Contacts of the helix formed by residues 159 - 166 (chain F) in PDB entry 7RDB
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 ASP 159 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B SER* 2.9 37.2 + - - +
155F CYS 3.5 7.7 - - - +
156F GLY* 4.4 0.2 - - - -
158F GLU* 1.3 82.0 - - - +
160F TYR* 1.3 58.3 + - + +
161F ARG* 3.3 20.9 + - - +
162F ASP* 2.8 42.0 + - - +
216F VAL 3.6 13.7 - - - +
217F ARG* 5.2 0.7 - - - -
218F GLY* 3.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F CYS* 3.4 36.6 + - + -
159F ASP* 1.3 78.2 - - + +
161F ARG* 1.3 105.6 + - + +
162F ASP 3.1 1.4 + - - -
163F TRP* 3.3 22.5 + - - +
181F VAL* 3.7 10.3 - - + +
202F THR* 2.7 33.3 + - - -
203F ILE* 3.6 14.8 + - + +
206F GLU 4.2 3.6 + - - -
207F ARG* 4.9 4.9 - - + -
210F VAL* 3.9 13.0 - - + +
214F ILE* 3.7 18.8 - - + -
215F TYR 3.9 5.6 - - - +
216F VAL* 3.1 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 4.0 24.4 - - + +
208B PHE* 3.4 39.2 + - - +
209B SER* 2.7 32.7 + - - +
159F ASP* 2.8 15.0 + - - +
160F TYR* 1.3 111.2 + - + +
162F ASP* 1.3 66.7 + - - +
163F TRP 3.0 3.3 + - - -
164F SER* 3.1 21.5 + - - -
203F ILE* 3.1 40.5 + - + +
206F GLU* 3.8 14.5 - - - +
207F ARG* 4.4 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 4.9 10.2 + - - +
125F ASN* 5.5 0.9 - - - +
128F ILE* 4.6 1.7 - - - +
129F ARG* 6.4 1.1 - - - -
132F ILE* 3.9 17.3 - - + +
156F GLY* 4.2 1.3 - - - -
157F GLY* 2.7 17.8 + - - +
158F GLU* 2.7 38.9 + - - +
159F ASP* 2.8 24.7 + - - +
161F ARG* 1.3 77.1 - - - +
163F TRP* 1.4 55.4 + - - +
164F SER* 4.3 0.2 - - - -
165F LYS* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ILE* 3.7 38.8 - - + -
135F TYR* 3.5 48.0 - + + -
145F MET* 3.9 11.7 - - + -
149F GLN* 3.1 38.9 + - - -
155F CYS* 3.5 9.7 - - - -
156F GLY* 3.5 7.7 - - - +
160F TYR 3.3 15.8 + - - +
161F ARG 3.0 1.8 + - - -
162F ASP* 1.4 75.8 - - - +
164F SER* 1.3 56.9 + - - +
165F LYS 2.8 7.5 + - - -
166F ASN* 2.9 20.0 + - + +
169F HIS* 3.3 23.9 - + - +
180F GLY 4.2 5.6 - - - +
181F VAL* 3.2 28.5 - - + -
182F PRO* 3.5 24.8 - - + +
203F ILE* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 2.8 29.9 + - - -
161F ARG 3.1 15.9 + - - -
162F ASP 2.9 0.6 + - - -
163F TRP* 1.3 76.4 - - - +
165F LYS* 1.3 68.4 + - - +
166F ASN 3.2 8.7 + - - +
169F HIS 4.1 13.0 - - - -
170F ASP* 3.6 26.2 + - - +
171F CYS* 4.7 4.4 + - - -
203F ILE* 3.7 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ASP* 3.3 44.3 + - - +
205B LYS* 5.4 1.3 - - - +
206B GLU* 5.3 1.6 + - - -
129F ARG* 5.0 13.5 - - + +
132F ILE* 4.3 11.0 - - + -
133F GLU* 4.2 32.2 - - + +
162F ASP* 2.9 20.2 + - + +
163F TRP 2.8 1.0 + - - -
164F SER* 1.3 86.0 + - - +
166F ASN* 1.3 60.7 + - - +
167F GLN* 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ILE* 2.9 33.8 + - + +
133F GLU* 3.8 14.1 + - - +
135F TYR* 3.9 5.3 - - - +
136F TYR* 3.7 20.4 - - - +
163F TRP* 2.9 14.7 + - + +
164F SER 3.5 2.5 - - - +
165F LYS* 1.3 80.3 - - - +
167F GLN* 1.3 70.2 + - - +
168F TYR* 2.8 41.1 + - - +
169F HIS* 3.1 18.5 + - + -
170F ASP* 3.1 20.4 + - - +
----------------------------------------------------------
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