.8 + - - -
162C ILE* 1.3 79.0 - - - +
164C THR* 1.3 60.6 + - - +
165C LEU 3.2 0.7 - - - -
166C GLY 3.3 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 4.8 4.3 - - - +
158C GLY 4.5 1.3 + - - -
159C ALA 4.9 0.2 - - - -
160C SER 3.0 16.2 + - - -
161C PRO* 3.6 7.9 - - - -
162C ILE 3.3 0.2 - - - -
163C GLY* 1.3 74.1 - - - +
165C LEU* 1.3 62.1 + - - +
166C GLY* 2.8 8.0 + - - -
167C TYR 3.2 10.9 + - - -
168C VAL* 3.6 9.6 + - + +
193C GLY* 3.7 17.3 + - - +
196C ALA* 3.9 8.3 - - + +
197C GLY* 3.4 31.1 - - - +
200C LEU* 4.7 0.7 - - + -
230C LEU* 3.5 22.6 - - + +
234C ALA* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.1 7.8 - - + +
12C PHE* 3.5 44.0 - - + -
60C TYR* 3.6 29.8 - - + -
161C PRO 3.6 12.7 + - - +
162C ILE* 3.6 20.0 - - + +
163C GLY 3.2 0.6 - - - -
164C THR* 1.3 77.5 - - - +
166C GLY* 1.3 63.4 + - - +
167C TYR 3.3 0.2 - - - -
168C VAL* 3.5 10.2 - - + +
169C ARG* 3.1 23.6 + - - +
200C LEU* 4.9 4.3 - - + -
234C ALA 4.9 0.4 - - - +
237C LEU* 4.7 4.9 - - + -
238C LEU* 3.2 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG* 3.6 34.9 + - - +
57C LYS* 4.3 3.4 - - - -
60C TYR* 4.2 8.0 - - - -
163C GLY 3.3 11.9 + - - -
164C THR 2.8 4.4 - - - -
165C LEU* 1.3 80.8 - - - +
167C TYR* 1.3 60.5 + - - -
169C ARG* 3.4 8.0 - - - +
170C ALA* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LYS* 6.0 1.1 - - + -
43C ASP* 2.4 32.8 + - - +
53C ASN* 3.1 50.4 - - + +
56C ARG* 3.3 15.0 - - + -
57C LYS* 3.9 14.3 - - + +
164C THR* 3.2 4.2 + - - +
166C GLY* 1.3 74.3 - - - +
168C VAL* 1.3 67.1 + - - +
169C ARG 2.9 1.6 - - - -
170C ALA* 3.1 21.1 - - + -
171C VAL* 2.8 30.1 + - - +
174C ILE* 5.9 0.4 - - + -
193C GLY 5.4 0.2 - - - +
194C THR* 3.7 28.9 - - + +
197C GLY* 3.9 20.4 - - - -
198C LEU* 4.1 13.7 - - + +
306C ILE* 4.2 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.4 27.9 - - + +
8C LEU* 6.4 0.4 - - + -
9C LEU* 4.0 13.2 - - + -
164C THR 3.6 14.8 + - - +
165C LEU* 3.5 14.6 - - - +
167C TYR* 1.3 79.0 - - - +
169C ARG* 1.3 60.1 + - - +
171C VAL* 3.8 2.6 + - - +
172C GLY 3.8 2.6 + - - -
197C GLY* 3.6 18.6 + - - +
200C LEU* 3.6 37.0 - - + -
201C GLY* 4.2 8.5 - - - -
204C ILE* 4.3 5.4 - - + -
238C LEU* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.8 26.5 - - - +
5C ILE* 4.4 2.7 - - - -
6C PHE* 5.2 13.3 - - - +
9C LEU* 3.5 33.7 - - + +
14C ARG* 3.4 44.9 - - - +
56C ARG* 5.9 4.7 - - - +
59C GLU* 4.5 6.0 + - - -
60C TYR* 3.3 24.9 + - - +
165C LEU 3.1 8.6 + - - +
166C GLY* 3.4 11.0 - - - +
168C VAL* 1.3 76.7 - - - +
170C ALA* 1.3 59.3 + - - +
172C GLY* 2.9 17.8 + - - -
173C GLU* 3.1 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LYS* 5.1 1.4 - - - -
56C ARG* 4.2 21.3 - - - +
166C GLY 3.2 4.5 + - - +
167C TYR* 2.9 48.3 + - + +
