Contacts of the helix formed by residues 265 - 271 (chain D) in PDB entry 5ON2
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 HIS 265 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TYR* 6.3 1.3 - + - -
242D THR 5.8 1.3 - - - -
243D LEU* 3.4 32.1 - - + +
244D THR 5.4 0.6 + - - -
261D VAL* 3.4 25.2 - - + +
262D ALA 3.8 7.4 + - - +
263D ALA 3.4 3.5 + - - +
264D GLY* 1.3 79.0 - - - +
266D PRO* 1.4 89.5 - - + +
267D LEU* 3.3 14.8 + - + +
268D ALA* 3.2 5.4 + - - +
269D GLN* 3.0 21.2 + - - +
328D MET* 3.4 14.9 - - + +
332D THR 3.9 15.9 + - - -
333D GLY 3.4 20.4 + - - +
334D ALA* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TYR* 3.8 17.7 + - + +
264D GLY 4.2 3.6 - - - +
265D HIS* 1.4 104.5 - - + +
267D LEU* 1.3 56.5 + - - +
269D GLN* 3.3 8.0 + - + +
270D LYS* 2.8 30.1 + - - +
328D MET* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D VAL* 4.2 20.9 - - + -
239D TYR* 3.7 38.0 + - + -
243D LEU* 4.6 17.3 - - + -
261D VAL* 4.9 4.5 - - + -
265D HIS* 3.3 17.1 + - + +
266D PRO* 1.3 77.7 - - - +
268D ALA* 1.3 59.4 + - - +
270D LYS* 3.5 4.7 + - - +
271D ALA* 3.1 25.3 + - - +
305D THR* 3.9 22.9 - - + +
307D PHE* 3.8 25.9 - - + -
320D VAL* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D VAL* 4.5 8.3 - - + +
262D ALA 4.0 13.0 - - - +
263D ALA 3.8 19.7 - - - +
265D HIS* 3.2 12.9 + - + +
267D LEU* 1.3 80.6 - - - +
269D GLN* 1.3 62.7 + - - +
271D ALA* 3.5 1.3 + - - -
272D ALA 3.3 15.8 + - - -
278D LEU* 3.6 16.3 - - + +
282D ILE* 3.7 15.7 - - + +
305D THR* 4.8 5.2 - - + -
322D ALA* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA 5.4 0.2 + - - -
264D GLY* 5.8 2.9 - - - +
265D HIS 3.0 13.0 + - - +
266D PRO* 3.3 10.5 + - + +
268D ALA* 1.3 72.4 - - - +
270D LYS* 1.3 66.0 + - - +
272D ALA* 3.2 20.2 + - - +
273D GLU* 3.2 21.2 + - - +
282D ILE* 4.7 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D TYR* 3.8 33.2 - - + -
240D ASP* 6.1 1.3 - - - -
266D PRO 2.8 16.6 + - - +
267D LEU 3.7 5.8 - - - +
268D ALA 3.4 0.2 - - - -
269D GLN* 1.3 77.4 - - - +
271D ALA* 1.3 58.5 + - - +
273D GLU* 3.0 29.0 + - - +
274D ASN* 4.7 1.4 - - - +
307D PHE* 4.6 11.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU 3.1 17.1 + - - +
269D GLN 3.3 0.6 - - - -
270D LYS* 1.3 73.9 - - - +
272D ALA* 1.3 59.6 + - - +
273D GLU 3.3 2.0 - - - -
274D ASN* 3.0 22.0 - - - +
275D ASN* 3.3 15.6 - - - +
278D LEU* 3.4 22.6 - - + +
305D THR* 4.0 19.5 - - - +
307D PHE* 3.7 20.2 - - + -
----------------------------------------------------------
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