Contacts of the helix formed by residues 2 - 24 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I SER* 1.3 71.7 - - - +
3I LEU* 1.3 62.9 + - + +
5I GLU* 3.2 9.1 + - - +
6I LEU* 3.0 30.0 + - - +
16K LYS* 4.0 17.7 - - + +
19K GLU* 5.5 2.7 - - + -
20K LEU* 3.7 34.3 - - + +
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Residues in contact with LEU 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I SER* 3.5 7.2 - - - -
2I LYS* 1.3 89.8 - - + +
4I LEU* 1.3 66.6 + - + +
6I LEU* 3.4 11.0 - - - +
7I LEU* 3.2 24.1 + - - +
3J LEU* 4.4 18.9 - - + +
4J LEU* 3.3 37.5 - - + -
7J LEU* 3.7 13.6 - - + +
20K LEU* 5.1 15.5 - - + -
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Residues in contact with LEU 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU 5.9 0.4 - - - +
22G GLU* 4.7 26.6 - - + +
24G TRP 5.6 4.5 - - - +
1I SER* 4.2 26.5 - - - +
2I LYS 3.3 0.2 - - - -
3I LEU* 1.3 83.6 - - + +
5I GLU* 1.3 64.6 + - - +
7I LEU* 3.3 14.4 + - + +
8I ARG* 3.1 23.9 + - - +
3J LEU* 4.0 24.7 - - + -
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Residues in contact with GLU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I SER 3.8 11.6 + - - +
2I LYS* 3.2 12.0 + - - +
4I LEU* 1.3 73.8 - - - +
6I LEU* 1.3 65.3 - - - +
8I ARG* 3.4 7.3 + - - +
9I LYS* 3.1 23.9 + - - +
13K ALA* 5.8 0.2 - - - -
16K LYS* 4.6 9.6 - - + -
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Residues in contact with LEU 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LYS 3.0 13.3 + - - +
3I LEU* 3.4 9.4 - - - +
5I GLU* 1.3 75.6 - - - +
7I LEU* 1.3 50.6 + - - +
9I LYS* 3.3 2.4 + - - +
10I LEU* 2.8 46.8 + - + +
7J LEU* 3.3 38.8 - - + -
13K ALA* 3.7 29.6 - - + +
16K LYS* 4.3 14.7 - - + +
17K ALA* 4.7 16.4 - - + +
20K LEU* 5.9 1.3 - - + -
14L LEU* 4.6 11.7 - - + -
18L ILE* 5.0 9.6 - - + -
21L LEU* 5.0 8.7 - - + -
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Residues in contact with LEU 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ILE* 4.0 23.3 - - + -
21G LEU* 4.4 13.0 - - + -
22G GLU* 5.2 11.0 - - + +
3I LEU 3.2 14.5 + - - +
4I LEU* 3.4 17.9 - - + +
5I GLU 3.2 0.4 - - - -
6I LEU* 1.3 72.6 - - - +
8I ARG* 1.3 66.2 + - - +
10I LEU* 3.4 4.6 - - - +
11I ALA* 3.1 24.4 + - - +
3J LEU* 4.0 22.9 - - + -
6J LEU* 3.8 17.9 - - + -
7J LEU* 3.6 14.1 - - + -
10J LEU* 3.2 31.9 - - + -
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Residues in contact with ARG 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ILE* 5.2 6.1 - - + -
22G GLU* 6.1 4.9 - - + -
4I LEU 3.1 12.4 + - - +
5I GLU* 3.8 6.3 - - - +
6I LEU 3.4 0.2 - - - -
7I LEU* 1.3 81.3 - - - +
9I LYS* 1.3 55.8 + - - +
11I ALA* 3.4 7.6 + - - +
12I GLU* 3.0 27.8 + - - +
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Residues in contact with LYS 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLU 3.1 17.3 + - - +
