Contacts of the strand formed by residues 242 - 248 (chain B) in PDB entry 1WZN
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 242 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 4.2 10.8 - - - +
26B GLU* 3.0 40.4 + - - +
113B PHE* 5.9 4.6 - - - -
114B SER* 6.1 0.7 - - - -
144B ASP* 3.1 26.4 + - - +
145B PHE 3.8 15.3 - - - +
146B PRO* 4.8 4.9 - - + -
230B GLY* 3.3 5.4 - - - -
231B ASN* 3.2 34.7 + - - +
232B LEU* 3.7 19.8 - - - +
240B ASP 3.7 0.6 - - - -
241B MET* 1.3 81.1 - - - +
243B TYR* 1.3 70.9 + - - +
244B TRP* 3.3 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR 4.0 0.2 - - - +
144B ASP* 3.1 8.5 - - - +
145B PHE* 2.9 67.0 + + + +
146B PRO 4.2 1.3 - - - -
147B CYS* 3.5 45.4 - - + +
212B PRO* 3.7 33.4 - - + -
228B ILE* 4.8 5.4 - - + -
229B TYR 3.4 5.6 - - - +
236B LEU* 4.0 22.2 - - + -
237B SER 5.8 0.2 - - - -
240B ASP* 3.0 37.0 + - + -
241B MET* 4.1 2.6 - - - -
242B ARG* 1.3 78.4 - - - +
244B TRP* 1.3 63.4 + - - +
245B ILE 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 4.1 12.3 - - + -
29B PHE* 3.6 33.9 - + + -
30B VAL* 4.3 10.5 - - + -
112B PHE* 3.7 31.0 - + - -
142B ILE* 3.6 23.6 - - + -
143B THR 3.4 5.8 - - - -
144B ASP* 3.6 30.2 - - + +
227B LYS 3.6 0.5 - - - +
228B ILE* 3.5 5.2 - - - +
229B TYR* 2.8 43.1 + - + +
230B GLY* 4.6 0.9 - - - -
231B ASN* 4.6 2.3 - - - +
232B LEU* 3.9 30.2 - - + +
242B ARG* 3.3 39.9 + - - +
243B TYR* 1.3 80.2 + - - +
245B ILE* 1.3 62.9 + - - +
246B VAL* 4.0 7.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 5.8 0.2 - - + -
141B PHE* 3.5 8.5 - - + +
142B ILE* 3.5 4.9 - - - -
143B THR* 2.9 41.7 + - + +
145B PHE* 3.2 31.2 - - + -
212B PRO 4.1 13.7 - - - +
215B VAL* 3.6 21.5 - - + -
216B ARG* 4.5 3.4 - - + +
219B ALA* 4.6 7.4 - - + -
226B VAL* 3.8 20.2 - - + -
227B LYS 3.5 0.7 - - - -
228B ILE* 3.7 33.9 - - + -
244B TRP* 1.3 76.7 - - - +
246B VAL* 1.3 66.1 + - - +
247B GLY* 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.8 37.7 - - + -
37B ASP* 4.3 9.2 - - + -
140B VAL* 4.5 5.6 - - + -
141B PHE 3.3 7.9 - - - +
142B ILE* 4.5 5.8 - - + -
225B LYS 3.8 0.5 - - - +
226B VAL* 3.2 7.0 - - - -
227B LYS* 2.8 44.3 + - + +
229B TYR* 3.9 26.9 - - + -
244B TRP* 4.7 3.1 - - + +
245B ILE* 1.3 79.0 - - - +
247B GLY* 1.3 63.0 + - - +
248B ILE* 4.0 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLY 3.8 0.3 - - - +
140B VAL* 3.1 8.1 - - - +
141B PHE* 2.8 42.1 + - - +
219B ALA* 6.1 0.2 - - - -
223B PHE* 3.8 26.5 - - - -
225B LYS 3.5 6.1 - - - -
226B VAL* 4.5 4.0 - - - -
245B ILE* 4.2 1.6 - - - +
246B VAL* 1.3 73.5 - - - +
248B ILE* 1.3 61.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 3.7 31.9 - - + +
39B LYS* 4.4 16.2 - - + -
138B GLY 4.4 2.5 - - - +
139B GLY 3.6 7.2 - - - +
140B VAL* 4.2 9.6 - - + -
223B PHE* 4.0 2.9 - - - +
224B GLU* 3.3 24.5 + - - +
225B LYS* 2.8 36.6 + - + +
227B LYS* 3.8 34.3 - - + -
246B VAL* 4.3 9.0 - - + +
247B GLY* 1.3 75.7 - - - +
249B ALA* 1.3 73.7 + - - +
----------------------------------------------------------
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