Contacts of the helix formed by residues 2 - 25 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H LYS* 5.3 4.2 - - + +
20H LEU* 4.2 20.0 - - + +
23H LYS* 6.5 0.7 - - + -
1J SER* 1.3 76.9 + - - +
3J LEU* 1.3 63.5 + - - +
5J GLU* 3.5 8.9 + - - +
6J LEU* 3.2 20.4 + - - +
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Residues in contact with LEU 3 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H LEU* 4.1 28.6 - - + +
24H TRP* 4.4 21.3 - - + -
3I LEU* 4.1 33.9 - - + -
4I LEU* 5.0 9.0 - - + +
7I LEU* 4.3 14.1 - - + -
1J SER 3.3 5.5 - - - +
2J LYS* 1.3 79.0 - - - +
4J LEU* 1.3 57.8 + - + +
6J LEU* 3.3 12.1 + - + +
7J LEU* 3.0 44.7 + - + +
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Residues in contact with LEU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 3.4 31.9 - - + -
1J SER* 3.6 26.8 + - - +
2J LYS 3.3 0.6 - - - -
3J LEU* 1.3 75.0 - - + +
5J GLU* 1.3 62.9 + - - +
7J LEU* 3.5 13.4 + - + +
8J ARG 3.2 17.7 + - - -
24K TRP* 4.4 9.0 - - + -
18L ILE* 4.6 2.0 - - + +
21L LEU* 4.1 34.1 - - + +
22L GLU* 3.6 28.8 - - + +
25L GLY* 4.1 22.4 - - - +
26L NH2 4.6 1.3 - - - +
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Residues in contact with GLU 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LYS* 4.0 23.6 - - + +
1J SER 3.4 10.5 + - - +
2J LYS* 3.6 11.4 - - - +
3J LEU 3.3 0.4 - - - -
4J LEU* 1.3 75.4 - - - +
6J LEU* 1.3 66.4 + - - +
8J ARG* 3.4 22.1 + - - +
9J LYS* 3.3 24.6 + - - +
22L GLU* 4.1 10.5 + - - +
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Residues in contact with LEU 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 5.4 1.6 - - + -
18G ILE* 6.0 1.3 - - + -
21G LEU* 3.9 19.7 - - + -
13H ALA* 3.8 24.9 - - - +
16H LYS* 4.5 15.8 - - + +
17H ALA* 4.2 13.5 - - + +
20H LEU* 3.8 26.5 - - + -
7I LEU* 4.2 12.1 - - + -
2J LYS 3.2 11.4 + - - +
3J LEU* 3.3 18.2 - - + +
5J GLU* 1.3 78.4 - - - +
7J LEU* 1.3 65.0 + - - +
9J LYS* 3.2 7.0 + - - +
10J LEU* 3.1 33.0 + - + +
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Residues in contact with LEU 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 4.4 15.0 - - + +
6I LEU* 4.0 24.7 - - + -
7I LEU* 3.5 35.0 - - + -
10I LEU* 4.0 17.2 - - + +
3J LEU* 3.0 32.1 + - + +
4J LEU* 3.7 25.1 - - + +
5J GLU 3.3 0.2 - - - -
6J LEU* 1.3 72.1 - - + +
8J ARG* 1.3 68.2 + - - +
10J LEU* 2.7 22.4 + - - +
11J GLY 2.9 10.0 + - - -
18L ILE* 3.9 15.7 - - + +
21L LEU* 5.6 2.5 - - + -
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Residues in contact with ARG 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LYS* 5.1 4.2 - - - +
4J LEU 3.2 5.5 + - - +
5J GLU* 3.4 25.4 + - - +
7J LEU* 1.3 76.1 - - - +
9J LYS* 1.3 84.8 + - - +
11J GLY* 3.1 2.6 + - - -
12J GLU* 2.8 48.7 + - + +
15L HIS* 4.5 8.1 + - + -
18L ILE* 3.5 16.2 - - + +
19L GLU* 4.7 19.7 - - + +
22L GLU* 2.3 42.4 + - - +
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Residues in contact with LYS 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LYS* 4.5 10.3 - - + +
12H GLU* 3.1 44.9 + - + +
13H ALA* 4.1 20.0 - - + +
16H LYS* 4.1 22.4 - - + +
5J GLU 3.3 10.9 + - - +
6J LEU* 3.2 10.2 + - - +
