Contacts of the helix formed by residues 164 - 176 (chain F) in PDB entry 3COA
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 164 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E G 4.4 14.4 - - - -
17E C 2.9 22.7 - - - -
158F ASN* 4.5 0.7 - - - +
160F TRP* 4.7 0.9 - - - -
162F ASN 3.7 2.4 + - - -
163F LEU* 1.3 75.7 - - - +
165F TYR* 1.3 64.3 + - - +
166F ALA* 3.4 9.9 + - - +
167F ASP* 2.9 43.8 + - - -
168F LEU* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E C 3.3 35.3 + + + +
18E A 2.6 29.1 + - - -
160F TRP* 3.6 23.8 - + - -
164F SER* 1.3 73.8 - - - +
166F ALA* 1.3 63.2 + - - +
168F LEU* 3.2 16.0 + - + +
169F ILE* 3.0 28.6 + - - +
190F MET* 5.4 0.9 - - - -
197F PHE* 4.0 20.9 - + - -
209F TRP* 3.7 27.7 - + + +
212F SER* 3.7 28.7 - - - -
213F ILE* 4.0 21.8 - - + -
216F ASN* 3.7 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E C 4.7 0.2 + - - -
164F SER* 3.1 9.5 + - - +
165F TYR* 1.3 79.4 - - - +
167F ASP* 1.3 57.9 + - - +
169F ILE* 3.3 3.0 + - - -
170F THR* 2.9 33.6 + - - -
216F ASN* 3.8 18.5 + - - +
220F HIS* 4.3 8.3 - - + +
222F LYS* 4.9 8.5 - - + +
223F PHE* 3.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162F ASN 4.7 1.0 - - - +
163F LEU* 3.8 25.7 - - + +
164F SER* 2.9 43.4 + - - +
166F ALA* 1.3 78.2 - - - +
168F LEU* 1.3 57.5 + - - +
170F THR* 3.2 8.4 + - - -
171F LYS* 2.9 31.5 + - - +
222F LYS* 5.0 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F TRP* 3.7 33.4 - - + +
163F LEU* 3.9 27.4 - - + -
164F SER 3.0 15.7 + - - +
165F TYR* 3.5 15.9 - - + +
167F ASP* 1.3 74.1 - - - +
169F ILE* 1.3 65.4 + - - +
171F LYS* 3.3 4.0 + - + +
172F ALA* 2.9 23.2 + - - +
189F TRP* 3.5 13.5 - - + -
190F MET* 3.3 31.2 - - + -
194F VAL* 4.1 19.5 - - + -
197F PHE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TYR 3.0 17.2 + - - +
166F ALA 3.7 5.2 - - - +
168F LEU* 1.3 74.8 - - - +
170F THR* 1.3 64.9 + - - +
172F ALA* 3.1 7.3 + - - +
173F ILE* 2.9 32.4 + - + +
186F ILE* 4.2 14.8 - - + -
190F MET* 5.4 0.7 - - - -
213F ILE* 3.9 39.0 - - + +
216F ASN* 3.7 28.9 - - + -
217F LEU* 3.7 27.6 - - + -
223F PHE* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ALA 2.9 20.0 + - - -
167F ASP* 3.3 11.9 - - - -
168F LEU 3.1 0.2 - - - -
169F ILE* 1.3 78.2 - - - +
171F LYS* 1.3 58.9 + - + +
173F ILE* 3.3 1.7 + - - +
174F GLU* 2.9 54.1 + - - +
222F LYS* 3.1 32.5 + - - +
223F PHE* 3.6 4.5 - - - -
239F LEU* 3.8 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F LEU* 3.4 31.9 - - + -
167F ASP* 2.9 13.8 + - + +
168F LEU* 3.7 8.7 - - + +
170F THR* 1.3 76.7 - - + +
172F ALA* 1.3 63.4 + - - +
174F GLU* 3.3 13.8 + - - +
175F SER* 2.9 24.6 + - - -
189F TRP* 3.7 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU 2.9 11.9 + - - +
169F ILE* 3.4 12.6 - - - +
171F LYS* 1.3 76.7 - - - +
173F ILE* 1.3 63.2 + - - +
175F SER* 2.8 21.5 + - - -
176F SER 3.5 0.9 + - - -
181F LEU* 3.3 18.9 - - + +
186F ILE* 4.5 11.7 - - + -
189F TRP* 3.4 43.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F ILE* 2.9 36.7 + - + +
170F THR 3.8 3.4 - - - +
172F ALA* 1.3 74.3 - - - +
174F GLU* 1.3 62.5 + - - +
176F SER* 2.8 25.5 + - - -
179F LYS* 3.6 32.3 - - + +
180F ARG 4.0 1.6 - - - +
181F LEU* 3.9 11.0 - - + -
186F ILE* 4.5 10.3 - - + -
223F PHE* 4.3 5.4 - - + -
237F TRP* 3.5 33.4 - - + +
238F MET* 3.9 11.4 - - - -
239F LEU* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F THR* 2.9 39.3 + - - +
171F LYS* 3.8 13.7 - - - +
172F ALA 3.2 0.2 - - - -
173F ILE* 1.3 76.1 - - - +
175F SER* 1.3 58.9 + - - +
179F LYS* 3.0 36.3 + - + +
239F LEU* 3.4 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F LYS 2.9 15.9 + - - -
172F ALA 2.8 13.8 + - - -
174F GLU* 1.3 75.2 - - - +
176F SER* 1.3 64.0 + - - +
177F ALA* 3.7 1.2 + - - -
181F LEU* 5.1 1.0 - - - +
189F TRP* 3.4 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ALA 3.5 0.4 + - - -
173F ILE 2.8 19.6 + - - -
174F GLU 3.5 1.7 - - - +
175F SER* 1.3 83.3 + - - +
177F ALA* 1.3 65.4 + - - +
178F GLU* 4.2 2.0 - - - -
179F LYS* 2.8 35.7 + - - +
180F ARG 2.9 12.9 + - - -
181F LEU* 3.7 28.7 - - - -
----------------------------------------------------------
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