6I LEU 3.3 3.6 + - - +
8I ARG* 1.3 73.9 - - - +
10I LEU* 1.3 54.7 + - - +
12I GLU* 3.4 9.2 + - - +
13I ALA* 3.0 33.8 + - - +
9K LYS* 4.1 9.3 - - - +
12K GLU* 4.2 10.5 - - + -
13K ALA* 3.8 29.6 - - + +
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Residues in contact with LEU 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 2.8 30.1 + - + +
7I LEU 3.4 5.6 - - - +
9I LYS* 1.3 68.7 - - - +
11I ALA* 1.3 55.2 + - - +
13I ALA* 3.5 6.7 + - - +
14I LEU* 2.9 34.5 + - - +
7J LEU* 3.3 40.4 - - + +
10J LEU* 3.3 54.5 - - + +
11J ALA* 3.5 10.1 - - + +
14J LEU* 4.7 9.5 - - + +
13K ALA* 4.3 4.3 - - + +
14L LEU* 4.5 11.9 - - + -
18L ILE* 5.2 0.9 - - + -
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU 6.3 0.2 - - - -
15G HIS* 6.2 3.1 - - - -
18G ILE* 3.6 32.1 - - + -
7I LEU 3.1 14.4 + - - +
8I ARG* 3.6 5.8 - - - +
10I LEU* 1.3 75.2 - - - +
12I GLU* 1.3 57.0 + - - +
14I LEU* 3.0 4.1 + - - +
15I HIS* 2.8 36.6 + - - +
10J LEU* 4.4 8.2 - - - +
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Residues in contact with GLU 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I ARG 3.0 13.9 + - - +
9I LYS* 3.4 13.2 - - - +
11I ALA* 1.3 76.4 - - - +
13I ALA* 1.3 60.9 + - - +
15I HIS* 3.5 6.3 - - - +
16I LYS* 3.1 24.7 + - - +
9K LYS* 4.8 5.8 - - + -
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Residues in contact with ALA 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LYS 3.0 13.4 + - - +
10I LEU* 3.6 7.9 - - - +
12I GLU* 1.3 75.1 - - - +
14I LEU* 1.3 53.0 + - - +
16I LYS* 3.5 4.5 + - - +
17I ALA* 2.6 38.2 + - - +
14J LEU* 4.0 22.2 - - + +
6K LEU* 4.6 7.1 - - + +
9K LYS* 3.4 33.4 - - + +
10K LEU* 4.6 1.3 - - - +
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Residues in contact with LEU 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ALA* 5.5 2.2 - - + +
14G LEU* 5.3 7.0 - - + -
10H LEU* 3.8 13.9 - - + -
10I LEU 2.9 18.6 + - - +
11I ALA* 3.0 6.5 + - - +
13I ALA* 1.3 71.3 - - - +
15I HIS* 1.3 66.8 + - - +
17I ALA* 4.0 1.1 - - + -
18I ILE* 3.1 47.1 + - + +
10J LEU* 3.9 20.6 - - + +
13J ALA* 3.5 28.3 - - + +
14J LEU* 3.3 38.1 - - + +
17J ALA* 4.2 2.0 - - + -
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Residues in contact with HIS 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ALA* 5.1 14.8 - - + +
15G HIS* 6.4 2.2 - - + -
11I ALA 2.8 16.0 + - - +
12I GLU* 3.5 7.9 - - - +
14I LEU* 1.3 75.1 - - - +
16I LYS* 1.3 51.9 - - - +
18I ILE* 4.1 0.7 - - - +
19I GLU* 2.9 37.6 + - - +
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Residues in contact with LYS 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I GLU 3.1 15.1 + - - +
13I ALA* 3.5 6.7 - - - +
15I HIS* 1.3 75.6 - - - +
17I ALA* 1.3 65.7 + - - +
19I GLU* 3.4 6.0 + - - +
20I LEU* 2.9 38.8 + - + +
2K LYS* 5.1 7.0 - - + +
5K GLU* 5.9 4.0 - - + -