7J LEU 2.8 4.2 + - - -
8J ARG* 1.3 97.0 - - - +
10J LEU* 1.3 56.3 + - - +
12J GLU* 3.2 26.0 + - - +
13J ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 3.7 35.9 - - + -
18G ILE* 4.4 11.7 - - + -
13H ALA* 4.2 8.3 - - + -
7I LEU* 3.3 33.9 - - + -
10I LEU* 4.2 30.0 - - + +
11I GLY 5.3 0.9 - - - +
14I LEU* 3.8 15.4 - - + +
6J LEU* 3.1 25.4 + - + +
7J LEU* 2.7 12.6 + - - +
9J LYS* 1.3 71.0 - - - +
11J GLY* 1.3 54.9 + - - +
13J ALA* 3.4 4.6 + - - +
14J LEU* 2.9 31.8 + - - +
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Residues in contact with GLY 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU* 4.6 4.4 - - - +
7J LEU 2.9 11.6 + - - -
8J ARG 3.4 4.3 - - - -
10J LEU* 1.3 76.8 - - - +
12J GLU* 1.3 56.3 + - - +
14J LEU* 3.5 5.5 + - - +
15J HIS* 2.9 30.8 + - - +
11L GLY 5.1 0.9 - - - +
14L LEU* 5.7 1.1 - - - -
15L HIS* 4.2 14.9 + - - +
18L ILE* 4.2 20.9 - - - +
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Residues in contact with GLU 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LYS* 3.4 33.5 + - + +
8J ARG* 2.8 45.3 + - - +
9J LYS* 3.2 32.9 + - - +
11J GLY* 1.3 69.6 - - - +
13J ALA* 1.3 65.3 + - - +
15J HIS* 3.5 9.3 + - - +
16J LYS* 3.1 23.4 + - - +
15L HIS* 3.5 23.1 - - + +
19L GLU* 5.4 0.5 - - - +
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Residues in contact with ALA 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.7 9.0 - - + +
9H LYS* 4.1 21.7 - - + +
10H LEU* 3.9 29.2 - - + -
13H ALA* 5.4 1.1 - - + -
14I LEU* 4.2 8.3 - - + -
9J LYS 2.9 17.0 + - - +
10J LEU* 3.7 6.3 - - - +
12J GLU* 1.3 73.3 - - - +
14J LEU* 1.3 62.3 + - - +
16J LYS* 3.3 2.5 + - - +
17J ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU* 4.1 16.4 - - + +
13I ALA* 3.9 18.8 - - + -
14I LEU* 3.8 35.1 - - + +
17I ALA* 4.4 11.0 - - + -
10J LEU 2.9 16.6 + - - +
11J GLY 3.8 4.7 - - - +
13J ALA* 1.3 72.0 - - - +
15J HIS* 1.3 66.4 + - - +
17J ALA* 3.3 3.1 + - - +
18J ILE* 3.1 47.1 + - + +
6K LEU* 5.0 1.6 - - + -
10K LEU* 3.7 20.0 - - + -
11L GLY* 5.7 2.0 - - - -
14L LEU* 3.7 20.4 - - + -
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Residues in contact with HIS 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J GLY 2.9 19.0 + - - +
12J GLU* 3.5 9.4 - - - +
14J LEU* 1.3 78.7 - - - +
16J LYS* 1.3 63.6 + - - +
18J ILE* 3.3 10.0 + - - +
19J GLU* 2.6 56.6 + - + +
8L ARG* 4.6 6.2 + - + +
11L GLY* 4.3 12.4 + - - +
12L GLU* 3.4 45.4 + - + +
15L HIS* 4.9 17.7 - + + -
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Residues in contact with LYS 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H LYS 5.6 2.2 - - - +
5H GLU* 5.0 11.9 - - + +
6H LEU* 4.4 23.8 - - + +
9H LYS* 5.4 4.3 - - + -
12J GLU 3.1 16.9 + - - +
13J ALA* 3.3 4.9 + - - +
15J HIS* 1.3 75.0 - - + +
17J ALA* 1.3 68.0 + - - +
19J GLU* 2.8 26.4 + - - +
20J LEU* 2.9 15.2 + - + +
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Residues in contact with ALA 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 4.1 13.6 - - + +
14I LEU* 4.6 6.5 - - + -
17I ALA* 4.0 18.8 - - + -
18I ILE* 5.6 0.9 - - + -
21I LEU* 3.9 23.9 - - + +
13J ALA 2.9 17.1 + - - +
14J LEU* 3.3 8.5 + - - +
