Contacts of the helix formed by residues 257 - 268 (chain D) in PDB entry 4OQB
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 SER 257 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL 4.2 1.0 + - - -
256D CYS* 1.3 76.4 - - - +
258D THR* 1.3 65.0 + - - +
259D ASN* 3.8 7.2 + - - +
260D ASP* 3.2 28.5 + - - +
261D LEU* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D SER* 1.3 74.6 - - - +
259D ASN* 1.3 56.7 + - - +
261D LEU* 3.1 11.9 + - + +
262D LYS* 2.8 46.6 + - - +
276D GLU* 4.5 24.1 + - + +
279D ILE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D SER* 3.3 8.6 + - - +
258D THR* 1.3 80.9 - - - +
260D ASP* 1.3 60.8 + - - +
262D LYS* 3.7 18.9 + - - +
263D GLU* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL 5.4 0.3 - - - +
256D CYS* 4.1 22.7 - - + -
257D SER* 3.2 29.7 + - - +
258D THR 3.2 0.4 - - - -
259D ASN* 1.3 79.2 - - - +
261D LEU* 1.3 59.7 + - - +
263D GLU* 3.5 6.8 + - - +
264D LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 4.0 38.6 - - + +
253D LYS* 5.6 3.8 - - - +
256D CYS* 4.2 13.5 - - + +
257D SER 3.4 19.1 - - - +
258D THR* 3.1 11.1 + - + +
260D ASP* 1.3 73.6 - - - +
262D LYS* 1.3 65.8 + - - +
264D LEU* 3.5 24.4 - - + +
265D LEU* 3.4 26.7 + - - +
276D GLU* 5.9 1.3 - - + +
279D ILE* 3.5 19.5 - - + -
280D LEU* 4.3 21.8 - - + -
283D VAL* 3.7 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D THR* 2.8 30.4 + - - +
259D ASN* 3.7 20.1 + - - +
260D ASP 3.3 0.2 - - - -
261D LEU* 1.3 73.9 - - - +
263D GLU* 1.3 59.1 + - + +
265D LEU* 3.3 6.7 + - - +
266D ILE* 3.1 37.6 + - + +
272D VAL* 3.7 27.9 - - + +
273D PRO 5.4 0.7 - - - -
279D ILE* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D ASN* 3.1 27.2 + - - +
260D ASP* 3.7 5.6 - - - +
262D LYS* 1.3 76.4 - - + +
264D LEU* 1.3 64.2 + - - +
265D LEU 3.4 0.2 - - - -
266D ILE* 3.9 16.2 - - + +
267D PHE* 3.2 24.3 + - - +
336D PRO* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 5.0 8.1 - - + -
256D CYS* 5.0 7.6 - - - -
260D ASP* 2.9 25.2 + - + +
261D LEU* 3.5 31.9 - - + +
263D GLU* 1.3 79.2 - - - +
265D LEU* 1.3 58.1 + - - +
267D PHE* 3.5 3.1 + - - +
268D ASN* 2.7 34.2 + - - -
283D VAL* 4.2 11.4 - - + -
287D MET* 5.9 3.4 - - - -
333D TRP* 4.1 22.9 - - + +
335D THR* 4.4 12.3 - - + -
336D PRO* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D LEU 3.4 14.3 + - - +
262D LYS 3.3 6.5 + - - +
264D LEU* 1.3 75.5 - - - +
266D ILE* 1.3 63.9 + - - +
268D ASN* 3.1 7.6 + - - -
269D LYS 3.2 0.2 + - - -
270D GLN* 2.9 52.0 + - + +
271D GLN 4.5 1.6 - - - +
272D VAL* 4.4 10.1 - - + -
273D PRO* 3.8 28.9 - - + -
279D ILE* 4.1 13.9 - - + +
282D ARG* 4.2 11.9 - - + +
283D VAL* 3.7 33.9 - - + +
333D TRP* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D LYS* 3.1 28.5 + - + +
263D GLU* 4.1 16.4 - - + +
265D LEU* 1.3 75.9 - - - +
267D PHE* 1.3 63.3 + - - +
269D LYS* 3.1 21.9 + - - +
270D GLN 4.2 6.7 - - - +
272D VAL* 3.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU 3.2 20.0 + - - +
264D LEU 3.6 5.2 - - - +
265D LEU 3.3 0.2 - - - -
266D ILE* 1.3 77.6 - - - +
268D ASN* 1.3 60.5 + - - +
269D LYS* 3.2 15.8 + - - +
334D VAL* 3.4 45.3 - - + -
336D PRO* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D LEU* 2.7 24.9 + - - +
265D LEU 3.1 7.6 + - - +
267D PHE* 1.3 79.5 - - - +
269D LYS* 1.3 71.8 + - - +
270D GLN* 3.3 15.1 + - + -
291D ALA* 4.0 11.8 - - + +
331D LYS* 5.3 8.6 + - - +
332D GLU 4.8 0.2 - - - +
333D TRP* 3.2 45.0 - - + +
334D VAL* 3.0 45.0 + - - +
----------------------------------------------------------
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