Contacts of the helix formed by residues 267 - 279 (chain K) in PDB entry 1OEY
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 LEU 267 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K PRO 3.8 1.2 + - - -
266K LEU* 1.3 71.1 - - - +
268K LYS* 1.3 65.5 + - - +
270K LEU* 3.0 7.6 + - + +
271K LEU* 2.9 37.2 + - + +
285K LEU* 4.1 22.4 - - + -
297K LEU* 4.4 15.5 - - + +
298K LEU* 3.4 13.2 - - - +
299K SER* 3.4 35.7 - - - +
300K ASP* 2.8 20.5 + - - +
303K VAL* 4.1 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J ARG* 5.3 0.9 - - - +
254J ASP* 4.9 8.4 + - - -
266K LEU* 3.2 29.3 - - + -
267K LEU* 1.3 79.3 - - - +
269K ASP* 1.3 69.9 + - - +
271K LEU* 3.6 10.7 + - - +
272K GLU* 3.1 29.2 + - - +
300K ASP* 5.6 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 269 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J ARG* 2.9 39.3 + - - -
317J LYS* 5.6 3.1 - - - -
259K GLU* 4.1 6.3 - - - +
265K PRO* 5.6 2.5 - - + -
266K LEU* 3.0 26.5 + - + +
268K LYS* 1.3 89.7 - - - +
270K LEU* 1.3 62.0 + - + +
272K GLU* 3.5 17.0 + - - +
273K LEU* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K LEU* 4.3 17.0 - - + -
257K VAL* 5.8 5.4 - - + -
265K PRO* 3.7 35.4 - - + -
266K LEU 3.1 14.7 + - - +
267K LEU* 3.0 8.6 + - + +
269K ASP* 1.3 76.0 - - - +
271K LEU* 1.3 59.3 + - - +
273K LEU* 3.6 9.4 + - + +
274K THR* 2.8 35.4 + - - +
285K LEU* 3.8 15.4 - - + +
297K LEU* 5.1 0.4 - - + -
303K VAL* 4.3 22.0 - - + -
306K MSE 4.6 3.8 - - + -
322K TRP* 4.2 11.4 - - + -
324K LEU* 4.4 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267K LEU* 2.9 36.8 + - + +
268K LYS* 3.8 9.0 - - - +
270K LEU* 1.3 74.5 - - - +
272K GLU* 1.3 58.8 + - - +
274K THR* 3.7 2.5 - - - +
275K ARG* 2.9 82.4 + - + +
283K ILE* 4.6 10.3 - - + +
284K ALA* 5.9 0.2 - - - -
285K LEU* 3.9 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317J LYS* 3.9 33.6 + - - +
268K LYS* 3.1 18.4 + - - +
269K ASP* 3.6 18.3 - - - +
271K LEU* 1.3 75.3 - - - +
273K LEU* 1.3 58.1 + - - +
275K ARG* 3.9 5.1 - - - +
276K ARG* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K LEU* 4.0 27.4 - - + -
255K ILE* 3.6 30.3 - - + -
256K ALA 3.6 13.5 - - - +
257K VAL* 4.0 20.6 - - + -
269K ASP 3.0 18.2 + - - +
270K LEU* 3.8 12.3 - - + +
272K GLU* 1.3 77.3 - - - +
274K THR* 1.3 67.5 + - + +
276K ARG* 3.4 30.3 + - - +
277K GLU* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K ILE* 4.5 9.6 - - + -
270K LEU 2.8 22.6 + - - +
271K LEU* 3.3 4.9 + - - -
273K LEU* 1.3 83.6 - - + +
275K ARG* 1.3 64.1 + - - +
277K GLU* 4.4 1.6 - - - -
278K PHE* 2.8 45.4 + - + +
283K ILE* 3.6 15.0 - - - +
285K LEU* 3.5 18.1 - - + +
324K LEU* 3.9 25.1 - - + -
326K ILE* 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271K LEU* 2.9 62.3 + - - +
272K GLU* 4.1 4.5 - - - +
274K THR* 1.3 75.0 - - - +
276K ARG* 1.3 58.5 + - - +
279K GLN* 2.9 29.8 + - - -
280K ARG 3.2 27.3 + - - +
281K GLU* 3.9 38.0 + - + +
283K ILE* 4.0 15.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256K ALA 4.7 6.9 + - - -
272K GLU* 2.9 28.1 + - - +
273K LEU* 3.4 45.9 - - - +
275K ARG* 1.3 78.2 - - - +
277K GLU* 1.3 71.8 + - - +
278K PHE 3.6 0.2 + - - -
279K GLN* 3.6 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253K LYS* 2.7 39.1 + - - +
255K ILE* 3.7 44.5 - - + +
256K ALA 5.4 0.2 + - - -
273K LEU 2.9 18.8 + - - +
274K THR 3.2 2.7 + - - +
276K ARG* 1.3 87.2 + - - +
278K PHE* 1.3 71.8 + - + +
279K GLN* 3.4 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242K VAL* 3.6 32.3 - - + -
244K TYR* 3.7 50.6 + + + -
253K LYS* 4.3 26.9 - - + -
255K ILE* 4.0 17.0 - - + -
274K THR* 2.8 27.4 + - - +
277K GLU* 1.3 81.6 - - + +
279K GLN* 1.3 72.0 + - - +
280K ARG* 3.2 19.9 + - + +
283K ILE* 5.3 3.1 - - + -
326K ILE* 4.7 10.8 - - + -
282M ASP* 3.5 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K ARG 2.9 13.6 + - - -
276K ARG* 3.8 13.2 - - - +
277K GLU 3.4 5.9 + - - +
278K PHE* 1.3 79.0 + - - +
280K ARG* 1.3 59.8 + - - +
281M GLU* 2.8 44.7 + - + +
282M ASP* 3.0 17.9 + - + +
329M LYS* 3.2 35.0 - - - +
----------------------------------------------------------
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