Contacts of the helix formed by residues 2 - 23 (chain O) in PDB entry 6O3N
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 LYS 2 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LYS* 4.3 14.0 - - + +
19M GLU* 6.2 0.4 - - + -
20M LEU* 2.8 42.9 - - + +
1O SER* 1.3 77.3 - - - +
3O LEU* 1.3 52.1 + - - +
5O GLU* 3.3 12.3 - - + +
6O LEU* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 3 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 3.2 17.9 - - + +
21N LEU* 4.2 25.8 - - + -
1O SER 4.1 15.7 - - - +
2O LYS* 1.3 73.6 - - - +
4O LEU* 1.3 60.5 + - + +
5O GLU 3.3 0.2 - - - -
6O LEU* 3.3 12.1 - - + +
7O LEU* 3.0 24.8 + - - +
3P LEU* 4.8 17.4 - - + +
4P LEU* 4.5 14.1 - - + -
7P LEU* 3.8 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 4 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O SER* 3.2 26.8 + - - +
3O LEU* 1.3 75.5 - - - +
5O GLU* 1.3 52.7 + - - +
7O LEU* 3.4 14.7 + - + +
8O ARG* 2.8 33.3 + - - +
3P LEU* 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 5 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ALA* 5.0 0.3 - - - -
16M LYS* 4.3 16.1 - - + +
1O SER 3.3 7.6 + - - +
2O LYS* 3.3 19.3 - - - +
3O LEU 3.3 0.2 - - - -
4O LEU* 1.3 74.5 - - - +
6O LEU* 1.3 62.2 + - - +
8O ARG* 3.3 9.1 + - - +
9O LYS* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ALA* 4.2 14.5 - - + +
16M LYS* 4.6 1.2 - - - +
17M ALA* 4.2 17.3 - - + -
20M LEU* 5.9 0.7 - - + -
14N LEU* 4.1 14.6 - - + -
18N ILE* 3.8 18.4 - - + -
21N LEU* 3.8 29.8 - - + -
2O LYS 2.8 17.0 + - - +
3O LEU* 3.3 11.9 - - - +
5O GLU* 1.3 70.9 - - - +
7O LEU* 1.3 58.7 - - - +
9O LYS* 3.4 4.6 + - - +
10O LEU* 3.0 44.5 + - + +
7P LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O LEU 3.0 15.2 + - - +
4O LEU* 3.5 19.5 - - + +
5O GLU 3.3 0.2 - - - -
6O LEU* 1.3 72.5 - - - +
8O ARG* 1.3 61.4 + - - +
10O LEU* 3.4 3.8 + - + +
11O ALA* 3.0 27.9 + - + +
3P LEU* 4.7 8.3 - - + -
6P LEU* 4.0 19.7 - - + -
7P LEU* 3.3 22.4 - - + -
10P LEU* 3.3 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O LEU 2.8 14.7 + - - +
5O GLU* 3.3 14.1 + - - +
7O LEU* 1.3 75.5 - - - +
9O LYS* 1.3 60.1 + - - +
11O ALA* 3.3 9.1 + - - +
12O GLU* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LYS* 3.5 11.1 - - - +
12M GLU* 4.1 5.2 - - + -
13M ALA* 2.8 49.2 - - + +
5O GLU 3.1 12.6 + - - +
6O LEU 3.8 0.4 - - - +
8O ARG* 1.3 73.4 - - - +
10O LEU* 1.3 59.2 + - - +
12O GLU* 3.4 7.7 + - - +
13O ALA* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ALA* 4.2 0.8 - - - +
14N LEU* 4.3 19.5 - - + -
18N ILE* 4.0 4.9 - - + -
6O LEU* 3.0 37.2 + - + +
7O LEU* 3.6 9.6 - - + +
8O ARG 3.3 0.2 - - - -
9O LYS* 1.3 73.9 - - - +
11O ALA* 1.3 58.3 + - - +
13O ALA* 3.4 6.0 - - - +
14O LEU* 3.0 29.6 + - + +
7P LEU* 3.6 26.7 - - - +
10P LEU* 3.6 47.5 - - + +
11P ALA* 3.9 6.5 - - - +
14P LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O LEU* 3.0 14.3 + - + +
8O ARG* 3.4 13.0 - - - +
9O LYS 3.3 0.2 - - - -
10O LEU* 1.3 74.3 - - - +
12O GLU* 1.3 59.9 + - - +
14O LEU* 3.2 8.0 + - - +
15O HIS* 2.9 32.0 + - - +
