Contacts of the strand formed by residues 163 - 174 (chain A) in PDB entry 2QBX
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 ARG 163 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASP* 4.5 0.7 - - - -
160A LEU* 2.7 57.7 + - + +
161A GLY 3.9 11.5 + - - -
162A GLY* 1.3 85.0 - - - +
164A VAL* 1.3 60.5 + - - +
3P GLU* 3.8 37.0 + - + -
4P TRP* 4.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLN* 3.9 29.2 - - + +
158A VAL 3.1 11.9 - - - +
159A ASP* 4.6 12.6 - - + +
162A GLY 5.5 1.6 - - - +
163A ARG* 1.3 73.2 - - - +
165A MET* 1.3 60.3 + - - +
1P SER* 3.2 38.4 - - - +
2P ASN* 2.9 33.4 + - - +
3P GLU* 3.7 7.6 + - - +
4P TRP* 3.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.9 26.9 - - + +
58A ASP 3.8 14.8 - - - +
59A GLU* 5.5 1.1 - - - -
61A MET* 3.8 30.1 - - - -
101A SER* 4.5 0.2 - - - +
156A SER 3.8 1.6 - - - +
157A GLN* 3.3 2.8 - - - -
158A VAL* 2.7 48.1 + - + +
160A LEU* 3.8 18.8 - - + -
163A ARG 3.7 1.8 + - - -
164A VAL* 1.3 72.5 - - - +
166A LYS* 1.3 61.4 + - - +
167A ILE* 4.1 23.1 + - + +
196A ILE* 5.5 0.7 - - - -
2P ASN* 3.6 2.0 - - - +
4P TRP* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE 4.0 0.2 - - - +
101A SER* 2.8 25.5 + - - -
102A VAL 4.5 2.2 + - - -
104A ASP* 5.2 5.5 + - - -
151A ALA* 5.2 6.0 - - + +
152A ASP 5.0 2.0 + - - -
153A GLU* 4.7 4.8 + - - -
155A PHE* 3.4 52.3 - - + -
156A SER 3.4 4.9 - - - +
157A GLN* 3.8 15.3 - - - +
164A VAL 3.8 0.2 + - - -
165A MET* 1.3 72.9 - - - +
167A ILE* 1.3 55.3 + - - +
168A ASN* 3.6 24.2 + - - +
1P SER* 3.6 25.6 - - - +
2P ASN* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR 4.0 9.6 - - - +
58A ASP* 3.6 10.1 - - - +
59A GLU* 3.4 58.8 - - + +
99A LYS* 4.1 20.0 - - + -
100A PHE 3.6 8.1 - - - +
101A SER* 3.8 1.8 - - - +
155A PHE* 3.8 14.2 - - - +
156A SER* 3.4 15.1 + - - +
165A MET* 4.1 18.6 + - + +
166A LYS* 1.3 72.6 - - - +
168A ASN* 1.3 71.3 + - - +
169A THR* 4.2 0.9 + - - +
196A ILE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 3.4 4.9 - - - -
100A PHE* 2.9 58.3 + - + +
102A VAL 5.2 3.3 + - - -
151A ALA* 3.2 26.2 - - - +
152A ASP* 3.1 24.3 + - - +
154A SER 3.0 28.0 + - - -
155A PHE* 3.4 9.5 - - - +
166A LYS* 3.6 17.7 - - - +
167A ILE* 1.3 74.5 - - - +
169A THR* 1.3 62.5 + - - +
170A GLU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 4.3 6.6 + - - -
97A GLU* 4.0 20.9 - - + +
98A MET 3.4 5.2 - - - +
99A LYS* 2.7 45.8 + - + +
152A ASP* 3.6 13.2 + - - +
154A SER 5.3 0.6 + - - -
167A ILE 4.2 0.9 + - - -
168A ASN* 1.3 75.9 - - - +
170A GLU* 1.3 79.4 + - - +
171A VAL* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL 3.7 1.0 - - - +
97A GLU* 3.6 2.3 - - - +
98A MET* 2.9 38.1 + - + +
100A PHE* 3.8 19.1 - - + -
149A ILE* 4.0 12.8 - - + -
150A ALA 3.8 20.6 - - - +
152A ASP* 3.0 38.0 - - - +
168A ASN* 5.5 0.2 - - + -
169A THR* 1.3 74.9 - - - +
171A VAL* 1.3 63.0 + - - +
172A ARG* 2.7 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 4.6 16.2 - - + +
96A VAL 3.4 15.3 - - - +
97A GLU* 3.9 26.7 - - + +
169A THR* 4.8 4.3 - - + -
170A GLU* 1.3 79.9 + - - +
172A ARG* 1.3 91.2 + - - +
173A SER* 5.6 0.2 - - - -
201A PHE* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 3.7 0.5 - - - -
96A VAL* 2.8 36.6 + - - +
98A MET* 4.1 7.6 - - + +
121A LEU* 4.4 2.9 - - + -
146A VAL* 3.7 21.1 - - + -
147A ASP* 2.7 38.0 + - - +
148A THR 4.2 6.3 + - - -
149A ILE* 3.6 32.5 - - + +
150A ALA 5.1 1.8 - - - +
170A GLU* 2.7 33.9 + - - +
171A VAL* 1.3 93.7 + - - +
173A SER* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.7 21.5 + - - -
94A ILE 3.1 7.6 - - - -
95A HIS* 3.0 39.0 + - - -
146A VAL* 4.0 9.1 - - - +
171A VAL* 5.6 0.4 - - - -
172A ARG* 1.3 75.6 - - - +
174A PHE* 1.3 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.6 14.3 - - - +
94A ILE* 2.8 66.0 + - + +
96A VAL* 3.6 28.5 - - + -
121A LEU* 5.9 0.2 - - + -
123A TYR* 3.3 64.4 - + + +
146A VAL* 3.8 21.3 - - + -
173A SER* 1.3 79.1 - - - +
175A GLY* 1.3 60.5 + - - +
177A VAL* 4.8 7.2 - - + -
182A PHE* 4.2 8.5 - + - -
184A LEU* 4.0 12.8 - - + -
----------------------------------------------------------
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