Contacts of the strand formed by residues 180 - 186 (chain D) in PDB entry 2W3S
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 ALA 180 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.5 27.6 - - + -
24D ASP* 5.0 4.0 - - + +
177D GLU* 5.1 4.3 - - + +
178D GLY 3.5 6.4 + - - +
179D GLN* 1.3 76.4 + - - +
181D ALA* 1.3 63.1 + - - +
194D CYS* 3.4 2.4 - - - +
195D SER* 2.9 34.5 + - - +
238D LEU* 3.7 5.1 - - - +
255D MET 3.2 9.9 - - - +
256D ARG* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.7 3.4 - - - -
180D ALA* 1.3 76.8 - - - +
182D LEU* 1.3 61.7 + - - +
192D ILE* 5.1 1.1 - - + -
193D HIS 3.6 6.3 - - - -
194D CYS* 4.1 9.4 - - + -
235D GLY 5.3 0.7 - - - +
238D LEU* 3.7 12.8 - - + +
239D ALA* 3.7 31.6 - - + +
242D CYS* 3.7 8.1 - - + -
254D LYS* 3.3 8.5 - - - +
255D MET 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.7 10.5 - - + +
26D LEU* 4.0 32.8 - - + -
27D PRO 5.6 0.7 - - - +
28D CYS* 4.7 16.6 - - + -
32D THR* 4.3 11.2 - - + -
181D ALA* 1.3 77.2 - - - +
183D ALA* 1.3 59.9 + - - +
184D LEU* 4.1 26.9 - - + -
191D VAL 3.6 1.2 - - - +
192D ILE* 3.5 5.5 - - - +
193D HIS* 2.8 46.7 + - + +
242D CYS* 4.3 1.3 - - - -
253D CYS 3.3 20.9 - - - +
254D LYS* 4.0 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 1.3 74.1 - - - +
184D LEU* 1.3 61.9 + - - +
185D PRO* 3.7 3.7 - - - +
190D VAL* 5.2 3.8 - - + -
191D VAL 3.4 4.3 - - - +
192D ILE* 3.8 16.6 - - + -
242D CYS* 3.6 12.2 - - + +
243D ALA* 3.6 33.0 - - + +
246D ALA* 4.0 4.6 - - + +
252D PRO* 3.6 5.7 - - - +
253D CYS 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D CYS* 5.4 0.7 - - + -
29D PRO* 4.5 15.5 - - + -
182D LEU* 4.1 22.7 - - + -
183D ALA* 1.3 76.3 - - - +
185D PRO* 1.3 69.7 - - + +
186D ALA* 3.4 3.5 + - + +
190D VAL* 4.5 2.0 - - - -
191D VAL* 2.8 49.6 + - + +
193D HIS* 4.2 23.1 - - + +
252D PRO* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 3.6 20.9 + - - +
183D ALA 3.7 8.5 - - - +
184D LEU* 1.3 83.0 - - - +
186D ALA* 1.3 59.0 + - - +
187D GLU 4.1 1.1 + - - -
189D GLY 3.7 9.0 - - - +
190D VAL* 4.5 5.1 - - + -
246D ALA* 4.0 21.1 - - + +
247D ARG* 5.9 1.8 - - - -
250D GLY* 4.0 28.3 - - - +
251D ARG 4.1 7.4 - - - +
252D PRO* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 4.5 14.8 - - - +
184D LEU* 3.4 7.4 + - + +
185D PRO* 1.3 74.3 - - - +
187D GLU* 1.3 74.2 + - + +
188D GLY 3.6 0.9 - - - -
189D GLY* 3.0 24.2 + - - +
190D VAL 5.1 0.2 - - - -
191D VAL* 4.6 17.0 - - + -
----------------------------------------------------------
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