Contacts of the helix formed by residues 2 - 25 (chain H) in PDB entry 6C4Z
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H SER* 1.3 77.6 + - - +
3H LEU* 1.3 64.4 + - - +
5H GLU* 3.5 14.5 - - - +
6H LEU* 3.1 20.4 + - - +
16J LYS* 5.6 2.3 - - - +
20J LEU* 3.8 25.1 - - + +
23J LYS* 4.9 15.2 - - + +
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Residues in contact with LEU 3 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G LEU* 3.8 31.6 - - + -
4G LEU* 4.1 20.4 - - + -
7G LEU* 4.1 23.3 - - + -
1H SER 3.3 5.5 - - - +
2H LYS* 1.3 76.1 - - - +
4H LEU* 1.3 55.9 + - + +
6H LEU* 2.8 17.8 + - + +
7H LEU* 2.7 52.5 + - + +
20J LEU* 3.9 17.9 - - + +
24J TRP* 4.8 12.3 - - + -
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Residues in contact with LEU 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 4.2 9.4 - - + -
18F ILE* 4.7 3.1 - - + +
21F LEU* 4.0 24.5 - - + +
22F GLU* 3.9 22.0 - - + +
25F GLY* 3.8 36.8 - - - +
26F NH2 4.4 0.4 - - - +
3G LEU* 3.6 31.2 - - + -
1H SER* 3.6 24.1 + - - +
3H LEU* 1.3 78.2 - - + +
5H GLU* 1.3 51.4 + - - +
7H LEU* 3.1 13.1 + - + +
8H ARG* 2.8 35.2 + - - +
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Residues in contact with GLU 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLU* 3.9 14.7 + - - +
1H SER 3.3 11.8 + - - +
2H LYS* 3.5 16.0 - - - +
4H LEU* 1.3 78.4 - - - +
6H LEU* 1.3 62.0 + - - +
8H ARG* 3.3 25.7 + - - +
9H LYS* 3.1 33.1 + - + +
16J LYS* 5.0 11.2 - - + +
19J GLU* 5.6 2.3 - - - +
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Residues in contact with LEU 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 4.2 17.9 - - + -
2H LYS 3.1 9.8 + - - +
3H LEU* 2.8 18.3 + - + +
5H GLU* 1.3 74.0 - - - +
7H LEU* 1.3 64.8 + - - +
9H LYS* 2.9 14.6 + - - +
10H LEU* 3.1 30.6 + - + -
14I LEU* 5.3 1.6 - - + -
18I ILE* 5.8 0.9 - - + -
21I LEU* 3.8 29.8 - - + -
13J ALA* 3.7 27.8 - - + +
16J LYS* 4.4 15.0 - - + +
17J ALA* 4.1 11.9 - - + +
20J LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ILE* 3.9 14.8 - - + +
21F LEU* 5.8 1.1 - - + -
3G LEU* 3.6 33.4 - - + +
6G LEU* 4.2 14.4 - - + -
7G LEU* 3.7 45.1 - - + +
10G LEU* 3.8 18.7 - - + +
3H LEU* 2.7 25.7 + - + +
4H LEU* 3.3 20.9 - - + +
6H LEU* 1.3 72.6 - - - +
8H ARG* 1.3 62.5 + - - +
10H LEU* 3.0 9.2 + - - +
11H GLY* 3.0 20.4 + - - -
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Residues in contact with ARG 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 4.7 3.4 + - + +
18F ILE* 3.6 16.3 - - + +
19F GLU* 4.4 25.1 - - + +
22F GLU* 3.0 36.5 + - + -
4H LEU 2.8 16.3 + - - +
5H GLU* 3.5 32.8 + - - +
6H LEU 3.2 0.2 - - - -
7H LEU* 1.3 72.8 - - - +
9H LYS* 1.3 86.8 + - - +
11H GLY* 3.5 1.8 + - - +
12H GLU* 3.3 45.2 + - + +
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Residues in contact with LYS 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLU* 3.1 23.7 + - + +
6H LEU* 2.9 11.4 + - - +
8H ARG* 1.3 100.6 - - - +
10H LEU* 1.3 60.9 + - - +
12H GLU* 3.6 17.4 + - - +
13H ALA* 3.1 26.9 + - - +
9J LYS* 4.5 8.8 - - + +
12J GLU* 3.4 40.9 + - + +
13J ALA* 4.1 25.6 - - + +
16J LYS* 5.4 3.4 - - + -
