Contacts of the strand formed by residues 185 - 190 (chain B) in PDB entry 2BEW
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 CYS 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.2 7.1 + - - +
131B THR* 3.3 4.5 - - - +
132B ILE* 2.9 29.1 + - - +
161B LYS* 3.4 26.0 - - + +
178B CYS* 3.9 50.5 - - + +
181B ASP* 3.9 14.4 - - - -
183B ASN 3.3 15.5 + - - -
184B PRO* 1.3 74.4 - - - +
186B ILE* 1.3 62.0 + - - +
210B LEU* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 4.3 8.1 - - + -
110B ILE* 4.1 12.1 - - + -
132B ILE* 3.4 24.7 - - + +
134B SER* 5.6 0.9 - - - -
154B PHE* 3.5 45.8 - - + -
160B ILE* 4.0 16.6 - - + -
161B LYS 2.8 15.0 + - - +
162B VAL* 3.4 6.8 - - + +
163B VAL* 3.0 28.1 + - - +
178B CYS* 5.3 0.2 - - - -
184B PRO 5.9 0.2 - - - -
185B CYS* 1.3 75.8 - - - +
187B PHE* 1.3 61.0 + - - +
188B PHE* 3.6 37.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.8 1.1 - - + -
131B THR* 4.6 3.4 - - + -
132B ILE 2.9 12.5 + - - +
133B ARG* 3.2 4.7 - - + -
134B SER 3.0 24.8 + - - -
163B VAL* 3.4 12.3 - - + -
165B PRO* 3.6 28.9 - - + -
171B ALA* 3.4 25.4 - - + -
174B LEU* 3.8 12.8 - - + -
175B LEU* 3.6 46.4 - - + -
178B CYS* 4.0 21.5 - - - -
185B CYS 4.1 0.2 - - - -
186B ILE* 1.3 72.3 - - - +
188B PHE* 1.3 60.9 + - - +
189B GLU* 3.4 38.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ALA* 3.7 22.9 - - + -
103B ILE* 4.4 5.8 - - + -
134B SER* 3.4 21.3 - - - -
136B TRP* 3.4 31.6 - + + -
150B PRO* 4.1 11.9 - - + -
151B GLU* 4.1 17.3 - - + -
154B PHE* 4.2 21.1 - + - -
162B VAL* 3.9 27.1 - - + -
163B VAL 3.0 7.2 + - - -
164B ILE* 3.7 19.3 - - + +
165B PRO* 3.1 23.4 - - - +
186B ILE* 3.6 26.5 - - + -
187B PHE* 1.3 71.7 - - - +
189B GLU* 1.3 61.4 + - - +
190B PRO* 3.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.4 4.0 - - + -
27B VAL* 3.7 19.5 - - + +
133B ARG* 2.8 43.7 + - - +
134B SER 2.9 13.0 + - - +
135B PRO* 3.3 3.5 - - - +
136B TRP* 2.8 24.5 + - - +
165B PRO* 4.7 1.1 - - - -
175B LEU* 4.3 0.3 - - - +
187B PHE* 3.4 37.5 - - + +
188B PHE* 1.3 71.6 - - - +
190B PRO* 1.3 69.0 - - + +
191B LYS* 3.0 1.6 + - - -
194B TYR* 2.5 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.5 11.2 - - + +
136B TRP* 3.4 33.0 - - + +
137B GLY* 6.0 0.2 - - - -
164B ILE* 4.2 2.5 - - + -
165B PRO* 3.4 33.0 - - + +
188B PHE 3.6 6.7 - - - +
189B GLU* 1.3 79.5 - - + +
191B LYS* 1.3 63.5 + - - +
192B ILE* 3.2 2.5 - - + +
193B LEU* 3.0 27.5 + - + +
194B TYR* 3.7 4.5 + - - -
228B GLY* 4.0 6.3 - - - -
229B THR* 3.6 22.7 - - - +
----------------------------------------------------------
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