16J LYS* 1.3 75.4 - - - +
18J ILE* 1.3 58.1 + - - +
20J LEU* 3.4 4.8 + - - +
21J LEU* 3.0 31.3 + - - +
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Residues in contact with ILE 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ALA* 5.2 1.3 - - + -
14J LEU* 3.1 35.2 + - + +
15J HIS* 3.7 6.7 - - - +
17J ALA* 1.3 73.0 - - + +
19J GLU* 1.3 62.2 + - - +
21J LEU* 3.2 18.9 + - + +
22J GLU* 2.9 27.2 + - - +
6K LEU* 5.1 5.6 - - + -
10K LEU* 4.0 31.0 - - + -
4L LEU* 4.7 2.2 - - + +
7L LEU* 3.8 18.4 - - + +
8L ARG* 3.5 36.1 - - + +
11L GLY* 4.2 11.2 - - - -
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Residues in contact with GLU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLU* 5.6 2.4 - - - +
15J HIS* 2.6 55.9 + - + +
16J LYS* 2.8 17.6 + - - +
18J ILE* 1.3 71.9 - - - +
20J LEU* 1.3 60.6 + - - +
22J GLU* 3.3 9.7 + - - +
23J LYS* 3.0 22.2 + - - +
8L ARG* 4.7 18.3 + - + +
12L GLU* 5.2 0.3 - - - +
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Residues in contact with LEU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LYS* 3.8 31.2 - - + +
3H LEU* 3.9 27.4 - - + +
6H LEU* 3.9 21.5 - - + -
21I LEU* 3.7 17.7 - - + -
16J LYS 2.9 11.1 + - - +
17J ALA 3.5 9.0 - - - +
19J GLU* 1.3 73.9 - - - +
21J LEU* 1.3 65.5 + - - +
23J LYS* 3.0 12.9 + - + +
24J TRP* 2.9 61.9 + - + +
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ALA* 4.3 15.7 - - + +
20I LEU* 3.5 40.6 - - + -
21I LEU* 3.8 26.4 - - + +
24I TRP* 3.4 22.9 - - + -
17J ALA 3.0 18.9 + - - +
18J ILE* 3.2 18.4 + - + +
20J LEU* 1.3 74.9 - - - +
22J GLU* 1.3 53.7 + - - +
24J TRP* 5.0 0.9 - - - -
25J GLY* 2.8 33.3 + - - -
6K LEU* 4.1 19.7 - - + -
4L LEU* 3.7 11.2 - - + +
7L LEU* 5.7 3.4 - - + -
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Residues in contact with GLU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ILE 2.9 12.2 + - - +
19J GLU* 3.3 8.3 - - - +
21J LEU* 1.3 76.4 - - - +
23J LYS* 1.3 62.6 + - - +
25J GLY 3.0 18.4 - - - +
4L LEU* 4.0 26.4 - - + +
8L ARG* 3.2 39.0 - - - +
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Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LYS* 4.9 13.1 - - + +
19J GLU 3.0 12.4 + - - +
20J LEU* 3.0 19.5 + - + +
22J GLU* 1.3 76.4 - - - +
24J TRP* 1.3 76.3 + - + +
25J GLY 3.8 2.8 - - - +
8L ARG* 5.2 0.6 - - - +
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Residues in contact with TRP 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 4.4 17.5 - - + -
3H LEU* 4.8 13.2 - - + -
21I LEU* 3.5 48.5 - - + -
24I TRP* 4.6 17.9 - + + +
25I GLY* 3.8 19.7 - - - -
20J LEU* 2.9 50.5 + - + +
21J LEU 4.4 1.1 - - - +
23J LYS* 1.3 86.6 - - + +
25J GLY* 1.3 63.9 + - - +
26J NH2 3.9 0.5 + - - -
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Residues in contact with GLY 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I TRP* 3.4 21.9 - - - -
21J LEU 2.8 24.5 + - - -
22J GLU 3.0 13.9 + - - +
23J LYS 3.8 3.8 - - - +
24J TRP* 1.3 75.3 - - - +
26J NH2 1.3 46.2 + - - -
1L SER* 5.7 1.0 - - - -
4L LEU* 3.6 13.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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