Contacts of the strand formed by residues 179 - 185 (chain H) in PDB entry 3WBR
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 179 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E HIS* 5.9 5.3 - - - -
151F ARG* 3.7 37.2 - - - +
153F TRP* 3.8 15.7 - - + -
174F ASN* 3.7 15.9 + - - +
145H SER* 3.2 6.1 - - - -
146H ASP* 2.7 33.4 + - + +
177H ASP 4.0 0.4 + - - -
178H GLU* 1.3 78.4 + - - +
180H CYS* 1.3 60.5 + - - +
195H ASP* 2.9 42.0 + - + +
196H ILE* 3.6 18.2 + - - +
197H HIS* 3.5 23.4 - - - +
198H CYS* 3.3 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F TRP* 4.2 5.4 - - - -
104H TRP* 3.4 40.8 - - + -
141H PHE* 3.9 14.1 - - + -
144H LEU 3.9 4.3 - - - -
145H SER* 3.9 7.0 - - - +
179H ARG* 1.3 76.4 - - - +
181H ALA* 1.3 60.5 - - - +
195H ASP* 3.3 2.8 - - - -
196H ILE* 2.8 36.9 + - - +
198H CYS* 2.1 48.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F TRP* 4.2 1.8 - - + -
168F TRP* 4.0 24.5 - - + -
141H PHE* 3.6 10.0 - - - -
142H LEU* 3.0 35.2 + - + +
144H LEU* 3.0 34.6 + - + +
180H CYS* 1.3 74.1 - - - +
182H ILE* 1.3 61.9 + - - +
193H TRP* 5.2 0.2 - - + -
194H ASN 3.2 9.2 - - - +
195H ASP* 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E PRO* 4.2 6.7 - - + -
139H SER* 3.4 9.9 - - - +
140H TYR 3.1 11.7 - - - +
141H PHE* 3.6 27.6 - - + -
142H LEU* 4.1 5.2 - - - +
181H ALA* 1.3 72.5 - - - +
183H ILE* 1.3 59.7 + - - +
184H ASN* 3.3 26.4 + - - +
193H TRP* 3.1 7.3 - - - +
194H ASN* 2.8 51.0 + - + +
196H ILE* 3.8 33.0 - - + -
202H GLN* 3.6 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H ILE* 5.1 0.2 - - + -
127H GLN* 3.6 34.5 - - - +
130H ILE* 4.7 7.6 - - + -
131H ILE* 4.3 10.5 - - + -
134H LEU* 4.0 19.3 - - + -
139H SER* 3.5 1.4 - - - -
140H TYR* 2.7 47.2 + - + +
142H LEU* 3.7 22.0 - - + +
182H ILE* 1.3 73.7 - - - +
184H ASN* 1.3 65.8 + - - +
191H TRP* 4.1 10.5 - - + -
192H GLY 3.4 14.4 - - - +
193H TRP* 4.3 5.8 - - + +
205H ILE* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E PRO* 3.8 13.7 - - + +
169F HIS* 3.0 40.8 + - - -
138H SER 3.7 10.3 - - - +
139H SER* 2.9 26.1 + - - +
182H ILE* 3.3 22.4 - - - +
183H ILE* 1.3 75.9 - - - +
185H PHE* 1.3 64.8 + - - +
186H ARG* 4.4 5.2 + - - +
191H TRP* 3.4 14.1 - - - -
192H GLY 3.0 18.4 + - - -
194H ASN* 4.8 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H ARG* 3.4 72.5 + - + +
138H SER 4.4 2.0 + - - -
184H ASN* 1.3 80.8 - - - +
186H ARG* 1.3 80.5 + - - +
187H SER* 4.0 9.4 - - - -
190H GLU* 3.4 39.9 - - + -
191H TRP* 3.4 38.1 - + + -
----------------------------------------------------------
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