Contacts of the strand formed by residues 154 - 157 (chain R) in PDB entry 2QJK
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 SER 154 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R CYS* 4.5 0.4 - - - -
148R PHE* 3.5 4.5 - - - -
149R CYS* 2.9 31.0 + - - -
153R GLY* 1.3 75.1 - - - +
155R HIS* 1.3 62.2 + - - +
156R TYR* 3.8 12.1 - - - -
164R LYS 3.2 8.3 - - - -
166R PRO* 3.0 30.1 - - - +
167R ALA* 3.3 26.4 + - - +
200R FES 3.6 12.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 155 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385M THR* 5.5 2.0 + - - -
142R GLY* 3.2 9.2 - - - -
143R ASP* 3.0 47.4 + - + +
144R PHE* 3.9 20.4 - + + -
147R TRP 3.7 3.4 - - - +
148R PHE* 3.7 23.7 - + - -
153R GLY* 3.6 12.5 + - - -
154R SER* 1.3 76.4 - - - +
156R TYR* 1.3 61.8 + - - +
162R ILE* 2.8 27.9 - - - +
163R ARG* 2.8 15.1 + - - -
164R LYS* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R CYS* 3.6 8.0 - - - -
130R THR* 3.2 27.5 + - - -
136R PRO* 4.7 6.1 - - + -
141R SER 4.0 1.6 - - - +
144R PHE* 4.1 8.4 + - - +
146R GLY* 3.1 6.8 + - - -
147R TRP* 2.9 48.4 + - + +
149R CYS* 4.7 4.9 - - + -
154R SER* 3.8 28.0 - - - -
155R HIS* 1.3 79.1 - - - +
157R ASP* 1.3 64.4 + - - +
160R GLY* 3.6 15.0 - - - -
161R ARG 2.9 13.0 - - - +
162R ILE* 3.8 3.8 - - + -
163R ARG* 4.9 0.2 - - - -
167R ALA* 3.4 18.7 - - + +
169R GLU 3.6 16.2 - - - -
171R LEU* 3.2 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88R VAL* 5.4 2.0 - - + -
93R LEU* 3.9 0.3 - - - +
144R PHE* 3.5 17.7 - - + +
146R GLY* 3.6 3.4 - - - -
147R TRP* 3.4 10.9 - - - -
156R TYR* 1.3 77.0 - - - +
158R SER* 1.3 62.3 + - - +
159R ALA* 2.7 22.5 + - - +
160R GLY 2.8 17.2 + - - -
161R ARG* 2.6 77.5 + - - +
163R ARG* 3.2 31.3 + - - +
----------------------------------------------------------
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