Contacts of the helix formed by residues 285 - 290 (chain B) in PDB entry 3KEU
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 285 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ARG 3.2 4.0 + - - -
284B PRO 1.3 70.1 - - - -
286B PRO* 1.3 78.6 - - - +
287B MET* 3.7 11.3 + - - +
288B GLN* 2.3 49.1 + - - +
289B LEU* 3.2 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 4.3 13.7 - - + +
48B GLY 3.8 18.4 - - - +
49B TYR* 3.7 36.6 + - + -
50B ALA 5.7 0.2 - - - +
285B SER* 1.3 87.2 - - - +
287B MET* 1.3 61.4 + - - +
289B LEU* 3.1 21.1 + - + +
290B GLU* 3.3 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 5.9 4.0 - - - +
72A ASN* 3.5 16.8 - - + +
73A ASN* 4.1 8.1 - - + +
74A MET* 3.2 33.7 - - + -
16B ARG* 4.2 17.9 - - - +
49B TYR* 3.2 25.1 - - + +
277B GLN* 6.1 2.9 - - - -
285B SER* 3.1 9.4 + - - +
286B PRO* 1.3 79.6 - - - +
288B GLN* 1.3 65.7 + - + +
289B LEU 3.4 0.3 + - - -
290B GLU* 3.5 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 4.1 3.8 - - - +
273B CYS 3.9 5.0 - - - +
274B ALA* 3.2 22.7 - - + +
277B GLN* 3.3 54.1 + - - +
278B ALA* 3.4 14.9 - - - +
283B ARG 3.5 3.6 - - - +
284B PRO* 3.0 16.2 - - + +
285B SER* 2.3 47.2 + - - +
287B MET* 1.3 80.1 - - + +
289B LEU* 1.3 60.1 + - - +
290B GLU 3.4 3.6 + - - +
292B ARG* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ALA* 3.9 17.3 - - + -
229B VAL* 3.8 24.7 - - + +
230B PHE* 3.7 35.4 - - + -
231B VAL 5.4 1.7 + - - +
270B THR* 3.5 11.5 - - + +
271B ILE* 4.4 4.9 - - + -
274B ALA* 4.1 9.6 - - + -
284B PRO* 3.6 44.9 - - + +
285B SER 3.2 13.0 + - - +
286B PRO* 3.1 10.6 + - + +
288B GLN* 1.3 77.7 - - - +
290B GLU* 1.3 66.5 + - - +
291B LEU* 3.3 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.3 6.2 - - + +
17B GLY* 3.2 22.2 - - - +
18B TYR* 2.7 33.2 + - + +
19B VAL* 5.0 0.3 - - - +
46B HIS* 3.5 16.8 + - - -
49B TYR* 2.6 41.8 + - - +
231B VAL 5.4 2.2 - - - +
270B THR* 3.4 7.3 - - - +
286B PRO 3.3 2.3 + - - +
287B MET* 3.6 15.5 - - + +
288B GLN 3.4 3.9 - - - +
289B LEU* 1.3 79.9 - - - +
291B LEU* 1.3 72.4 + - - +
292B ARG* 3.2 9.4 + - - +
----------------------------------------------------------
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