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Residues in contact with LEU 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 3.3 33.4 - - + +
10G LEU* 4.5 25.5 - - + +
11G GLY* 5.1 1.3 - - - +
14G LEU* 3.8 15.5 - - + +
6H LEU* 3.1 23.9 + - + +
7H LEU* 3.0 10.6 + - - +
9H LYS* 1.3 75.7 - - - +
11H GLY* 1.3 60.6 + - - +
13H ALA* 3.4 4.1 + - + +
14H LEU* 2.9 32.2 + - - +
14I LEU* 3.7 34.3 - - + -
18I ILE* 4.3 11.9 - - + -
13J ALA* 3.9 10.3 - - + -
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Residues in contact with GLY 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLY 5.2 0.7 - - - +
14F LEU* 5.8 1.3 - - - -
15F HIS* 4.3 15.0 - - - +
18F ILE* 4.1 20.5 - - - +
10G LEU* 4.7 4.2 - - - +
7H LEU 3.0 13.1 + - - -
8H ARG* 3.9 4.0 - - - -
9H LYS 3.4 0.2 - - - -
10H LEU* 1.3 76.9 - - - +
12H GLU* 1.3 51.5 + - - +
14H LEU* 3.3 6.5 + - - +
15H HIS* 2.8 35.2 + - - +
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Residues in contact with GLU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 3.3 30.3 + - + +
19F GLU* 5.0 1.0 - - - +
8H ARG* 3.3 34.8 + - - +
9H LYS* 3.8 17.6 + - - +
10H LEU 3.3 0.2 - - - -
11H GLY* 1.3 73.0 - - - +
13H ALA* 1.3 55.8 + - - +
15H HIS* 3.1 10.1 + - - +
16H LYS* 2.8 39.7 + - + +
9J LYS* 3.1 41.2 + - + +
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Residues in contact with ALA 13 (chain H).
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* 4.3 7.9 - - + -
9H LYS 3.1 14.6 + - - +
10H LEU* 3.6 9.4 - - + +
12H GLU* 1.3 78.3 - - - +
14H LEU* 1.3 57.9 + - - +
16H LYS* 3.3 4.6 + - - +
17H ALA* 2.9 29.8 + - - +
6J LEU* 3.8 5.6 - - + +
9J LYS* 4.1 24.0 - - + +
10J LEU* 4.2 26.5 - - + +
13J ALA* 5.4 0.7 - - + -
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 5.0 1.1 - - + -
10E LEU* 3.7 21.1 - - + -
11F GLY* 5.8 1.1 - - - -
14F LEU* 3.8 7.9 - - + -
10G LEU* 3.8 30.1 - - + +
13G ALA* 4.0 18.2 - - + +
14G LEU* 3.9 35.1 - - + +
17G ALA* 4.4 7.4 - - + -
10H LEU 2.9 17.5 + - - +
11H GLY* 3.5 4.5 - - - +
13H ALA* 1.3 73.0 - - - +
15H HIS* 1.3 67.0 + - - +
17H ALA* 3.3 2.2 + - - +
18H ILE* 3.0 49.6 + - + +
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Residues in contact with HIS 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ARG* 4.8 3.1 - - + -
11F GLY* 4.1 11.8 + - - +
12F GLU* 3.3 43.1 + - + +
15F HIS* 4.5 20.6 + + + -
11H GLY 2.8 21.3 + - - +
12H GLU* 3.3 9.5 + - - +
14H LEU* 1.3 74.3 - - - +
16H LYS* 1.3 69.4 + - - +
18H ILE* 3.4 8.9 + - + +
19H GLU* 2.7 58.0 + - + +
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Residues in contact with LYS 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H GLU* 2.8 26.3 + - + +
13H ALA* 3.6 4.7 - - - +
15H HIS* 1.3 80.1 - - - +
17H ALA* 1.3 63.7 - - - +
19H GLU* 3.3 19.5 + - - +
20H LEU* 3.0 24.7 + - - +
2J LYS 5.3 2.9 - - - +
5J GLU* 4.0 26.5 - - + +
6J LEU* 4.5 20.4 - - + +
8J ARG* 5.1 4.8 - - - +
9J LYS* 4.1 28.4 - - + +
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Residues in contact with ALA 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 4.4 7.4 - - + -
17G ALA* 4.3 16.6 - - + -
18G ILE* 5.6 1.3 - - + -
