Contacts of the helix formed by residues 159 - 170 (chain F) in PDB entry 3A68
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
----------------------------------------------------------
40F LYS 3.5 10.3 - - - +
41F TYR* 3.3 16.6 - - - -
42F VAL 4.9 0.2 + - - -
45F SER* 4.2 10.9 + - - +
105F ARG* 2.8 45.4 + - - -
154F ALA* 2.8 21.7 + - - +
155F THR* 4.7 0.6 - - - +
157F ASN* 3.1 5.5 - - + +
158F GLY* 1.3 72.7 - - - +
160F VAL* 1.3 61.9 + - - +
161F GLN* 3.6 3.3 + - - +
162F LEU* 3.1 18.5 + - + -
163F ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F GLY 3.0 13.8 + - - +
159F ASP* 1.3 72.7 + - - +
161F GLN* 1.3 58.0 + - - +
163F ALA* 3.4 7.6 + - - +
164F ASP* 3.0 25.6 + - - +
148G LEU* 4.1 17.3 - - + +
151G HIS* 3.4 44.6 - - + +
167G GLU* 3.6 11.1 - - + +
171G LEU* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F TYR* 2.4 40.2 + - - -
105F ARG* 3.6 12.6 + - - +
159F ASP* 3.3 2.3 + - - +
160F VAL* 1.3 76.2 - - - +
162F LEU* 1.3 60.4 + - - +
164F ASP* 3.3 9.8 + - + +
165F PHE* 2.9 33.2 + - - +
148G LEU* 5.3 3.2 - - + +
171G LEU* 3.7 40.2 - - + +
172G GLY* 3.7 16.9 - - - +
175G VAL* 3.6 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 4.4 4.5 - - + -
45F SER* 3.9 27.4 - - - +
49F VAL* 4.0 23.3 - - + -
101F TYR* 3.2 35.8 + - + +
105F ARG* 4.0 1.6 - - - +
150F LEU* 4.4 11.7 - - + -
154F ALA* 3.6 22.4 - - + +
159F ASP* 3.1 22.3 + - - +
161F GLN* 1.3 76.2 - - - +
163F ALA* 1.3 64.1 + - - +
165F PHE* 3.2 4.8 + - + +
166F VAL* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F HIS* 3.4 26.0 - - + +
154F ALA* 3.7 8.6 - - + +
155F THR* 3.8 21.1 - - + -
159F ASP 3.2 12.8 + - - +
160F VAL* 3.6 10.3 - - - +
162F LEU* 1.3 79.1 - - - +
164F ASP* 1.3 61.4 + - - +
166F VAL* 3.3 1.9 + - - +
167F GLU* 3.0 30.8 + - - +
167G GLU* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F VAL 3.0 17.5 + - - +
161F GLN* 3.6 15.3 + - + +
162F LEU 3.3 0.2 - - - -
163F ALA* 1.3 76.1 - - - +
165F PHE* 1.3 66.1 + - - +
167F GLU* 3.3 9.1 + - - +
168F THR* 2.9 42.3 + - - -
164G ASP* 5.2 0.2 - - - +
167G GLU* 3.6 49.3 + - + +
168G THR* 4.5 8.5 + - - -
172G GLY* 5.3 2.6 + - - -
341O CA 4.0 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LYS* 4.1 20.4 - - + -
98F LEU* 3.7 15.9 - - + -
101F TYR* 3.6 57.0 - + + -
104F LYS* 6.1 2.9 - - - -
161F GLN* 2.9 23.0 + - - +
162F LEU* 3.2 5.1 + - + +
164F ASP* 1.3 79.2 + - - +
166F VAL* 1.3 67.6 + - + +
168F THR* 4.9 1.6 - - - -
169F GLU* 2.9 58.7 + - + +
170F TYR* 3.6 29.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LEU* 3.9 26.7 - - + +
150F LEU* 3.6 30.5 - - + -
151F HIS* 4.2 14.4 - - + +
162F LEU* 3.0 32.2 + - + +
163F ALA 3.8 3.6 - - - +
164F ASP 3.3 0.2 - - - -
165F PHE* 1.3 82.7 - - + +
167F GLU* 1.3 64.0 + - - +
170F TYR* 3.0 33.7 + - + +
171F LEU* 3.2 21.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F HIS* 2.6 35.9 + - + +
163F ALA* 3.0 18.4 + - - +
164F ASP* 3.8 10.9 - - - +
166F VAL* 1.3 78.6 - - - +
168F THR* 1.3 62.2 + - - +
171F LEU* 3.4 24.3 + - + +
172F GLY 3.9 4.2 + - - -
167G GLU* 4.2 5.3 - - - +
160O VAL* 3.7 17.2 - - + +
164O ASP* 3.6 29.6 - - - +
167O GLU* 4.1 3.2 - - - +
341O CA 2.7 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ASP* 2.9 32.5 + - - -
165F PHE* 4.2 2.5 - - - -
167F GLU* 1.3 78.7 - - - +
169F GLU* 1.3 76.4 + - - +
173F GLU* 3.5 1.7 - - - +
215F CA 2.4 30.5 - - - -
164O ASP* 4.7 8.0 + - - -
168O THR* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F HIS* 6.1 0.7 - - - -
97F LYS* 2.8 36.8 + - + +
165F PHE* 2.9 46.9 + - + +
168F THR* 1.3 91.5 - - - +
170F TYR* 1.3 79.5 + - + +
173F GLU* 3.3 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 4.4 6.5 - - - -
94F HIS* 2.8 53.7 + + + -
97F LYS* 3.3 22.6 - - + +
98F LEU* 3.3 24.2 + - + +
147F LEU* 3.9 33.9 - - + +
165F PHE* 3.6 26.9 - + - -
166F VAL* 3.0 27.1 + - + +
168F THR 3.5 0.6 - - - -
169F GLU* 1.3 92.5 - - + +
171F LEU* 1.3 60.7 + - - +
172F GLY 3.5 1.8 - - - -
173F GLU* 3.4 7.4 + - - +
174F GLN* 2.9 31.4 + - - +
----------------------------------------------------------
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