Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 5BZR
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 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 3.2 24.0 + - - -
137A VAL 5.6 0.2 - - - -
138A THR* 6.1 0.8 - - - +
151A THR* 3.8 20.3 - - + +
152A ILE 3.2 12.1 - - - +
153A VAL* 3.7 26.8 - - + +
154A ASN* 5.3 1.6 - - - -
157A GLY 3.4 13.9 + - - +
158A THR* 1.3 77.4 - - - +
160A TYR* 1.3 60.8 + - - +
161A SER* 5.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL 4.5 2.0 + - - +
138A THR* 3.3 38.6 - - + -
139A ASP* 3.8 17.3 + - - -
140A LEU* 3.7 19.3 - - + -
150A ILE 3.8 0.8 - - - +
151A THR* 3.4 0.5 - - - -
152A ILE* 2.7 52.4 + - + +
159A ARG* 1.3 74.8 - - - +
161A SER* 1.3 76.4 + - - +
162A LYS* 3.7 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A THR* 4.5 11.2 - - - +
150A ILE 3.2 5.2 - - - -
151A THR* 2.8 32.5 + - - +
159A ARG* 5.2 1.6 - - - +
160A TYR* 1.3 87.8 - - - +
162A LYS* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 4.6 3.4 + - - -
140A LEU* 2.8 34.3 + - + -
141A PRO* 4.7 4.4 + - - +
143A SER* 2.7 31.8 + - - +
149A THR* 4.6 4.5 - - - -
150A ILE* 2.8 37.0 + - + +
160A TYR* 3.7 33.1 + - + +
161A SER* 1.3 76.8 - - - +
163A LYS* 1.3 70.0 + - - +
164A GLY 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 5.2 0.3 + - - -
144A PHE 4.6 0.7 - - - +
145A ASP* 4.3 15.9 + - - -
146A GLY 2.8 31.7 + - - +
147A PRO* 4.0 15.4 - - + +
148A VAL 3.2 11.4 - - - +
149A THR* 4.5 5.4 - - - +
162A LYS* 1.3 85.3 - - - +
164A GLY* 1.3 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A SER* 5.1 4.3 - - - -
144A PHE 3.2 14.4 - - - -
146A GLY* 3.4 14.9 + - - -
148A VAL* 2.8 37.3 + - - +
150A ILE* 3.7 10.9 - - - +
162A LYS 3.8 1.0 + - - -
163A LYS* 1.3 75.4 - - - +
165A GLU* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 5.2 0.7 - - - +
143A SER* 3.7 2.8 - - - -
144A PHE* 2.8 57.4 + - + -
145A ASP 3.9 9.0 - - - +
146A GLY* 4.0 5.2 - - - -
147A PRO* 4.6 5.4 - - + +
148A VAL* 3.6 11.3 - - - +
150A ILE* 3.9 7.4 - - - +
164A GLY* 1.3 75.5 - - - +
166A TYR* 1.3 81.4 + - - +
167A ARG* 2.8 59.5 + - - +
173A ILE* 4.5 9.9 - - + +
----------------------------------------------------------
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