Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 1KV0
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 ASN 18 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 3.7 1.1 - - - +
17A LEU* 1.3 92.7 - - - +
19A ASN* 1.3 64.8 + - - +
20A GLU* 3.7 19.7 - - + +
21A TYR* 3.3 24.5 + - + +
22A CYS* 3.5 8.5 + - - -
36A CYS* 3.6 11.1 - - - +
38B ILE* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 1.3 71.5 - - - +
20A GLU* 1.3 68.6 + - - +
22A CYS* 3.1 3.8 + - - +
23A ASN* 2.9 30.5 + - - +
34A GLY 3.9 3.4 - - - +
35A TYR* 3.7 17.1 - - + +
36A CYS* 2.8 44.6 + - - +
5B TYR* 3.8 9.0 + - - -
37B ASN* 4.2 7.5 - - - +
38B ILE* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 3.2 17.7 - - + +
19A ASN* 1.3 83.9 + - - +
21A TYR* 1.3 65.8 + - - +
23A ASN* 3.4 7.9 + - - +
24A ASN* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.0 33.7 - + - +
15A GLY 3.5 21.9 + - - -
16A CYS* 3.8 18.8 - - + -
17A LEU 5.1 2.0 - - - -
18A ASN* 3.3 17.9 + - + +
19A ASN 3.2 0.4 - - - -
20A GLU* 1.3 81.2 - - - +
22A CYS* 1.3 62.7 + - - +
24A ASN* 3.1 12.2 + - + +
25A LEU* 2.9 42.3 + - + -
46A CYS* 3.7 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 3.5 22.9 - - - -
18A ASN 3.5 0.8 + - - -
19A ASN 3.1 5.1 + - - +
21A TYR* 1.3 79.2 - - - +
23A ASN* 1.3 57.5 + - - +
25A LEU* 4.4 1.3 - - - -
26A CYS* 2.9 35.7 + - - +
34A GLY 4.1 1.8 - - - -
35A TYR 3.5 29.2 - - - +
36A CYS* 3.6 6.1 - - - -
46A CYS* 2.0 58.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN 2.9 15.6 + - - +
20A GLU* 3.7 8.7 + - - +
22A CYS* 1.3 78.4 - - - +
24A ASN* 1.3 60.7 + - - +
26A CYS* 4.1 0.2 - - - -
27A THR* 2.8 43.0 + - - +
32A LYS 4.6 0.5 - - - +
33A ILE* 3.4 32.7 - - - +
34A GLY 3.7 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.0 13.6 + - - +
21A TYR* 3.1 14.9 + - - +
23A ASN* 1.3 78.4 - - - +
25A LEU* 1.3 63.2 + - - +
27A THR* 3.3 5.8 + - - -
28A LYS* 3.0 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.8 21.5 - - + -
14A TYR* 3.6 52.3 - - + +
21A TYR* 2.9 32.4 + - + +
22A CYS* 3.9 2.7 - - - +
24A ASN* 1.3 80.8 - - - +
26A CYS* 1.3 62.5 + - - +
28A LYS* 3.5 5.6 + - + +
29A ASP* 2.9 40.7 + - - +
46A CYS* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.6 0.9 - - - -
22A CYS 2.9 27.6 + - - +
23A ASN 4.1 0.2 - - - +
25A LEU* 1.3 75.0 - - - +
27A THR* 1.3 62.0 + - - +
29A ASP* 3.1 13.3 + - - +
30A GLY 3.2 0.3 + - - -
31A ALA* 3.0 24.1 + - + +
33A ILE 3.7 13.5 - - - +
34A GLY* 3.6 9.4 - - - +
46A CYS* 4.5 10.1 - - - -
47A TRP 3.9 3.4 - - - -
48A CYS* 2.0 61.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.8 42.0 + - - +
24A ASN* 3.3 7.8 + - - -
26A CYS* 1.3 74.6 - - - +
28A LYS* 1.3 62.9 + - - +
30A GLY* 2.9 18.9 + - - -
31A ALA 3.5 19.9 - - - +
32A LYS 3.6 19.7 - - - +
33A ILE* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 3.0 57.4 + - - +
25A LEU* 3.9 7.0 - - + +
27A THR* 1.3 77.7 - - - +
29A ASP* 1.3 60.9 + - - +
30A GLY 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.4 31.6 - - + +
14A TYR* 5.6 0.2 + - - -
25A LEU* 2.9 29.6 + - - +
26A CYS 3.1 9.7 + - - +
27A THR 3.1 0.8 - - - -
28A LYS* 1.3 79.1 - - - +
30A GLY* 1.3 57.3 + - - +
31A ALA 3.5 0.7 - - - -
51A LEU* 3.9 4.9 - - + +
52A PRO* 3.4 19.8 - - - +
55A VAL* 3.7 18.4 - - + +
----------------------------------------------------------
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