169C ARG* 1.3 79.8 - - - +
171C VAL* 1.3 61.5 + - - +
172C GLY 3.1 0.3 + - - -
173C GLU* 3.2 6.0 + - - +
174C ILE* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.6 22.0 - - + -
167C TYR 2.8 17.7 + - - +
168C VAL 3.8 3.8 - - - +
169C ARG 3.3 0.2 - - - -
170C ALA* 1.3 74.1 - - - +
172C GLY* 1.3 59.1 + - - +
174C ILE* 3.5 14.5 - - + +
175C ALA* 2.8 28.4 + - - +
185C ILE* 5.9 0.4 - - + -
198C LEU* 3.6 26.0 - - + -
201C GLY* 3.8 14.4 - - - -
202C LEU* 4.0 24.9 - - + +
205C LEU* 3.8 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.1 32.5 - - - -
2C HIS* 3.8 5.8 + - - -
5C ILE* 3.9 9.6 - - - -
168C VAL 3.8 0.8 + - - -
169C ARG 2.9 5.9 + - - -
171C VAL* 1.3 81.3 - - - +
173C GLU* 1.3 60.8 + - - +
175C ALA* 3.2 8.5 + - - +
176C THR* 3.1 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 4.1 11.2 - - + +
18C ILE* 5.7 0.5 - - - +
20C TRP 4.1 5.4 - - - +
21C GLU* 2.9 59.9 - - + +
41C LYS* 3.7 11.6 + - - -
56C ARG* 3.4 33.0 + - - +
169C ARG* 3.1 11.7 + - + +
170C ALA* 3.7 7.9 - - - +
172C GLY* 1.3 72.6 - - - +
174C ILE* 1.3 60.2 + - - +
176C THR* 3.5 3.5 + - - -
177C GLN* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 4.4 2.7 - - + -
41C LYS* 3.8 32.8 - - + -
167C TYR* 5.9 0.4 - - + -
170C ALA* 2.9 29.2 + - + +
171C VAL* 3.5 16.8 - - + +
173C GLU* 1.3 72.5 - - - +
175C ALA* 1.3 54.7 + - - +
176C THR 2.8 9.0 + - - -
177C GLN* 3.0 8.4 + - - +
178C SER* 2.7 48.0 + - - +
182C PHE* 5.6 2.2 - - + -
185C ILE* 5.5 4.7 - - + -
198C LEU* 4.7 6.7 - - + -
304C LEU* 4.1 27.6 - - + -
306C ILE* 4.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HIS* 4.9 12.6 - - + -
171C VAL 2.8 18.4 + - - +
172C GLY* 3.4 6.7 - - - +
174C ILE* 1.3 77.2 - - - +
176C THR* 1.3 60.7 + - - +
178C SER* 4.0 12.2 - - - +
205C LEU* 3.8 22.2 - - + -
207C GLU* 5.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 2.8 32.1 + - - +
2C HIS* 3.8 6.1 + - - -
21C GLU* 3.9 15.9 - - - +
172C GLY 3.1 7.0 + - - -
173C GLU 3.7 7.6 - - - -
174C ILE 2.8 2.0 + - - -
175C ALA* 1.3 81.1 - - - +
177C GLN* 1.3 61.5 + - - +
178C SER 3.7 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 4.0 25.4 - - - +
22C THR 3.1 16.0 + - - +
23C PRO* 4.3 5.5 - - - +
24C ILE* 4.0 20.9 + - + +
41C LYS* 2.7 35.0 - - - +
173C GLU* 3.1 26.7 + - - +
174C ILE* 3.0 9.1 + - - +
176C THR* 1.3 77.0 - - - +
178C SER* 1.3 62.6 + - - +
179C GLU* 3.5 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 4.0 19.5 - - - -
174C ILE* 2.7 30.7 + - - -
175C ALA* 4.0 12.3 - - - +
176C THR 3.4 1.6 - - - +
177C GLN* 1.3 74.0 - - - +
179C GLU* 1.3 61.5 + - - +
180C VAL* 3.5 4.1 + - - +
182C PHE* 2.9 32.2 - - - -
----------------------------------------------------------
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