Contacts of the helix formed by residues 23 - 30 (chain F) in PDB entry 7KHI
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 THR 23 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LYS* 4.9 12.3 - - - +
21F TYR* 4.4 5.1 - - + -
22F LEU* 1.3 76.0 - - - +
24F TYR* 1.3 74.3 + - - +
25F ALA* 3.8 14.3 + - + +
26F GLU* 3.1 45.5 + - + +
27F VAL* 3.7 5.0 + - - +
55F VAL* 3.9 10.4 - - - +
57F GLU 4.9 0.5 + - - -
58F GLU* 4.5 5.4 - - - -
59F ALA* 3.6 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ARG* 5.8 4.0 - - - +
22F LEU 3.8 0.8 + - - -
23F THR* 1.3 76.9 + - - +
25F ALA* 1.3 64.9 + - - +
26F GLU 3.0 1.2 + - - -
27F VAL* 3.3 18.9 - - + +
28F ASN* 3.1 22.5 + - - +
45F ILE* 4.9 17.0 - - + -
54F GLN* 5.4 1.4 - - - -
55F VAL* 3.2 20.1 + - + +
56F MET 3.0 31.9 - - - -
57F GLU* 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ARG* 4.6 23.6 + - - +
200C ARG* 5.0 12.9 - - - +
23F THR* 3.2 15.9 + - + +
24F TYR* 1.3 78.2 - - - +
26F GLU* 1.3 67.5 + - + +
28F ASN* 3.2 6.5 + - - +
29F ASP* 3.1 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C LYS* 5.8 1.6 + - - -
12F LEU* 4.1 14.4 - - + -
19F GLN* 5.8 3.1 - - - +
22F LEU* 5.1 6.3 - - + -
23F THR* 3.1 30.5 + - + +
25F ALA* 1.3 73.9 - - - +
27F VAL* 1.3 56.2 + - + +
28F ASN 2.6 15.5 + - - -
29F ASP* 2.4 27.7 - - - +
30F HIS* 2.3 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.2 24.7 - - + +
22F LEU* 4.6 18.6 - - + +
23F THR 3.7 7.6 + - - +
24F TYR* 3.3 30.5 + - + +
26F GLU* 1.3 72.1 - - - +
28F ASN* 1.3 60.4 + - + +
30F HIS* 4.2 3.6 - - - -
31F LEU* 4.2 13.0 + - - +
41F ILE* 5.7 5.1 - - + +
44F ILE* 5.1 13.9 - - + +
45F ILE* 4.8 22.0 - - + -
48F ILE* 5.9 6.5 - - + -
53F ILE* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ARG 5.1 10.5 - - - +
201C ARG 5.5 5.6 - - - +
202C ARG* 4.9 5.6 + - - +
24F TYR 3.1 12.8 + - - +
25F ALA* 3.3 12.3 - - - +
26F GLU 2.6 5.9 + - - -
27F VAL* 1.3 76.8 - - + +
29F ASP* 1.3 62.9 + - - +
31F LEU* 3.7 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ARG* 4.6 9.2 + - - +
201C ARG 4.8 2.4 + - - +
202C ARG* 3.8 23.8 - - + +
203C LYS* 4.3 38.1 - - + +
8F GLN* 3.1 13.0 + - - -
25F ALA* 3.2 15.0 - - - +
26F GLU* 2.4 33.3 + - - +
28F ASN* 1.3 73.2 - - - +
30F HIS* 1.3 85.3 + - - +
31F LEU 3.1 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLN* 2.6 54.0 + - - +
9F LEU* 3.9 8.5 - - + +
11F LEU* 3.5 30.9 - - + +
12F LEU* 4.3 20.9 - - + +
26F GLU* 2.3 63.4 + - + +
27F VAL* 4.8 1.8 - - - -
29F ASP* 1.3 82.9 + - - +
31F LEU* 1.3 60.8 + - - +
32F PRO 3.7 0.3 - - - -
----------------------------------------------------------
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