Contacts of the strand formed by residues 170 - 179 (chain O) in PDB entry 4WNC
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 ILE 170 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161O ALA* 4.0 35.9 - - + +
164O ILE* 3.9 23.8 - - + -
165O HIS* 3.1 15.4 + - + +
169O GLY* 1.3 73.9 - - - +
171O VAL* 1.3 65.1 + - - +
172O GLU* 3.7 26.5 - - - +
173O GLY 4.3 1.3 - - - +
224O LEU* 3.9 20.1 - - + +
227O LYS* 3.7 17.1 - - + +
228O LEU* 4.4 13.0 - - + -
245O LEU* 4.7 12.8 - - + -
247O CYS* 4.2 11.9 - - + -
248O ARG 3.6 4.7 - - - +
249O LEU* 4.7 0.2 - - + -
250O GLU* 4.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170O ILE* 1.3 74.1 - - - +
172O GLU* 1.3 74.5 + - + +
227O LYS* 3.7 21.4 + - - +
248O ARG* 2.7 33.8 + - + +
249O LEU 3.9 3.1 - - - +
250O GLU* 3.6 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170O ILE* 3.5 6.4 - - - -
171O VAL* 1.3 90.5 - - + +
173O GLY* 1.3 58.4 + - - +
227O LYS* 3.3 12.6 - - - +
247O CYS* 3.3 2.6 - - - +
248O ARG* 2.8 52.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172O GLU* 1.3 76.8 - - - +
174O LEU* 1.3 65.9 + - - +
227O LYS 2.9 8.6 + - - +
228O LEU* 3.3 23.3 - - - +
229O THR 3.3 21.1 + - - -
245O LEU* 4.5 1.3 - - - -
246O THR 3.3 10.3 - - - -
247O CYS* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173O GLY* 1.3 76.4 - - - +
175O MET* 1.3 60.2 + - - +
229O THR* 3.3 36.3 - - + +
230O GLY* 4.6 2.7 - - - +
244O ASP 3.9 1.0 - - - +
245O LEU* 4.4 2.2 - - - +
246O THR* 2.8 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 175 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153O THR* 3.8 23.6 - - + -
157O LEU* 3.8 24.7 - - + -
174O LEU* 1.3 74.6 - - - +
176O THR* 1.3 72.4 + - - +
177O THR* 4.2 9.4 - - + +
211O THR* 3.9 21.5 - - + -
214O ALA* 4.1 16.4 - - + +
228O LEU* 6.4 0.4 - - + -
229O THR 2.9 12.6 + - - +
230O GLY* 3.0 6.6 - - - -
231O MET* 3.0 52.5 + - - +
243O VAL* 4.0 19.5 - - + -
244O ASP 3.4 8.7 - - - +
245O LEU* 4.5 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O MET* 1.3 78.4 + - - +
177O THR* 1.3 69.0 + - - +
178O VAL* 4.2 7.4 + - + +
231O MET* 3.3 17.2 - - - +
233O PHE* 3.6 35.0 - - + -
242O VAL 4.0 0.2 - - - +
243O VAL* 3.6 1.0 - - - -
244O ASP* 2.8 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153O THR* 4.3 18.4 - - + +
175O MET* 4.2 10.5 - - + +
176O THR* 1.3 76.0 - - - +
178O VAL* 1.3 62.1 + - - +
179O HIS* 4.0 8.2 - - + +
211O THR* 4.8 2.7 - - + -
231O MET 3.0 6.4 + - - +
232O ALA* 3.3 24.5 - - + -
233O PHE 2.8 32.1 + - - +
242O VAL 3.2 12.9 + - - -
243O VAL* 4.3 4.7 - - - -
314O TYR* 2.8 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176O THR* 4.2 11.9 - - + +
177O THR* 1.3 73.1 - - - +
179O HIS* 1.3 60.4 + - - +
233O PHE* 3.5 11.4 - - + +
235O VAL* 3.8 34.5 - - + -
240O VAL 4.8 0.3 - - - +
241O SER* 3.3 3.6 - - - -
242O VAL* 2.9 53.3 + - + +
244O ASP* 6.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 179 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O CYS* 3.8 24.5 - - - -
153O THR* 3.8 7.4 + - - -
177O THR* 4.0 13.5 - - + +
178O VAL* 1.3 75.9 - - - +
180O ALA* 1.3 87.7 + - - +
182O THR* 3.9 19.3 - - + -
232O ALA* 5.1 2.2 - - + -
233O PHE 2.8 9.9 + - - +
234O ARG* 3.4 28.1 + - - +
235O VAL* 3.0 29.1 + - - +
241O SER* 3.4 13.0 + - - -
314O TYR* 3.3 24.0 - - - -
316O ASN* 3.9 16.1 - - + +
----------------------------------------------------------
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