Contacts of the helix formed by residues 286 - 294 (chain B) in PDB entry 4KEU
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 ASP 286 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 3.3 13.8 - - - +
236B ASN* 2.9 21.5 + - - -
277B ARG* 2.4 40.5 + - - +
282B LEU* 2.9 24.7 + - + +
285B GLU* 1.3 81.0 - - - +
287B THR* 1.3 60.7 + - - +
289B PRO* 3.0 6.9 - - - +
290B PHE* 2.9 29.5 + - - +
293B ARG* 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 3.1 39.8 - - + +
236B ASN* 3.1 30.0 + - - +
239B THR* 5.1 0.9 - - + -
253B ILE* 4.6 9.9 - - + -
282B LEU* 3.9 2.0 + - - +
283B ILE* 3.4 20.9 + - + +
286B ASP* 1.3 79.9 + - - +
288B ILE* 1.3 66.5 + - + +
290B PHE* 3.0 4.7 + - - +
291B LEU* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.3 3.1 - - + -
283B ILE* 2.7 46.9 + - + +
284B PHE* 4.1 20.2 - - + +
287B THR* 1.3 76.1 - - + +
289B PRO* 1.3 67.2 - - + +
291B LEU* 3.2 11.3 + - + +
292B LYS* 3.0 47.4 + - + +
298B GLU* 6.2 0.2 - - - +
301B ILE* 4.3 26.2 - - + -
305B PHE* 4.1 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 5.1 2.5 - - + -
285A GLU* 4.0 24.7 - - + +
283B ILE 3.6 0.2 - - - +
284B PHE 3.1 25.6 - - - +
285B GLU 3.7 11.2 - - - +
286B ASP 3.0 14.4 - - - +
288B ILE* 1.3 97.2 - - + +
290B PHE* 1.3 55.6 + - - +
292B LYS* 3.3 11.6 + - + +
293B ARG* 3.0 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 6.4 0.4 - - - -
236B ASN* 3.5 57.0 - - + +
237B GLU* 4.5 11.4 - - + -
240B LEU* 4.1 25.1 - - + -
286B ASP* 2.9 16.0 + - - +
287B THR 3.0 8.5 + - - +
289B PRO* 1.3 76.1 - - - +
291B LEU* 1.3 71.8 + - + +
293B ARG* 3.4 30.5 + - - +
294B ASN* 2.8 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ASN 4.6 0.7 - - - +
239B THR* 4.3 9.9 - - + -
240B LEU* 4.1 30.5 - - + +
243B ILE* 4.1 26.9 - - + -
253B ILE* 4.8 6.7 - - + -
287B THR* 2.9 32.9 + - + +
288B ILE* 3.2 12.7 + - + +
290B PHE* 1.3 87.4 - - + +
292B LYS* 1.3 62.2 + - - +
294B ASN* 2.8 20.3 + - - -
296B VAL* 3.2 32.4 + - + +
301B ILE* 4.8 14.8 - - + -
304B ILE* 5.4 2.5 - - + -
305B PHE* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 4.2 30.6 - - - +
58A GLN* 4.7 5.9 - - - +
288B ILE* 3.0 43.8 + - + +
289B PRO* 3.7 8.5 - - + +
291B LEU* 1.3 76.2 - - - +
293B ARG* 1.3 61.8 + - + +
294B ASN 3.0 1.4 + - - -
295B GLY* 3.2 11.1 + - - -
296B VAL 3.5 18.2 - - - +
297B ASN 5.5 0.9 - - - -
298B GLU* 3.1 31.7 + - - +
301B ILE* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO 5.7 4.0 - - - -
277A ARG* 6.1 10.3 - - - +
285A GLU* 4.5 7.9 + - - -
286B ASP* 5.0 2.4 + - - -
289B PRO* 3.0 40.8 + - + +
290B PHE* 3.6 39.5 + - - +
291B LEU 3.2 0.2 - - - -
292B LYS* 1.3 75.8 - - + +
294B ASN* 1.3 62.4 + - - +
295B GLY 3.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.8 38.6 - - + +
244B LYS* 5.4 7.3 - - - +
290B PHE* 2.8 36.1 - - - +
291B LEU 2.8 9.7 + - - +
293B ARG* 1.3 85.3 + - - +
295B GLY* 1.3 57.6 + - - +
296B VAL* 3.3 10.1 + - - +
----------------------------------------------------------
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