Contacts of the helix formed by residues 2 - 13 (chain D) in PDB entry 1KVO
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 LEU 2 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASN* 1.3 77.4 - - - +
3D VAL* 1.3 59.1 + - + +
5D PHE* 4.1 7.9 - - + -
6D HIS* 2.9 29.7 + - - +
51D TYR* 4.7 4.5 - - - +
62D LYS* 2.9 41.1 + - + +
63D PHE* 5.9 2.7 - - + -
190D OAP 3.2 79.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 3 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TYR* 3.5 48.7 - - + +
1D ASN* 2.7 20.4 - - - +
2D LEU* 1.3 70.5 - - + +
4D ASN* 1.3 62.5 + - - +
6D HIS* 3.3 7.9 + - + +
7D ARG* 2.9 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 4 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASN* 2.7 38.4 + - - +
3D VAL* 1.3 74.0 - - - +
5D PHE* 1.3 57.6 + - - +
7D ARG* 3.2 6.0 + - - +
8D MET* 2.8 35.3 + - - +
65D SER* 3.7 2.5 - - - -
66D TYR* 3.5 53.4 + - + +
68D PHE* 3.7 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ASN 3.3 10.2 + - - +
2D LEU* 3.8 16.4 - - + +
4D ASN* 1.3 79.7 - - - +
6D HIS* 1.3 62.5 + - - +
8D MET* 3.1 6.5 + - - +
9D ILE* 2.9 49.8 + - + +
47D HIS* 3.4 33.7 - + - -
51D TYR* 4.6 0.9 - - - +
66D TYR* 3.6 5.1 + - - -
91D ASP* 3.4 50.9 - - + +
94D ALA* 3.7 14.4 - - + -
95D ALA* 4.3 0.7 - - + -
98D PHE* 4.8 1.1 - + - -
190D OAP 3.6 42.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A TYR* 6.1 2.6 - - - -
2D LEU 2.9 21.3 + - - +
3D VAL* 3.4 8.9 + - + +
5D PHE* 1.3 76.6 - - - +
7D ARG* 1.3 65.1 + - - +
9D ILE* 3.4 3.6 + - - +
10D LYS* 3.2 29.7 + - + +
16D GLU* 2.7 34.1 + - - -
17D ALA* 3.6 28.4 + - + +
18D ALA* 3.7 11.6 + - + +
190D OAP 3.8 18.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 4.3 26.6 - - + +
3D VAL* 2.9 13.8 + - + +
4D ASN* 3.4 9.6 - - - +
6D HIS* 1.3 80.0 + - - +
8D MET* 1.3 63.1 + - - +
10D LYS* 2.9 19.2 + - - +
11D LEU* 3.1 46.5 + - - +
68D PHE* 4.4 14.6 - - + -
70D ASN* 4.9 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASN 2.8 16.8 + - - +
5D PHE* 3.1 5.8 + - - +
7D ARG* 1.3 73.7 - - - +
9D ILE* 1.3 61.1 + - - +
11D LEU* 3.4 12.3 + - - +
12D THR* 3.2 25.6 + - + +
66D TYR* 3.5 24.7 - - + +
68D PHE* 3.9 32.5 - - + -
75D ILE* 4.0 24.5 - - + -
88D CYS* 4.4 4.9 - - - +
91D ASP* 3.6 12.3 - - + +
92D LYS* 3.4 36.3 - - - +
95D ALA* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PHE* 2.9 52.2 + - + +
6D HIS 3.7 4.3 - - - +
7D ARG 3.2 0.2 - - - -
8D MET* 1.3 75.8 - - - +
10D LYS* 1.3 55.8 + - - +
12D THR* 3.2 5.7 + - - -
13D THR* 2.6 50.0 + - + +
15D LYS 4.4 1.6 - - - +
17D ALA* 3.6 31.9 - - + -
21D TYR* 3.8 19.1 - - + -
95D ALA* 4.2 8.1 - - + -
98D PHE* 4.3 15.9 - - + -
190D OAP 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D HIS* 3.2 20.6 + - + +
7D ARG* 2.9 14.7 + - - +
9D ILE* 1.3 79.3 - - - +
11D LEU* 1.3 57.9 + - - +
14D GLY* 2.8 39.2 + - - +
15D LYS 3.2 22.9 - - - +
16D GLU* 4.0 25.5 - - - +
17D ALA 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG* 3.1 51.6 + - - +
8D MET* 3.9 7.9 - - - +
9D ILE 3.3 0.4 - - - -
10D LYS* 1.3 77.8 - - + +
12D THR* 1.3 60.4 + - - +
14D GLY 4.7 0.3 + - - -
68D PHE* 4.4 13.7 - - + -
70D ASN* 3.6 43.7 - - + +
72D GLY 4.3 4.3 - - - +
73D SER* 4.2 13.7 - - - -
75D ILE* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D MET* 3.2 15.1 + - + +
9D ILE* 3.2 9.0 + - - -
11D LEU* 1.3 80.1 - - - +
13D THR* 1.3 62.7 + - - +
14D GLY 3.6 0.2 - - - -
73D SER* 3.9 21.3 - - - +
75D ILE* 3.9 25.1 - - + -
95D ALA* 3.0 37.0 + - + +
96D THR* 4.8 8.3 - - - +
99D ALA* 3.6 18.9 - - - +
102D LYS* 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 2.6 27.1 + - + +
12D THR* 1.3 85.1 - - - +
14D GLY* 1.3 58.7 + - - +
15D LYS* 3.0 25.3 + - - +
21D TYR* 3.6 21.8 - - - +
98D PHE* 3.7 9.9 - - + -
99D ALA* 3.6 29.4 - - - +
102D LYS* 2.7 38.9 + - + +
----------------------------------------------------------
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