Contacts of the helix formed by residues 275 - 280 (chain Y) in PDB entry 2CKV
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 THR 275 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Y LEU* 4.0 15.9 - - - +
170Y LEU* 3.6 19.3 - - + -
226Y GLN* 3.5 43.0 + - + +
229Y PHE* 3.1 32.6 - - - -
269Y PRO* 5.2 1.3 - - - -
274Y LYS* 1.3 79.4 + - - +
276Y PHE* 1.3 67.9 + - - +
277Y LEU* 3.0 13.9 - - + +
278Y ASP* 3.0 27.0 + - - +
279Y ILE* 4.2 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 276 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y ASN* 5.8 5.6 - - + -
36Y LEU* 3.6 26.9 - - + -
37Y SER* 5.0 9.2 - - - -
40Y LEU* 5.4 3.1 - - + -
74Y LEU* 5.2 8.7 - - + -
77Y LEU* 3.6 33.0 - - + -
126Y LEU* 6.2 0.7 - - + -
129Y LEU* 4.3 18.8 - - + +
133Y LEU* 3.6 11.4 - - - +
167Y MET* 4.2 22.4 - - + -
170Y LEU* 3.7 17.9 - - + -
223Y GLU* 4.7 5.2 - - + -
226Y GLN* 3.2 33.6 + - - -
265Y ALA 5.2 1.8 - - - -
266Y GLN* 4.9 14.6 - - + -
269Y PRO* 5.6 4.5 - - + -
275Y THR* 1.3 76.1 - - + +
277Y LEU* 1.3 58.3 + - - +
278Y ASP 3.3 0.2 - - - -
279Y ILE* 3.2 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129Y LEU* 5.3 0.9 - - - -
133Y LEU* 4.1 2.4 - - - +
169Y VAL* 5.9 0.7 - - + -
170Y LEU* 3.2 57.0 - - + +
173Y THR* 3.6 15.3 - - + +
174Y CYS* 3.3 30.5 - - + +
177Y LYS* 5.5 2.9 - - - +
229Y PHE* 4.5 2.5 - - + -
230Y VAL* 3.9 27.6 - - + -
275Y THR* 3.0 6.6 - - + +
276Y PHE* 1.3 77.9 - - - +
278Y ASP* 1.3 66.6 + - - +
279Y ILE 3.1 3.7 + - - -
280Y ASN* 2.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Y LEU* 4.8 5.6 - - + -
229Y PHE* 3.3 27.4 - - - -
273Y GLY 4.0 4.3 - - - +
274Y LYS* 3.6 29.6 - - + +
275Y THR* 3.0 24.1 + - - +
277Y LEU* 1.3 78.4 - - - +
279Y ILE* 1.3 57.2 + - - +
280Y ASN* 3.3 5.9 + - - +
281Y LYS 4.3 2.1 + - - -
282Y ASP* 3.5 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Y LEU* 5.4 2.0 - - + -
40Y LEU* 3.9 24.0 - - + -
77Y LEU* 3.1 48.5 - - + +
80Y GLY* 3.5 30.5 - - - +
81Y VAL* 5.3 4.9 - - + -
133Y LEU* 3.6 23.4 - - + +
134Y PHE* 5.9 0.3 - - - -
275Y THR 4.6 2.0 - - - +
276Y PHE* 3.2 17.3 - - - +
277Y LEU 3.1 0.4 + - - -
278Y ASP* 1.3 77.6 - - - +
280Y ASN* 1.3 63.8 + - - +
281Y LYS 3.5 0.4 - - - -
282Y ASP* 3.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 280 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Y LEU* 3.4 36.7 - - - +
174Y CYS* 3.5 19.9 + - - +
177Y LYS* 4.7 19.0 - - + +
178Y SER* 3.2 23.4 + - - +
277Y LEU* 2.7 27.6 + - - +
278Y ASP 3.3 2.6 - - - +
279Y ILE* 1.3 79.3 - - - +
281Y LYS* 1.3 71.6 + - + +
282Y ASP 3.8 0.2 - - - -
----------------------------------------------------------
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