10P LEU* 5.5 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 5.2 0.2 - - - -
9M LYS* 3.5 23.5 - - + +
8O ARG 3.2 10.3 + - - +
9O LYS* 3.4 8.0 + - - +
11O ALA* 1.3 74.1 - - - +
13O ALA* 1.3 63.3 + - - +
15O HIS* 3.6 6.3 + - - +
16O LYS* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 3.1 20.7 - - + +
9M LYS* 3.9 5.4 - - + +
10M LEU* 4.4 13.2 - - + +
13M ALA* 6.3 0.4 - - + -
9O LYS 3.1 13.3 + - - +
10O LEU* 3.4 11.9 - - + +
12O GLU* 1.3 75.8 - - - +
14O LEU* 1.3 51.3 + - - +
17O ALA* 2.7 38.9 + - - +
14P LEU* 3.3 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O LEU* 3.0 18.4 + - + +
11O ALA* 3.2 9.4 + - - +
13O ALA* 1.3 73.3 - - - +
15O HIS* 1.3 57.7 + - - +
17O ALA* 4.2 1.3 - - - -
18O ILE* 2.9 67.0 + - + +
10P LEU* 4.0 28.5 - - + +
13P ALA* 5.5 4.5 - - + -
14P LEU* 3.8 26.7 - - + +
17P ALA* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ALA 2.9 17.4 + - - +
12O GLU* 3.7 7.6 - - - +
14O LEU* 1.3 74.8 - - - +
16O LYS* 1.3 56.0 + - - +
18O ILE* 4.4 1.3 - - - +
19O GLU* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M LYS* 4.2 11.0 - - + +
5M GLU* 5.2 3.8 - - + -
6M LEU* 3.6 33.7 - - + +
12O GLU 3.2 14.6 + - - +
13O ALA 3.9 0.2 - - - +
15O HIS* 1.3 75.4 - - - +
17O ALA* 1.3 59.2 + - - +
19O GLU* 3.5 6.5 + - - +
20O LEU* 3.0 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 3.5 16.5 - - + +
13O ALA 2.7 23.8 + - - +
14O LEU 3.6 2.2 - - - +
16O LYS* 1.3 72.0 - - - +
18O ILE* 1.3 60.2 + - + +
20O LEU* 3.3 21.9 - - - +
21O LEU* 3.3 13.9 + - - +
14P LEU* 3.5 27.4 - - + -
17P ALA* 5.7 0.9 - - + -
18P ILE* 4.1 14.6 - - + +
21P LEU* 4.8 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O LEU* 2.9 47.9 + - + +
15O HIS* 4.5 2.0 - - - +
17O ALA* 1.3 73.8 - - + +
19O GLU* 1.3 67.6 + - - +
20O LEU 3.2 1.1 - - - -
21O LEU* 3.2 16.1 + - + +
22O GLU* 3.0 26.3 + - + +
17P ALA* 5.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O HIS 3.1 22.1 + - - +
16O LYS* 3.5 9.2 - - - +
18O ILE* 1.3 73.3 - - - +
20O LEU* 1.3 65.7 + - + +
22O GLU* 3.4 5.6 + - - +
23O LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M LYS* 5.2 6.7 - - + -
3M LEU* 3.2 49.6 - - + +
6M LEU* 3.4 30.7 - - + -
7N LEU* 6.3 2.0 - - + -
16O LYS* 3.0 21.4 + - + +
17O ALA* 3.3 9.2 - - - +
19O GLU* 1.3 75.6 - - + +
21O LEU* 1.3 57.8 + - - +
23O LYS* 2.9 24.9 + - + +
24O TRP* 3.1 12.0 + - - +
18P ILE* 6.6 0.2 - - + -
21P LEU* 4.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O ALA 3.3 9.7 + - - +
18O ILE* 3.2 18.9 + - + +
20O LEU* 1.3 79.4 - - - +
22O GLU* 1.3 60.0 + - - +
24O TRP* 3.4 23.4 + - + +
17P ALA* 3.5 34.1 - - + +
18P ILE* 6.0 0.7 - - + -
20P LEU* 4.5 17.5 - - + -
21P LEU* 3.7 38.4 - - + -
24P TRP* 5.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O ILE* 3.0 18.0 + - + +
19O GLU* 3.9 5.4 - - - +
21O LEU* 1.3 74.0 - - - +
23O LYS* 1.3 56.4 + - - +
24O TRP 3.2 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O GLU 3.0 12.9 + - - +
20O LEU* 2.9 15.7 + - + +
22O GLU* 1.3 74.0 - - - +
24O TRP* 1.3 57.3 + - - +
----------------------------------------------------------
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