Contacts of the strand formed by residues 33 - 38 (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 ILE 33 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 3.4 20.9 - - + +
26A CYS* 3.7 9.0 - - - +
27A THR* 4.1 2.2 - - - -
31A ALA* 3.4 1.5 - - - +
32A LYS* 1.3 86.3 - - + +
34A GLY* 1.3 73.8 + - - +
35A TYR* 3.8 29.2 - - + +
48A CYS* 3.7 2.3 - - - -
49A ILE* 3.0 50.5 + - + +
3B ASP* 5.3 6.3 - - - +
47B TRP* 6.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.9 3.5 - - - +
22A CYS* 3.8 2.7 - - - -
23A ASN* 3.6 29.9 + - - +
26A CYS* 3.6 16.2 - - - -
33A ILE* 1.3 81.2 - - - +
35A TYR* 1.3 73.7 + - - -
47A TRP 3.2 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.7 11.9 - - + +
22A CYS* 3.5 7.5 - - - +
33A ILE* 3.8 36.0 - - + +
34A GLY* 1.3 78.1 - - - -
36A CYS* 1.3 60.7 + - - +
37A ASN* 3.4 4.7 + - + +
46A CYS* 3.4 3.6 - - - -
47A TRP* 2.9 41.4 + + - +
49A ILE* 3.7 28.1 - - + +
3B ASP* 4.3 3.6 + - - -
35B TYR* 4.3 18.2 - + - -
37B ASN* 3.3 35.9 - - - +
47B TRP* 3.5 25.4 + + - -
49B ILE* 3.2 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 2.0 63.5 - - - -
17A LEU 3.9 2.0 - - - -
18A ASN 3.6 20.4 - - - +
19A ASN* 2.8 19.0 + - - +
22A CYS* 3.6 2.7 - - - +
35A TYR* 1.3 71.2 - - - +
37A ASN* 1.3 57.1 + - - +
44A ASN* 3.5 9.6 - - - -
37B ASN* 3.5 3.1 - - - -
38B ILE* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 2.8 31.8 + - - -
35A TYR* 4.1 2.0 - - + +
36A CYS* 1.3 74.3 - - - +
38A ILE* 1.3 74.8 + - - +
40A GLY 4.3 1.0 + - - -
44A ASN* 3.2 4.3 - - - -
45A ALA 2.9 36.1 + - - +
47A TRP* 3.7 29.3 - - + +
19B ASN* 2.9 30.4 + - - +
35B TYR* 3.8 7.1 - - - +
36B CYS 3.2 3.2 - - - +
37B ASN* 2.9 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 2.8 23.4 + - - -
37A ASN* 1.3 74.3 + - - +
39A VAL* 1.3 71.0 - - + +
43A GLY 3.9 7.4 - - - +
44A ASN* 3.4 9.6 + - - +
16B CYS 4.3 1.6 - - - +
17B LEU* 3.2 45.8 - - + +
18B ASN* 4.4 0.4 - - - -
19B ASN* 3.5 17.0 + - - +
36B CYS* 3.0 36.0 + - + +
44B ASN* 3.9 26.2 - - - +
----------------------------------------------------------
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