Contacts of the strand formed by residues 276 - 281 (chain B) in PDB entry 1WG8
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 LYS 276 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL 3.7 1.4 - - - +
232B ILE* 3.6 2.8 - - - +
233B ALA* 2.8 36.3 + - - +
234B PHE 4.1 10.3 + - - -
236B SER* 4.1 22.8 + - - +
239B ASP* 3.7 46.8 + - - +
258B PRO* 4.1 12.8 - - + -
259B LEU 3.6 5.4 - - - -
260B VAL* 4.5 11.2 - - + -
274B SER* 3.3 17.6 + - - +
275B ALA* 1.3 80.4 - - - +
277B LEU* 1.3 61.5 + - - +
278B ARG* 3.8 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.4 31.6 - - + +
13B GLU* 4.5 3.1 - - + -
14B ALA* 3.9 32.8 - - + +
17B LEU* 3.4 32.3 - - + -
230B VAL* 4.2 7.6 - - + -
231B VAL 3.5 4.9 - - - +
232B ILE* 3.8 22.0 - - + +
258B PRO* 3.2 5.7 - - - +
259B LEU* 2.9 48.0 + - + +
276B LYS* 1.3 72.0 - - - +
278B ARG* 1.3 72.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B VAL* 3.6 0.7 - - - -
231B VAL* 2.9 34.3 + - - +
239B ASP* 2.7 41.3 + - - -
242B VAL* 4.1 14.1 - - + -
243B LYS* 3.6 52.2 - - - +
246B LEU* 3.7 17.4 - - + +
255B THR* 3.2 17.2 + - - +
256B LYS 4.6 8.9 + - - -
258B PRO* 3.0 42.6 - - + +
276B LYS* 4.5 4.2 - - - +
277B LEU* 1.3 84.2 - - - +
279B ALA* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.7 35.2 - - + +
228B ARG* 5.7 0.4 - - + -
229B LEU 3.1 12.6 - - - +
230B VAL* 4.1 11.9 - - + -
246B LEU* 4.1 4.8 - - - +
253B VAL* 3.8 3.8 - - - +
254B LEU* 2.8 29.6 + - + -
255B THR* 2.9 15.1 + - + +
278B ARG* 1.3 76.7 - - - +
280B ALA* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 3.3 5.5 - - - +
229B LEU* 2.8 33.6 + - + +
246B LEU* 4.0 20.2 - - + +
251B LEU* 3.6 33.4 - - + -
252B LYS 3.3 9.9 - - - +
253B VAL* 4.2 6.1 - - + -
254B LEU* 4.0 4.0 - - - +
279B ALA* 1.3 76.1 - - - +
281B GLU* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLY* 3.9 15.5 - - - +
227B GLY 3.3 7.6 - - - +
228B ARG* 2.9 43.0 + - - +
251B LEU* 3.6 6.7 - - - -
252B LYS* 2.7 67.2 + - + +
254B LEU* 4.0 6.7 - - + -
280B ALA* 1.3 74.6 - - - +
282B LYS* 1.3 77.2 + - - +
283B GLU* 5.0 2.8 - - - +
----------------------------------------------------------
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