Contacts of the helix formed by residues 167 - 176 (chain A) in PDB entry 3DC1
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 VAL 167 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.9 4.5 - - - +
160A ALA* 2.8 21.6 + - + +
161A SER 3.7 15.5 - - - +
162A ASP* 3.7 22.0 - - + +
165A GLY 3.1 0.4 + - - -
166A ILE* 1.3 69.6 - - - +
168A PRO* 1.4 70.0 - - + +
169A ASP* 4.2 11.9 - - + +
170A SER* 3.1 34.2 + - - +
171A LEU 3.2 4.7 + - - -
212A ARG* 3.7 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.2 13.4 - - + +
167A VAL* 1.4 80.5 - - + +
169A ASP* 1.3 57.6 + - - +
170A SER 3.0 1.6 - - - -
171A LEU* 3.0 11.8 + - + +
172A ARG* 2.7 42.9 + - - +
212A ARG* 3.7 23.3 - - + +
215A GLU* 3.8 44.9 - - + +
216A ILE* 4.3 13.0 - - + +
219A LEU* 4.8 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 3.4 11.2 - - + -
168A PRO* 1.3 81.4 - - - +
170A SER* 1.3 57.6 + - - +
172A ARG* 2.9 27.4 + - - +
173A ASP* 3.0 39.7 + - - +
215A GLU* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.9 3.7 - - - +
160A ALA* 2.9 43.3 + - - +
167A VAL* 3.1 17.4 + - - +
168A PRO 3.0 0.2 - - - -
169A ASP* 1.3 77.9 - - - +
171A LEU* 1.3 65.6 + - - +
173A ASP* 3.2 7.3 + - - +
174A ILE* 3.0 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.8 24.9 - - + -
159A VAL* 3.9 24.2 - - + +
166A ILE* 4.6 3.8 - - + -
167A VAL 3.2 4.5 + - - +
168A PRO* 3.0 16.0 + - + +
170A SER* 1.3 79.5 + - - +
172A ARG* 1.3 60.8 + - - +
174A ILE* 3.5 2.9 + - + +
175A LEU* 3.1 55.3 + - + +
194A LEU* 4.6 8.5 - - + -
216A ILE* 3.8 37.7 - - + -
219A LEU* 4.2 17.7 - - + -
225A PHE* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 2.7 18.2 + - - +
169A ASP* 2.9 41.8 + - - +
171A LEU* 1.3 70.0 - - - +
173A ASP* 1.3 65.3 + - - +
175A LEU* 3.2 2.9 + - - +
176A SER* 2.9 29.3 + - - -
215A GLU* 3.8 35.0 + - - +
218A GLU* 5.6 3.8 + - - -
219A LEU* 3.7 40.9 - - + +
223A TYR* 5.3 0.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 3.0 21.9 + - - +
170A SER* 3.2 6.6 + - - +
172A ARG* 1.3 80.5 - - - +
174A ILE* 1.3 61.1 + - + +
176A SER* 2.6 22.4 + - - +
177A ARG* 4.2 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 4.0 14.4 - - + -
157A ILE* 3.7 22.2 - - + -
158A ASN 3.1 27.6 - - - +
159A VAL* 3.6 22.4 - - + -
170A SER* 3.0 24.8 + - - +
171A LEU* 3.9 5.6 - - - +
173A ASP* 1.3 77.6 - - + +
175A LEU* 1.3 65.8 + - + +
176A SER 3.4 0.3 + - - -
177A ARG* 2.9 52.4 + - - +
178A TRP* 3.9 6.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
136A LEU* 4.1 10.8 - - + -
171A LEU* 3.1 42.1 + - + +
172A ARG 3.2 4.9 + - - +
174A ILE* 1.3 77.5 - - + +
176A SER* 1.3 49.6 + - - +
177A ARG 3.0 5.1 - - - -
178A TRP* 2.7 48.9 + - + +
191A PRO* 3.9 30.1 - - + -
219A LEU* 3.7 17.0 - - + -
223A TYR* 3.7 32.9 + - + -
225A PHE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG 2.9 10.9 + - - -
173A ASP* 2.6 31.9 + - - -
174A ILE 3.3 0.2 - - - -
175A LEU* 1.3 74.6 - - - +
177A ARG* 1.3 60.0 + - - +
178A TRP 3.1 11.4 + - - +
179A LYS* 5.9 0.5 + - - +
223A TYR* 4.3 6.2 + - - -
----------------------------------------------------------
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