Contacts of the helix formed by residues 2 - 24 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P SER* 1.3 75.1 - - - +
3P LEU* 1.3 60.1 + - - +
5P GLU* 3.2 11.7 + - + +
6P LEU* 3.1 27.9 + - - +
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Residues in contact with LEU 3 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O SER 6.2 0.2 - - - +
3O LEU* 4.8 15.5 - - + +
4O LEU* 3.9 33.0 - - + -
7O LEU* 4.7 3.8 - - + -
1P SER 3.2 7.3 - - - +
2P LYS* 1.3 76.4 - - - +
4P LEU* 1.3 54.9 + - + +
6P LEU* 3.4 19.8 + - + +
7P LEU* 2.7 55.0 + - + +
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Residues in contact with LEU 4 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ILE* 4.2 4.0 - - + +
21N LEU* 3.4 44.2 - - + +
22N GLU* 3.2 44.6 - - + +
24N TRP 4.9 5.2 - - - +
3O LEU* 4.5 15.3 - - + -
1P SER* 3.3 19.8 + - - +
3P LEU* 1.3 74.7 - - - +
5P GLU* 1.3 58.6 + - - +
7P LEU* 3.7 8.7 - - + +
8P ARG* 3.1 29.8 + - - +
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Residues in contact with GLU 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N GLU* 6.0 0.7 - - - -
1P SER 3.3 6.2 + - - +
2P LYS* 3.2 19.6 + - + +
4P LEU* 1.3 75.7 - - - +
6P LEU* 1.3 64.6 + - - +
8P ARG* 3.6 5.9 - - - +
9P LYS* 3.1 22.6 + - - +
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Residues in contact with LEU 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O LEU* 4.0 28.7 - - + -
2P LYS 3.1 11.7 + - - +
3P LEU* 3.4 15.7 + - + +
5P GLU* 1.3 76.0 - - - +
7P LEU* 1.3 65.5 + - + +
9P LYS* 3.2 9.2 + - + +
10P LEU* 2.9 44.1 + - + +
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Residues in contact with LEU 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ILE* 2.9 32.9 - - + +
3O LEU* 3.8 31.9 - - + +
6O LEU* 3.9 13.7 - - + -
7O LEU* 3.3 44.6 - - + +
10O LEU* 3.6 5.4 - - + +
3P LEU* 2.7 43.0 + - + +
4P LEU* 3.7 9.0 - - + +
5P GLU 3.3 0.2 - - - -
6P LEU* 1.3 80.9 - - + +
8P ARG* 1.3 61.9 + - - +
10P LEU* 3.5 3.2 + - - -
11P ALA 3.2 13.7 + - - -
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Residues in contact with ARG 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N ILE* 2.9 30.3 - - + +
19N GLU* 5.4 2.0 - - - +
22N GLU* 5.0 7.6 - - + -
4P LEU 3.1 12.5 + - - +
5P GLU* 3.6 7.4 - - - +
7P LEU* 1.3 71.5 - - - +
9P LYS* 1.3 59.1 - - - +
11P ALA* 3.4 5.1 + - - +
12P GLU* 3.0 29.3 + - - +
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Residues in contact with LYS 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P GLU 3.1 12.0 + - - +
6P LEU* 3.2 15.5 + - + +
8P ARG* 1.3 77.4 - - - +
10P LEU* 1.3 57.3 - - - +
12P GLU* 3.4 7.6 + - - +
13P ALA* 2.8 29.1 + - - +
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Residues in contact with LEU 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O LEU* 3.3 34.1 - - + +
10O LEU* 3.6 39.5 - - + +
11O ALA* 5.5 1.3 - - - +
14O LEU* 4.0 29.2 - - + +
6P LEU* 2.9 29.7 + - + +
7P LEU 3.8 0.4 - - - +
8P ARG 3.3 0.4 - - - -
9P LYS* 1.3 72.1 - - - +
11P ALA* 1.3 58.7 + - - +
13P ALA* 3.4 12.0 - - + +
14P LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N ALA* 4.8 4.2 - - - +
14N LEU* 4.1 9.4 - - + +
15N HIS* 4.0 28.9 - - - +
18N ILE* 3.9 16.4 - - + -
10O LEU* 3.9 9.7 - - - +
7P LEU 3.2 13.0 + - - +
8P ARG* 3.4 10.3 - - - +
10P LEU* 1.3 73.7 - - - +
12P GLU* 1.3 56.2 + - - +
14P LEU* 3.2 6.7 + - - +
15P HIS* 3.1 29.3 + - - +
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Residues in contact with GLU 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15N HIS* 4.9 6.3 - - + +
8P ARG 3.0 11.0 + - - +
9P LYS* 3.5 11.9 - - - +
11P ALA* 1.3 73.9 - - - +
13P ALA* 1.3 57.9 + - - +
15P HIS* 3.4 7.6 + - - +
16P LYS* 2.9 31.4 + - - +
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Residues in contact with ALA 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O LEU* 5.5 6.1 - - + -
9P LYS 2.8 21.6 + - - +
10P LEU* 3.4 19.1 - - + +
11P ALA 3.3 0.2 - - - -
12P GLU* 1.3 71.1 - - - +
14P LEU* 1.3 53.1 + - - +
16P LYS* 3.3 5.6 + - - +
17P ALA* 2.8 36.8 + - - +
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Residues in contact with LEU 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 5.2 0.2 - - + -
