Contacts of the strand formed by residues 169 - 175 (chain A) in PDB entry 2XHC
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 GLN 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.5 12.1 + - - -
92A VAL* 4.1 4.2 - - - +
161A VAL* 3.7 25.7 - - + +
162A VAL 3.2 5.6 - - - +
163A GLN* 2.5 35.6 + - + +
167A GLY 4.0 4.8 + - - +
168A GLU* 1.3 84.6 - - - +
170A ASP* 1.3 62.4 + - - +
171A VAL* 4.4 7.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 2.8 34.8 + - - +
87A ARG* 2.8 46.3 + - - +
160A VAL 3.6 1.2 - - - +
161A VAL* 3.4 4.2 - - - +
162A VAL* 2.8 40.4 + - + +
164A THR* 5.6 1.0 + - - -
169A GLN* 1.3 73.8 - - - +
171A VAL* 1.3 62.6 + - - +
172A TYR* 3.6 30.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
159A LYS* 4.0 22.2 - - + -
160A VAL 3.4 3.6 - - - +
161A VAL* 4.2 16.4 - - + -
169A GLN* 5.2 7.2 - - + +
170A ASP* 1.3 78.9 - - - +
172A TYR* 1.3 70.6 + - - +
173A TYR* 3.5 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 4.0 19.1 - - + -
84A TYR 3.6 18.2 - - - -
85A ALA* 3.3 8.8 - - - +
86A ARG* 2.7 39.7 + - + +
87A ARG 3.9 4.2 + - - -
158A LYS 3.4 0.9 - - - +
159A LYS* 3.5 2.9 - - - -
160A VAL* 2.7 53.5 + - + +
162A VAL* 3.8 22.5 - - + +
170A ASP* 3.6 31.1 + - + +
171A VAL* 1.3 79.7 - - - +
173A TYR* 1.3 64.4 + - - +
174A ILE* 3.9 16.8 - - + -
196A LEU* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 3.9 9.4 - - - +
97A VAL* 4.0 13.5 - - + -
114A TYR* 3.5 65.0 - + + +
157A MET* 3.3 29.2 - - + +
158A LYS 3.4 3.8 - - - -
159A LYS* 3.7 41.6 + - + +
171A VAL* 3.5 24.0 - - + +
172A TYR* 1.3 76.2 - - - +
174A ILE* 1.3 60.8 + - - +
175A PRO* 3.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 3.7 30.5 - - + -
157A MET* 3.1 3.6 - - - -
158A LYS* 2.7 44.6 + - + +
160A VAL* 3.8 26.0 - - + -
172A TYR* 4.5 8.7 - - + +
173A TYR* 1.3 72.9 - - - +
175A PRO* 1.3 83.4 - - + +
176A LEU 3.1 0.9 + - - -
178A VAL* 4.2 0.4 - - + -
179A PHE* 3.9 20.6 - - + +
184A ILE* 5.0 7.2 - - + -
196A LEU* 4.5 12.8 - - + +
197A ALA* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ILE* 4.1 12.1 - - + -
155A GLU* 3.6 11.4 - - + +
156A ARG 3.9 4.3 - - - +
157A MET* 3.3 18.1 - - + -
173A TYR 3.5 9.4 - - - +
174A ILE* 1.3 85.7 - - + +
176A LEU* 1.3 65.9 + - - +
177A ASP* 3.2 11.2 - - - +
178A VAL* 2.9 31.6 + - + +
179A PHE 3.3 4.3 + - - -
200A ARG* 3.5 38.8 - - - +
----------------------------------------------------------
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