Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 2QQK
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 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 3.5 48.4 - - + +
65A ASN* 4.0 21.3 + - - +
67A LYS* 3.8 12.0 + - - -
147A GLU 5.5 0.7 - - - +
149A CYS* 4.5 5.4 - - - -
150A SER* 4.9 2.4 + - - -
172A ASN 4.2 3.3 + - - -
173A LEU* 1.3 75.8 + - - +
175A CYS* 1.3 58.8 + - - +
176A THR* 5.2 3.8 - - - +
248A THR* 6.1 0.9 - - - +
249A PHE 3.5 2.9 - - - +
250A HIS* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A CYS* 2.1 51.6 - - - -
150A SER* 3.3 18.2 - - - -
163A PRO* 5.3 0.9 - - - -
173A LEU* 4.7 9.0 - - + -
174A ASP* 1.3 71.1 - - - +
176A THR* 1.3 63.9 + - - +
177A PHE* 3.9 28.3 + - + -
247A LEU 3.7 0.3 - - - +
248A THR* 3.3 6.3 - - - +
249A PHE* 2.8 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 5.4 4.3 + - - -
63A GLU* 5.7 5.8 - - + -
64A PRO* 5.1 17.3 - - + -
150A SER* 2.9 40.8 + - - +
151A LYS 3.6 4.0 + - - +
152A ASN* 5.7 0.2 - - - +
174A ASP 5.2 1.3 - - - +
175A CYS* 1.3 79.1 - - - +
177A PHE* 1.3 63.3 + - - +
178A THR* 4.0 7.4 + - - -
220A PRO* 4.4 18.8 - - + -
247A LEU 3.2 9.2 - - - -
248A THR* 4.4 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A CYS 4.4 7.0 - - - -
151A LYS* 3.6 22.2 - - + -
153A PHE* 4.3 17.5 - + + -
160A ILE* 3.8 23.6 - - + -
161A GLU 3.9 19.5 - - - -
163A PRO* 4.0 15.7 - - + -
175A CYS* 3.9 29.6 - - + -
176A THR* 1.3 74.8 - - - +
178A THR* 1.3 60.7 + - - +
179A ILE* 5.5 2.0 - - + +
245A LEU 4.1 0.3 - - - +
246A SER* 3.2 2.3 - - - -
247A LEU* 2.7 55.9 + - + +
249A PHE* 4.1 19.3 - - + -
260A PHE* 4.1 18.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 5.7 1.0 + - - -
151A LYS 3.2 6.5 + - - -
152A ASN* 3.4 21.6 - - - +
153A PHE* 3.0 29.8 + - - -
176A THR* 4.0 9.8 + - - -
177A PHE* 1.3 72.5 - - - +
179A ILE* 1.3 68.2 + - - +
180A LEU* 4.0 23.5 + - + -
219A ILE* 5.7 3.5 - - + +
220A PRO* 4.6 5.5 - - - +
244A ILE* 4.2 9.0 - - + -
245A LEU 3.6 2.9 - - - -
246A SER* 2.7 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 4.0 17.0 - - + +
160A ILE* 5.4 4.0 - - + -
177A PHE 5.5 1.6 - - - +
178A THR* 1.3 75.8 - - - +
180A LEU* 1.3 66.2 + - - +
187A ILE* 3.4 46.1 - - + +
189A LEU* 4.3 14.6 - - + -
244A ILE* 3.3 7.1 - - - +
245A LEU* 2.7 44.1 + - + +
247A LEU* 6.3 2.0 - - + -
264A TYR* 3.7 45.5 - - + -
266A LEU* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A NAG 5.8 2.0 - - - +
152A ASN* 4.3 28.7 - - + +
153A PHE 3.3 19.6 + - - +
154A THR* 4.6 5.7 - - - +
178A THR* 4.0 12.8 - - + +
179A ILE* 1.3 77.1 - - - +
181A ALA* 1.3 61.7 + - - +
243A GLY 3.4 2.5 - - - +
244A ILE* 3.4 35.7 - - + -
266A LEU* 4.0 12.0 - - - +
444A LEU* 4.8 6.3 - - + -
----------------------------------------------------------
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