Contacts of the helix formed by residues 229 - 243 (chain T) in PDB entry 6O81
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 229 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228T LEU* 1.3 79.3 - - - +
230T TYR* 1.3 57.6 + - - +
232T ILE* 3.4 7.0 + - - +
233T GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 230 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228T LEU 3.4 3.4 - - - +
229T LYS* 1.3 76.5 - - - +
231T ASN* 1.3 60.6 + - - +
233T GLU* 3.3 6.0 + - - +
234T VAL* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223T PRO 5.8 4.7 - - - +
228T LEU* 3.7 12.4 + - - +
229T LYS 3.4 0.4 - - - -
230T TYR* 1.3 75.6 - - - +
232T ILE* 1.3 60.9 + - - +
234T VAL* 3.4 6.8 + - - +
235T VAL* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60T ALA* 4.7 22.2 - - + +
61T ILE* 5.2 10.1 - - + +
228T LEU 3.3 16.4 + - - +
229T LYS* 3.7 7.4 - - - +
230T TYR 3.3 0.2 - - - -
231T ASN* 1.3 77.9 - - - +
233T GLU* 1.3 56.8 + - - +
235T VAL* 3.4 6.4 + - - +
236T CYS* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229T LYS 2.9 17.9 + - - +
230T TYR* 3.3 7.2 + - - +
231T ASN 3.3 0.2 - - - -
232T ILE* 1.3 74.8 - - - +
234T VAL* 1.3 58.9 + - - +
236T CYS* 3.3 6.7 + - - +
237T GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230T TYR 2.9 17.0 + - - +
231T ASN* 3.8 7.4 - - - +
232T ILE 3.3 0.2 - - - -
233T GLU* 1.3 76.7 - - - +
235T VAL* 1.3 57.8 + - - +
237T GLU* 3.4 6.4 + - - +
238T TYR* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188T LEU* 5.5 9.9 - - + -
222T ILE* 5.5 12.1 - - + -
231T ASN 2.9 17.9 + - - +
232T ILE* 3.8 7.6 - - - +
234T VAL* 1.3 75.2 - - - +
236T CYS* 1.3 56.8 + - - +
238T TYR* 3.4 6.4 + - - +
239T ILE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 236 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61T ILE* 6.3 3.1 - - + -
88T ILE* 5.2 15.4 - - + +
232T ILE 2.9 17.8 + - - +
233T GLU* 3.7 7.9 - - - +
235T VAL* 1.3 75.4 - - - +
237T GLU* 1.3 59.5 + - - +
239T ILE* 3.4 6.8 + - - +
240T VAL* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233T GLU 2.9 17.8 + - - +
234T VAL* 3.8 7.4 - - - +
236T CYS* 1.3 77.6 - - - +
238T TYR* 1.3 57.3 + - - +
240T VAL* 3.3 6.5 + - - +
241T LYS* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 238 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221T ILE 5.7 4.5 - - - +
222T ILE* 6.0 4.0 - - + -
234T VAL 2.9 18.6 + - - +
235T VAL* 3.8 7.2 - - - +
236T CYS 3.3 0.2 - - - -
237T GLU* 1.3 75.3 - - - +
239T ILE* 1.3 57.7 + - - +
241T LYS* 4.2 4.2 - - - +
242T LYS* 2.9 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235T VAL 2.9 18.1 + - - +
236T CYS* 3.8 6.7 - - - +
237T GLU 3.3 0.2 - - - -
238T TYR* 1.3 76.4 - - - +
240T VAL* 1.3 62.9 + - - +
242T LYS* 4.9 0.7 - - - -
243T ILE* 3.2 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88T ILE* 5.2 12.3 - - + +
236T CYS 2.9 17.9 + - - +
237T GLU* 3.3 7.2 + - - +
239T ILE* 1.3 78.1 - - - +
241T LYS* 1.3 60.8 + - - +
243T ILE 4.4 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237T GLU 2.9 16.9 + - - +
238T TYR* 4.2 4.0 - - - +
240T VAL* 1.3 79.0 - - - +
242T LYS* 1.3 59.1 + - + +
243T ILE 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238T TYR* 2.9 20.4 + - + +
239T ILE* 4.9 0.7 - - - -
241T LYS* 1.3 80.2 - - - +
243T ILE* 1.3 65.2 + - - +
244T PRO* 3.3 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154T ALA* 4.4 23.1 - - + -
184T HIS* 5.8 9.6 - - + -
239T ILE* 3.2 24.8 + - + +
240T VAL* 4.4 7.8 - - - +
241T LYS 5.2 0.2 - - - -
242T LYS* 1.3 76.3 - - - +
244T PRO* 1.3 64.8 - - - +
----------------------------------------------------------
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