Contacts of the strand formed by residues 156 - 161 (chain P) in PDB entry 2BDI
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 156 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P ILE* 3.4 27.8 - - + -
19P GLY 4.2 3.8 - - - +
20P GLU* 3.3 22.0 + - - +
21P ASP* 3.3 23.9 + - - +
22P CYS* 3.0 6.0 - - - -
139P SER* 2.8 36.9 - - - -
140P GLY 2.9 10.0 + - - +
144P LEU* 3.8 27.8 - - + +
152P PRO* 3.8 16.2 - - + +
154P VAL* 2.9 28.7 + - - +
155P LEU* 1.3 77.2 + - - +
157P CYS* 1.3 53.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P ILE* 4.1 1.8 - - - -
19P GLY* 3.2 4.3 - - - -
20P GLU* 2.8 37.9 + - + +
21P ASP 5.1 0.4 - - - +
22P CYS* 2.1 44.6 - - + -
27P GLN* 4.0 11.7 - - - -
137P LEU* 3.8 21.1 - - + -
138P VAL 3.6 2.0 - - - -
139P SER* 3.7 13.0 - - - -
156P GLN* 1.3 70.4 - - - +
158P VAL* 1.4 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P ILE* 3.4 24.0 - - + -
17P ILE 4.2 1.1 - - - +
18P ASN 3.5 25.6 - - - +
19P GLY* 3.8 2.9 - - - -
137P LEU* 3.3 6.6 - - - +
138P VAL* 3.0 51.5 + - + +
157P CYS* 1.4 75.1 - - - +
159P ASN* 1.3 75.4 + - - +
160P VAL* 4.3 9.2 - - + -
188P LYS* 3.7 27.6 - - + +
189P ASP 4.5 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P SER* 3.6 17.0 + - - +
136P CYS* 3.0 22.4 + - - +
137P LEU* 3.9 15.2 - - - +
158P VAL* 1.3 82.2 - - - +
160P VAL* 1.3 70.1 + - - +
186P ASP* 5.1 1.0 - - - +
188P LYS* 3.7 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P SER* 4.5 0.7 - - - -
136P CYS* 2.9 25.4 + - - +
138P VAL* 3.8 22.0 - - + -
158P VAL* 4.3 9.6 - - + -
159P ASN* 1.3 84.6 - - - +
161P SER* 1.3 63.1 + - - +
183P ALA* 4.0 19.4 - - + +
184P GLY* 3.7 16.6 - - - -
188P LYS* 3.7 30.1 - - + +
189P ASP* 4.4 4.9 - - - +
199P LEU* 4.0 10.3 - - + -
228P TYR* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M ASN* 6.1 1.1 - - - -
133P GLY* 3.6 16.0 + - - -
134P ASN 3.1 10.8 - - - -
135P SER* 3.7 15.4 + - - -
160P VAL* 1.3 76.0 - - - +
162P VAL* 1.3 70.4 + - - +
163P VAL* 3.3 2.4 + - - +
183P ALA* 3.1 2.6 - - - -
184P GLY* 2.7 30.8 + - - +
----------------------------------------------------------
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