Contacts of the strand formed by residues 179 - 186 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ARG* 3.2 41.7 - - - +
153C TRP* 3.7 20.4 - - + -
174C ASN* 3.6 20.6 + - - +
145G SER* 3.3 3.3 - - - -
146G ASP* 2.7 36.2 + - + +
177G ASP* 3.6 5.1 + - - +
178G GLU* 1.3 79.6 - - - +
180G CYS* 1.3 58.8 + - - +
195G ASP* 2.8 42.4 + - - +
196G ILE* 3.5 14.8 + - - +
197G HIS* 3.9 16.8 - - - +
198G CYS* 3.2 9.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TRP* 4.3 4.3 - - - -
104G TRP* 3.2 41.3 - - + -
141G PHE* 3.8 14.6 - - + -
144G LEU 3.7 4.3 - - - -
145G SER* 3.8 7.0 - - - +
179G ARG* 1.3 75.9 - - - +
181G ALA* 1.3 61.1 + - - +
195G ASP* 3.4 1.6 - - - -
196G ILE* 2.9 34.5 + - - +
198G CYS* 2.0 47.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C TRP* 4.4 1.0 - - + -
168C TRP* 3.9 16.2 - - + -
141G PHE* 3.6 8.7 - - - -
142G LEU* 2.9 39.6 + - + +
144G LEU* 2.9 42.2 + - + +
180G CYS* 1.3 74.9 - - - +
182G ILE* 1.3 61.8 + - - +
193G TRP* 4.9 0.4 - - + -
194G ASN 3.3 6.5 - - - +
195G ASP* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 4.2 7.6 - - + -
139G SER* 3.5 8.3 - - - +
140G TYR 3.0 10.5 - - - +
141G PHE* 3.5 32.3 - - + -
142G LEU* 4.2 3.8 - - - +
181G ALA* 1.3 72.8 - - - +
183G ILE* 1.3 60.3 + - - +
184G ASN* 3.2 25.4 - - - +
193G TRP* 3.1 7.4 - - - +
194G ASN* 2.8 50.7 + - + +
196G ILE* 3.7 28.3 - - + -
202G GLN* 3.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ILE* 4.9 2.5 - - + -
127G GLN* 3.5 35.7 - - - +
130G ILE* 5.0 4.5 - - + -
131G ILE* 4.3 15.3 - - + -
134G LEU* 3.9 14.1 - - + -
139G SER* 3.5 1.2 - - - -
140G TYR* 2.7 42.6 + - + +
142G LEU* 3.6 26.2 - - + +
182G ILE* 1.3 73.2 - - - +
184G ASN* 1.3 63.1 + - - +
191G TRP* 4.1 10.5 - - + -
192G GLY 3.3 15.7 - - - +
193G TRP* 4.0 9.0 - - + +
205G ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 3.7 16.1 - - + +
169C HIS* 3.0 22.7 + - - -
138G SER 4.0 3.6 - - - +
139G SER* 2.9 32.1 + - - +
182G ILE* 3.2 23.0 - - - +
183G ILE* 1.3 75.7 - - - +
185G PHE* 1.3 64.1 + - - +
186G ARG* 4.7 3.6 + - - +
191G TRP* 3.4 14.8 - - - -
192G GLY 3.1 15.5 + - - -
194G ASN* 2.6 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ARG* 3.6 68.3 + - + +
138G SER 4.8 0.2 + - - -
184G ASN* 1.3 78.1 - - - +
186G ARG* 1.3 68.7 + - - +
187G SER* 3.6 26.5 - - - -
188G SER 5.2 0.2 - - - -
190G GLU* 3.4 45.8 - - + -
191G TRP* 3.8 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C HIS* 3.5 27.8 - - - +
170C SER* 3.4 17.2 + - - -
172C GLU* 3.4 19.2 + - - +
184G ASN* 4.7 3.3 + - - +
185G PHE* 1.3 79.4 - - - +
187G SER* 1.3 63.0 + - - +
189G GLU* 2.7 44.7 + - + -
190G GLU* 2.5 44.0 + - - +
194G ASN* 2.7 26.6 + - - -
----------------------------------------------------------
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