Contacts of the helix formed by residues 2 - 25 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M SER* 1.3 77.2 - - - +
3M LEU* 1.3 62.8 + - - +
5M GLU* 3.6 16.1 - - + +
6M LEU* 3.3 20.1 + - - +
16O LYS* 5.4 2.4 - - - +
20O LEU* 3.6 28.6 - - + +
23O LYS* 5.8 7.2 - - + +
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Residues in contact with LEU 3 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M SER 3.3 8.3 - - - +
2M LYS* 1.3 77.6 - - - +
4M LEU* 1.3 59.1 + - - +
6M LEU* 3.4 5.5 + - + +
7M LEU* 2.8 28.6 + - - +
3N LEU* 3.7 29.2 - - + -
4N LEU* 3.9 20.6 - - + -
7N LEU* 4.3 17.8 - - + +
20O LEU* 3.7 23.1 - - + -
24O TRP* 3.8 34.5 - - + -
21P LEU* 5.1 2.0 - - + -
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Residues in contact with LEU 4 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU* 3.7 25.8 - - + +
22K GLU* 4.4 13.8 - - + +
25K GLY* 3.4 36.8 - - - +
26K NH2 4.0 1.8 - - - +
24L TRP* 4.0 20.6 - - + -
1M SER* 3.7 24.3 + - - +
2M LYS 3.4 0.2 - - - -
3M LEU* 1.3 75.7 - - - +
5M GLU* 1.3 66.0 + - - +
7M LEU* 3.4 19.8 - - + +
8M ARG* 3.0 25.6 + - - +
3N LEU* 4.5 11.2 - - + -
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Residues in contact with GLU 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M SER* 3.5 16.3 + - - +
2M LYS* 3.6 17.3 - - - +
3M LEU 3.3 0.4 - - - -
4M LEU* 1.3 79.4 - - - +
6M LEU* 1.3 62.3 + - - +
8M ARG* 3.2 31.4 + - - +
9M LYS* 3.2 24.9 + - - +
16O LYS* 3.2 32.6 + - + +
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Residues in contact with LEU 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M LYS 3.3 11.7 + - - +
3M LEU* 3.6 5.8 - - + +
5M GLU* 1.3 75.1 - - - +
7M LEU* 1.3 67.1 + - - +
9M LYS* 3.3 4.1 + - - +
10M LEU* 3.0 36.3 + - + +
7N LEU* 3.8 24.0 - - + -
13O ALA* 3.7 28.3 - - + +
16O LYS* 4.3 16.1 - - + +
17O ALA* 4.3 12.8 - - + +
20O LEU* 3.7 25.4 - - + -
14P LEU* 4.9 2.7 - - + -
18P ILE* 5.0 5.2 - - + -
21P LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K ILE* 3.8 28.0 - - + +
21K LEU* 4.4 13.2 - - + -
22K GLU* 5.6 0.9 - - + +
3M LEU 2.8 21.1 + - - +
4M LEU* 3.4 21.8 - - + +
6M LEU* 1.3 73.0 - - - +
8M ARG* 1.3 53.3 + - - +
10M LEU* 3.0 8.6 + - - +
11M GLY* 2.8 31.9 + - - -
3N LEU* 4.1 17.3 - - + -
6N LEU* 4.1 15.0 - - + -
7N LEU* 3.7 21.7 - - + +
10N LEU* 3.3 33.2 - - + -
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Residues in contact with ARG 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K ILE* 4.3 15.7 - - + -
22K GLU* 5.4 12.9 - - + +
4M LEU 3.0 12.2 + - - +
5M GLU* 3.4 39.3 + - - +
7M LEU* 1.3 77.8 - - - +
9M LYS* 1.3 71.5 + - - +
11M GLY* 3.2 2.3 + - - -
12M GLU* 2.6 59.8 + - + +
16O LYS* 6.2 0.4 - - - +
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Residues in contact with LYS 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M GLU 3.2 12.5 + - - +
6M LEU* 3.6 8.1 - - - +
7M LEU 3.3 0.2 - - - -
8M ARG* 1.3 94.1 - - + +
10M LEU* 1.3 58.6 + - - +
12M GLU* 3.1 23.7 + - - +
13M ALA* 2.9 30.1 + - - +
9O LYS* 5.1 5.3 - - + +
12O GLU* 2.7 47.0 + - + +
13O ALA* 4.1 20.0 - - + +
16O LYS* 4.3 31.7 - - + +
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Residues in contact with LEU 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LEU* 3.0 25.0 + - + +
7M LEU* 3.3 8.5 - - - +
9M LYS* 1.3 74.9 - - - +
11M GLY* 1.3 63.1 + - - +
13M ALA* 3.5 2.8 + - - +
14M LEU* 3.1 24.7 + - - +
7N LEU* 3.9 28.5 - - + -
10N LEU* 4.4 23.0 - - + +
11N GLY* 4.8 6.5 - - - +
14N LEU* 4.1 14.0 - - + +
13O ALA* 4.5 3.3 - - + +
14P LEU* 3.6 32.8 - - + -
18P ILE* 3.5 29.4 - - + -
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Residues in contact with GLY 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K HIS* 6.4 2.0 - - - -
18K ILE* 4.1 22.0 - - - -
7M LEU 2.8 16.5 + - - -
8M ARG 3.5 3.4 - - - -
10M LEU* 1.3 72.2 - - - +
12M GLU* 1.3 61.6 + - - +
13M ALA 3.2 0.3 + - - -
14M LEU* 3.2 8.4 + - - +
15M HIS* 3.0 24.2 + - - +