10M LEU* 4.6 16.8 - - + -
11N ALA* 4.7 7.0 - - + -
14N LEU* 5.6 2.9 - - + -
10O LEU* 4.6 11.2 - - + +
13O ALA* 3.3 33.7 - - + -
14O LEU* 3.8 22.4 - - + +
17O ALA* 3.5 29.2 - - + -
10P LEU 3.0 14.3 + - - +
11P ALA* 3.2 7.6 + - - +
13P ALA* 1.3 75.0 - - - +
15P HIS* 1.3 58.6 + - - +
17P ALA* 3.4 6.3 - - + +
18P ILE* 3.0 50.7 + - + +
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Residues in contact with HIS 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N ALA* 3.7 29.5 - - + +
12N GLU* 5.2 1.6 - - - +
15N HIS* 5.2 6.3 - - + -
11P ALA 3.1 13.8 + - - +
12P GLU* 3.6 11.9 - - - +
14P LEU* 1.3 76.0 - - - +
16P LYS* 1.3 52.3 + - - +
18P ILE* 4.1 0.9 - - - +
19P GLU* 2.9 35.3 + - - +
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Residues in contact with LYS 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P GLU 2.9 19.0 + - - +
13P ALA* 3.8 4.9 - - - +
15P HIS* 1.3 72.9 - - - +
17P ALA* 1.3 64.0 + - - +
19P GLU* 3.4 19.6 - - - +
20P LEU* 3.4 10.2 + - - +
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Residues in contact with ALA 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O LEU* 5.6 2.5 - - + -
17O ALA* 5.7 0.7 - - + -
18O ILE* 5.3 10.8 - - + -
21O LEU* 3.5 22.9 - - + +
13P ALA 2.8 21.5 + - - +
14P LEU* 3.4 18.8 - - + +
16P LYS* 1.3 73.5 - - - +
18P ILE* 1.3 60.6 + - + +
20P LEU* 3.5 8.1 - - - +
21P LEU 3.1 17.8 + - - -
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Residues in contact with ILE 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M LEU* 5.1 8.7 - - + -
10M LEU* 5.2 10.1 - - + -
4N LEU 5.4 0.9 - - - +
7N LEU* 4.5 36.6 - - + +
8N ARG* 4.8 6.5 - - + +
11N ALA* 5.7 4.3 - - + -
17O ALA* 4.1 15.9 - - + +
20O LEU* 6.5 0.2 - - + -
21O LEU* 6.0 0.9 - - + -
14P LEU* 3.0 45.4 + - + +
15P HIS* 4.3 1.6 - - - +
17P ALA* 1.3 74.5 - - + +
19P GLU* 1.3 60.5 + - - +
20P LEU 3.2 1.1 - - - -
21P LEU* 3.7 23.8 - - + -
22P GLU* 2.8 34.5 + - + +
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Residues in contact with GLU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ARG* 6.4 1.8 - - - -
15P HIS 2.9 20.4 + - - +
16P LYS* 3.4 12.6 - - - +
18P ILE* 1.3 77.5 - - - +
20P LEU* 1.3 59.3 + - - +
22P GLU* 3.8 4.9 - - - +
23P LYS* 3.2 19.5 + - - +
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Residues in contact with LEU 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O LEU* 4.5 19.5 - - + -
16P LYS 3.4 7.1 + - - +
17P ALA* 3.5 13.2 - - - +
19P GLU* 1.3 78.3 - - - +
21P LEU* 1.3 65.4 + - - +
23P LYS* 3.1 19.7 + - + +
24P TRP* 3.1 16.8 + - + +
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Residues in contact with LEU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M LEU* 6.3 0.9 - - + -
4N LEU* 5.0 11.1 - - + +
7N LEU* 5.9 4.5 - - + -
17O ALA* 4.8 5.4 - - - +
20O LEU* 4.4 25.6 - - + -
21O LEU* 3.7 44.2 - - + +
24O TRP* 5.2 8.7 - - + -
17P ALA 3.1 7.4 + - - +
18P ILE* 3.2 31.6 + - + +
20P LEU* 1.3 77.6 - - - +
22P GLU* 1.3 64.8 + - - +
24P TRP* 3.2 21.7 + - + +
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Residues in contact with GLU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N LEU* 3.3 48.7 - - + +
8N ARG* 6.1 3.1 - - + -
18P ILE* 2.8 22.7 + - + +
19P GLU* 3.8 5.6 - - - +
21P LEU* 1.3 74.6 - - - +
23P LYS* 1.3 68.1 + - - +
24P TRP 3.2 4.0 + - - -
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Residues in contact with LYS 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P GLU 3.2 11.1 + - - +
20P LEU* 3.1 16.5 + - + +
22P GLU* 1.3 82.1 - - - +
24P TRP* 1.3 58.4 + - - +
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Residues in contact with TRP 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O LEU* 5.8 4.0 - - + -
24O TRP* 6.2 4.3 - - + -
20P LEU* 3.1 14.8 + - + +
21P LEU* 3.6 20.4 - - + +
22P GLU 3.2 4.7 - - - -
23P LYS* 1.3 81.2 - - - +
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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) + - + + + + + -
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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