Contacts of the helix formed by residues 168 - 180 (chain C) in PDB entry 3CB4
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 168 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS* 3.8 12.7 + - - -
159C VAL* 4.1 0.9 - - - +
160C ARG 3.6 17.5 - - - -
161C CYS* 3.6 6.5 - - - -
166C GLY 3.6 0.6 + - - -
167C VAL* 1.3 72.1 - - - +
169C VAL* 1.3 51.9 + - - +
170C GLN 3.2 2.7 - - - -
171C ASP* 2.9 20.2 + - - +
172C VAL* 2.8 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.1 22.2 - - + -
23C ARG* 4.1 35.9 - - + +
24C ILE* 4.3 11.4 - - + -
27C ILE* 4.5 11.0 - - + -
161C CYS* 4.2 12.3 - - + -
162C SER 4.3 7.9 - - - +
166C GLY* 3.4 31.4 + - - +
167C VAL 3.2 0.2 - - - -
168C GLY* 1.3 77.6 - - - +
170C GLN* 1.3 55.9 + - - +
172C VAL* 3.3 11.0 + - + +
173C LEU* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A THR 3.9 8.3 + - - +
535A HIS* 4.0 12.1 - - + -
536A ILE* 3.3 53.5 + - - +
539A ARG* 4.2 7.5 - - - +
27C ILE* 4.0 20.0 - - + +
63C TYR* 3.8 19.6 + - + +
64C LYS 5.2 1.2 + - - -
166C GLY 4.5 2.9 + - - +
168C GLY 3.2 1.0 - - - +
169C VAL* 1.3 77.9 - - - +
171C ASP* 1.3 67.0 + - - +
173C LEU* 3.2 4.9 + - - +
174C GLU* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS* 4.3 16.9 + - - -
159C VAL* 3.7 17.1 - - + +
168C GLY* 2.9 17.6 + - - +
170C GLN* 1.3 83.5 - - - +
172C VAL* 1.3 63.9 + - - +
174C GLU* 3.8 11.1 - - - +
175C ARG* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.5 9.6 - - + -
24C ILE* 5.6 1.1 - - + -
99C LEU* 3.9 28.1 - - + +
127C VAL* 5.6 1.3 - - + +
129C VAL* 3.7 35.4 - - + -
159C VAL* 3.8 17.5 - - + -
161C CYS* 3.8 15.7 - - - -
168C GLY 2.8 19.5 + - - +
169C VAL* 3.4 11.4 - - + +
171C ASP* 1.3 77.5 - - - +
173C LEU* 1.3 61.4 + - + +
175C ARG* 3.4 3.1 + - - +
176C LEU* 3.1 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 5.6 0.2 - - + -
24C ILE* 3.8 37.9 - - + -
27C ILE* 3.7 25.6 - - + -
28C CYS* 3.9 13.2 - - - -
63C TYR* 3.6 38.8 - - + -
73C LEU* 4.1 17.0 - - + +
169C VAL 3.0 11.6 + - - +
170C GLN 3.2 9.2 + - - +
172C VAL* 1.3 80.3 - - + +
174C GLU* 1.3 61.4 + - - +
176C LEU* 3.4 16.1 - - + +
177C VAL* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TYR* 2.6 21.8 + - - +
65C ALA* 3.4 11.0 - - - +
66C SER* 2.9 43.8 + - - -
67C ASP 5.2 0.3 + - - -
170C GLN* 3.0 24.9 + - + +
171C ASP* 3.8 11.4 - - - +
172C VAL 3.3 0.2 - - - -
173C LEU* 1.3 76.9 - - - +
175C ARG* 1.3 56.5 + - - +
177C VAL* 3.5 7.2 + - - +
178C ARG* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C VAL* 3.8 20.6 - - + +
157C ASP* 2.8 49.9 + - - +
158C ALA* 4.8 0.8 - - - +
159C VAL* 3.7 28.3 - - + +
171C ASP 3.2 15.5 + - - +
172C VAL 3.7 4.3 - - - +
174C GLU* 1.3 74.9 - - - +
176C LEU* 1.3 58.8 + - - +
178C ARG* 3.5 30.8 - - - +
179C ASP* 2.8 57.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
5C ARG* 3.8 20.4 - - + -
7C PHE* 3.6 52.9 - - + -
24C ILE* 5.6 0.2 - - + -
73C LEU* 4.0 8.3 - - + -
99C LEU* 3.9 18.4 - - + -
127C VAL* 4.8 6.2 - - - +
172C VAL 3.1 13.2 + - - +
173C LEU* 3.4 25.1 - - + +
175C ARG* 1.3 75.5 - - - +
177C VAL* 1.3 62.3 + - - +
180C ILE* 3.0 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.8 42.3 + - + +
63C TYR* 4.4 18.6 - - + -
65C ALA* 5.0 4.9 - - + -
71C TYR* 3.9 39.5 - - + +
73C LEU* 4.2 22.4 - - + -
173C LEU 3.1 14.6 + - - +
174C GLU* 3.7 9.2 - - - +
176C LEU* 1.3 78.3 - - - +
178C ARG* 1.3 64.9 + - - +
180C ILE 3.6 2.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
157C ASP* 5.0 4.8 + - - -
174C GLU 2.9 19.5 + - - +
175C ARG* 3.5 37.3 - - - +
177C VAL* 1.3 80.4 - - - +
179C ASP* 1.3 95.9 + - - +
180C ILE 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLU* 3.4 34.1 - - - +
127C VAL* 4.6 9.6 - - + +
175C ARG* 2.8 28.2 + - - +
178C ARG* 1.3 119.2 + - - +
180C ILE* 1.3 63.8 + - - +
181C PRO* 3.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.0 39.8 + - + -
6C ASN 4.2 7.4 - - - +
7C PHE* 4.1 10.5 - - + -
96C GLU* 3.8 2.7 - - + -
97C GLY* 3.7 34.1 - - - +
98C ALA 4.1 1.3 - - - +
99C LEU* 4.5 3.1 - - + -
125C GLU* 3.8 19.7 - - + +
127C VAL* 3.9 18.8 - - + -
176C LEU* 3.0 41.6 + - + +
177C VAL 3.6 2.3 - - - +
178C ARG 5.0 0.6 - - - -
179C ASP* 1.3 74.0 - - - +
181C PRO* 1.3 75.0 - - + +
----------------------------------------------------------
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