21G LEU* 4.1 18.7 - - + +
13H ALA 2.9 20.6 + - - +
14H LEU* 3.3 8.3 + - - +
16H LYS* 1.3 72.7 - - - +
18H ILE* 1.3 58.2 + - - +
20H LEU* 3.4 3.9 + - - +
21H LEU* 3.0 31.3 + - - +
6J LEU* 4.2 19.9 - - + +
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Residues in contact with ILE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LEU* 5.1 13.0 - - + -
10E LEU* 3.8 37.7 - - + -
4F LEU* 4.8 2.6 - - + +
7F LEU* 3.8 12.3 - - + +
8F ARG* 3.5 35.7 - - + +
11F GLY* 4.2 16.8 - - - -
17G ALA* 5.1 3.1 - - + -
14H LEU* 3.0 34.0 + - + +
15H HIS* 3.8 4.7 - - + +
17H ALA* 1.3 72.2 - - + +
19H GLU* 1.3 60.9 + - - +
21H LEU* 3.2 11.9 + - + +
22H GLU* 2.9 27.1 + - + +
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Residues in contact with GLU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ARG* 4.0 24.5 - - + +
12F GLU* 4.5 5.0 - - - +
15H HIS* 2.7 51.6 + - + +
16H LYS* 3.3 24.3 + - - +
18H ILE* 1.3 77.0 - - - +
20H LEU* 1.3 60.6 + - - +
22H GLU* 3.3 11.2 + - - +
23H LYS* 3.0 21.7 + - - +
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 3.7 22.0 - - + -
16H LYS 3.0 13.6 + - - +
17H ALA 3.5 8.5 - - - +
19H GLU* 1.3 73.4 - - - +
21H LEU* 1.3 65.9 + - - +
23H LYS* 3.0 11.7 + - + +
24H TRP* 2.9 56.8 + - + +
2J LYS* 4.2 26.5 - - + +
3J LEU* 4.1 24.9 - - + +
6J LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 4.1 19.3 - - + -
4F LEU* 4.7 9.6 - - + -
7F LEU* 5.5 2.9 - - + -
17G ALA* 4.1 13.0 - - + +
20G LEU* 4.0 36.3 - - + -
21G LEU* 3.9 19.4 - - + +
24G TRP* 3.4 45.4 - - + -
17H ALA 3.0 15.2 + - - +
18H ILE* 3.2 15.3 - - + +
20H LEU* 1.3 74.8 - - - +
22H GLU* 1.3 52.7 + - - +
24H TRP* 3.1 3.1 + - + -
25H GLY* 2.7 34.0 + - - -
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Residues in contact with GLU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F SER 5.3 1.5 - - - +
4F LEU* 3.9 34.2 - - + +
5F GLU* 3.8 12.3 - - - +
8F ARG* 2.8 47.3 + - + +
18H ILE 2.9 12.4 + - - +
19H GLU* 3.4 12.6 - - - +
21H LEU* 1.3 74.8 - - - +
23H LYS* 1.3 64.4 + - - +
25H GLY 3.0 18.5 + - - +
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Residues in contact with LYS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H GLU 3.0 12.9 + - - +
20H LEU* 3.0 15.7 + - + +
22H GLU* 1.3 78.4 + - - +
24H TRP* 1.3 70.0 + - + +
25H GLY 3.8 4.0 - - - +
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Residues in contact with TRP 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 3.5 30.7 - - + -
24G TRP* 4.5 16.7 - + + +
25G GLY* 3.4 36.1 - - - -
20H LEU* 2.9 50.5 + - + +
21H LEU* 3.8 3.4 - - - +
23H LYS* 1.3 83.8 - - + +
25H GLY* 1.3 64.1 + - - +
4I LEU* 4.2 18.6 - - + -
7I LEU* 6.4 0.2 - - + -
3J LEU* 4.4 17.7 - - + -
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Residues in contact with GLY 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 4.1 8.6 - - - +
24G TRP* 3.4 27.5 - - - -
21H LEU 2.7 16.9 + - - -
22H GLU 3.0 15.6 + - - +
23H LYS 3.8 4.2 - - - +
24H TRP* 1.3 77.4 - - - +
26H NH2 1.3 47.5 + - - -
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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