6K LEU* 5.1 8.1 - - + +
9K LYS* 6.0 0.9 - - + -
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Residues in contact with ALA 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ALA 2.6 21.5 + - - +
14I LEU* 3.6 6.5 - - - +
15I HIS 3.5 0.2 - - - -
16I LYS* 1.3 73.0 - - - +
18I ILE* 1.3 58.3 + - - +
20I LEU* 3.4 9.7 - - - +
21I LEU* 3.1 27.9 + - - +
14J LEU* 3.7 21.8 - - + -
17J ALA* 4.4 10.6 - - + +
18J ILE* 4.2 16.4 - - + -
21J LEU* 4.7 5.7 - - - +
6K LEU* 4.8 7.8 - - + +
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Residues in contact with ILE 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G LEU* 3.2 41.5 - - + +
8G ARG* 5.3 2.7 - - - +
11G ALA* 5.2 15.3 - - + -
6H LEU* 4.4 0.4 - - + -
10H LEU* 3.8 28.7 - - + -
14I LEU* 3.1 34.2 + - + +
15I HIS 4.3 0.7 - - - +
17I ALA* 1.3 71.3 - - - +
19I GLU* 1.3 57.8 + - - +
20I LEU 3.2 1.3 - - - -
21I LEU* 3.7 9.1 - - + +
22I GLU* 2.8 37.9 + - + +
17J ALA* 3.6 23.8 - - + -
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I HIS 2.9 22.6 + - - +
16I LYS* 3.5 8.1 - - - +
18I ILE* 1.3 77.2 - - - +
20I LEU* 1.3 62.2 + - + +
22I GLU* 3.5 13.4 + - - +
23I LYS* 4.2 6.4 + - - +
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I LYS* 2.9 25.0 + - + +
17I ALA* 3.4 8.7 - - - +
19I GLU* 1.3 80.6 - - + +
21I LEU* 1.3 59.9 + - - +
22I GLU 3.5 0.2 + - - -
23I LYS* 4.4 3.3 + - - +
24I TRP* 4.0 13.9 + - - +
21J LEU* 4.9 13.4 - - + +
2K LYS* 3.3 53.6 - - + +
3K LEU* 3.9 22.2 - - + +
6K LEU* 4.8 5.2 - - + -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 5.0 6.1 - - + -
7G LEU* 4.7 4.5 - - + -
3H LEU* 5.1 2.5 - - + -
6H LEU* 4.0 9.4 - - + -
17I ALA 3.1 11.7 + - - +
18I ILE* 3.2 23.0 + - + +
20I LEU* 1.3 75.7 - - - +
22I GLU* 1.3 72.5 + - - +
23I LYS 3.5 0.2 - - - -
24I TRP* 3.2 28.8 + - - +
17J ALA* 3.2 37.0 - - + +
20J LEU* 3.3 33.4 - - + -
21J LEU* 4.3 21.3 - - + +
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 2.8 52.8 - - + +
7G LEU* 5.7 0.2 - - + -
8G ARG* 6.1 4.7 - - + -
18I ILE* 2.8 24.3 + - + +
19I GLU* 3.5 8.5 + - - +
20I LEU 3.4 1.6 - - - -
21I LEU* 1.3 79.5 - - - +
23I LYS* 1.3 61.2 + - - +
24I TRP 4.4 2.6 - - - -
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 5.4 1.9 - - - +
19I GLU 4.2 5.5 + - - +
20I LEU 4.4 4.5 + - - +
22I GLU* 1.3 79.0 - - - +
24I TRP* 1.3 60.9 + - - +
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Residues in contact with TRP 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU 4.0 10.9 + - - +
21I LEU* 3.2 24.7 + - - +
22I GLU 4.4 2.2 - - - -
23I LYS* 1.3 82.0 - - - +
21J LEU* 6.0 4.3 - - + -
24J TRP* 4.5 25.0 - - + +
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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
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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