Contacts of the strand formed by residues 161 - 168 (chain B) in PDB entry 3QNF
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 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B HIS* 1.3 72.4 - - - +
162B PHE* 1.3 58.5 + - - -
163B TYR* 3.4 4.0 - - - -
180B THR* 3.1 5.9 - - - -
181B GLN 2.8 43.0 + - - +
182B PHE* 3.7 7.4 - - - -
186B ALA* 3.5 28.0 - - - +
189B MET* 4.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.7 15.9 - - + -
69B ALA* 3.6 27.1 - - + -
76B PHE* 3.8 24.4 - + + -
154B ASN 4.8 0.3 - - - +
155B LEU* 3.5 29.0 - - + -
156B SER* 2.8 22.8 + - - -
160B HIS 3.7 0.8 + - - -
161B GLY* 1.3 70.3 - - - -
163B TYR* 1.3 59.6 + - - +
178B ALA* 3.7 20.6 - - + -
179B SER 3.4 15.7 - - - -
180B THR* 4.0 4.5 - - + +
182B PHE* 4.2 0.6 - - - -
189B MET* 4.7 5.5 + - - +
190B ALA* 4.0 20.9 - - + +
249B PHE* 3.6 34.8 - + - -
251B ILE* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.6 4.3 - - - -
156B SER* 3.2 18.8 - - - +
159B PHE* 3.6 51.6 - + + +
160B HIS 3.7 4.9 - - - +
161B GLY 3.4 9.9 - - - -
162B PHE* 1.3 75.8 - - - +
164B LYS* 1.3 73.6 + - - +
165B SER* 3.6 11.3 + - - -
178B ALA* 3.5 5.2 - - - -
179B SER* 2.8 62.1 + - - -
180B THR 3.7 22.2 - - - -
181B GLN* 3.7 10.3 - - + +
311B ILE* 4.0 3.4 - - + +
313B ASP 5.6 1.1 - - - -
314B PHE* 3.2 33.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.7 9.0 - - + -
155B LEU* 4.2 22.1 - - + +
156B SER 3.0 15.2 + - - +
157B GLU* 4.4 24.1 - - - +
159B PHE* 4.3 9.5 - - - -
163B TYR* 1.3 78.2 - - - +
165B SER* 1.3 61.0 + - - +
166B THR* 5.4 3.8 - - + -
176B ILE* 4.6 12.3 - - + -
177B LEU 3.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 4.9 5.4 - - - -
163B TYR* 3.6 17.9 + - - -
164B LYS* 1.3 73.2 - - - +
166B THR* 1.3 65.0 + - - +
176B ILE* 3.5 4.5 - - - +
177B LEU* 2.7 61.2 + - - +
311B ILE* 4.2 2.6 - - - +
312B PRO* 4.0 5.9 - - - +
313B ASP* 3.5 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LYS* 5.4 3.8 - - + -
165B SER* 1.3 83.8 + - - +
167B TYR* 1.3 67.2 + - - +
174B LEU* 4.8 17.9 - - + -
175B ARG 3.3 6.3 - - - +
176B ILE* 4.0 26.0 - - + -
177B LEU 4.9 0.2 - - - +
312B PRO* 3.7 13.2 - - - +
313B ASP* 4.6 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 1.3 77.6 - - - +
168B ARG* 1.3 68.2 + - - +
169B THR* 4.6 6.3 - - - -
174B LEU* 3.7 3.2 - - - +
175B ARG* 2.9 76.9 + - + +
176B ILE 5.1 0.4 - - - -
177B LEU* 4.0 20.9 - - + -
253B ASP* 2.6 31.4 + - - -
254B PHE* 5.1 0.2 - + - -
272B VAL* 3.6 36.3 - - + -
273B PRO* 3.6 13.7 - - + +
274B ASP* 4.6 9.9 - - - -
312B PRO* 3.9 15.5 - - + -
329B GLU* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B TYR* 1.3 81.7 - - - +
169B THR* 1.3 68.1 + - - +
170B LYS 4.0 0.2 + - - -
172B GLY* 4.4 9.4 - - - +
173B GLU 3.4 8.1 - - - +
174B LEU* 4.6 2.9 - - + +
274B ASP* 4.1 2.9 - - - +
----------------------------------------------------------
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