10N LEU* 4.7 5.0 - - - +
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Residues in contact with GLU 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K HIS* 6.6 0.2 - - - -
8M ARG* 2.6 47.5 + - + +
9M LYS* 3.1 29.3 + - - +
11M GLY* 1.3 73.3 - - - +
13M ALA* 1.3 64.1 + - - +
15M HIS* 3.4 14.7 + - - +
16M LYS* 3.5 16.5 + - - +
9O LYS* 3.5 29.4 - - + -
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Residues in contact with ALA 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M LYS 2.9 17.0 + - - +
10M LEU* 3.9 4.5 - - - +
12M GLU* 1.3 67.8 - - - +
14M LEU* 1.3 57.8 + - - +
15M HIS 3.0 1.3 - - - -
16M LYS* 2.4 35.3 + - - +
17M ALA* 3.0 8.8 + - - -
14N LEU* 4.2 21.3 - - + -
6O LEU* 4.4 8.5 - - + -
9O LYS* 3.9 30.6 - - + +
10O LEU* 4.7 2.9 - - + +
13O ALA* 5.8 1.8 - - + -
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Residues in contact with LEU 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K GLY* 6.5 0.2 - - - -
14K LEU* 4.0 6.3 - - + -
6L LEU* 5.1 1.1 - - + -
10L LEU* 3.6 25.1 - - + -
10M LEU 3.1 13.9 + - - +
11M GLY* 3.5 4.9 - - - +
13M ALA* 1.3 76.6 - - - +
15M HIS* 1.3 61.6 + - - +
17M ALA* 3.4 2.3 + - + +
18M ILE* 3.0 49.4 + - + +
10N LEU* 3.4 34.8 - - + +
13N ALA* 4.3 9.4 - - + +
14N LEU* 4.0 40.2 - - + +
17N ALA* 4.7 6.1 - - + -
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Residues in contact with HIS 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K GLY* 5.5 12.3 - - - -
12K GLU* 5.8 4.4 - - + +
15K HIS* 5.3 20.5 - + + -
11M GLY 3.0 11.4 + - - +
12M GLU* 3.4 14.4 + - - +
13M ALA 2.7 3.6 + - - -
14M LEU* 1.3 73.6 - - - +
16M LYS* 1.3 71.7 + - - +
18M ILE* 3.3 9.2 + - + +
19M GLU* 2.9 57.0 + - + +
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Residues in contact with LYS 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M GLU* 3.5 16.7 + - - +
13M ALA* 2.4 23.1 + - - +
15M HIS* 1.3 79.5 + - - +
17M ALA* 1.3 62.4 + - - +
19M GLU* 3.2 9.2 + - - +
20M LEU* 3.1 23.4 + - - +
2O LYS 5.2 2.0 - - - +
5O GLU* 4.6 26.0 - - + -
6O LEU* 4.5 19.1 - - + +
9O LYS* 4.0 30.8 - - + +
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Residues in contact with ALA 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ALA 3.0 5.5 + - - +
14M LEU 3.6 8.3 - - - +
16M LYS* 1.3 77.1 - - - +
18M ILE* 1.3 57.2 + - - +
20M LEU* 3.4 3.4 + - - +
21M LEU* 3.0 28.9 + - - +
14N LEU* 4.1 24.5 - - + -
17N ALA* 4.2 18.4 - - + -
18N ILE* 5.2 1.8 - - + -
21N LEU* 3.9 19.8 - - + +
6O LEU* 4.3 13.9 - - + +
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Residues in contact with ILE 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K LEU* 3.7 42.8 - - + +
8K ARG* 4.5 15.5 - - + -
11K GLY* 4.3 16.8 - - - -
6L LEU* 5.4 6.3 - - + -
10L LEU* 4.1 13.7 - - + -
14M LEU* 3.0 47.1 + - + +
15M HIS* 3.8 7.4 - - + +
17M ALA* 1.3 72.4 - - + +
19M GLU* 1.3 61.1 + - + +
21M LEU* 3.2 8.8 + - - +
22M GLU* 2.8 32.1 + - + +
17N ALA* 5.4 2.5 - - + -
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Residues in contact with GLU 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M HIS* 2.9 56.3 + - + +
16M LYS* 3.2 10.1 + - - +
18M ILE* 1.3 76.0 - - + +
20M LEU* 1.3 63.1 + - - +
22M GLU* 3.3 20.9 + - - +
23M LYS* 3.1 21.7 + - - +
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Residues in contact with LEU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LYS 3.1 12.5 + - - +
17M ALA* 3.6 8.3 - - - +
19M GLU* 1.3 77.0 - - - +
21M LEU* 1.3 57.5 + - - +
23M LYS* 3.1 9.2 + - + +
24M TRP* 2.9 59.2 + - + +
21N LEU* 3.6 30.1 - - + -
2O LYS* 3.8 26.7 - - + -
3O LEU* 3.6 33.7 - - + +
6O LEU* 4.7 7.6 - - + -
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Residues in contact with LEU 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 4.7 2.8 - - + +
7K LEU* 3.9 14.8 - - + -
3L LEU* 4.6 4.5 - - + -
6L LEU* 3.4 33.2 - - + -
17M ALA 3.0 19.1 + - - +
18M ILE* 3.2 8.0 + - - +
20M LEU* 1.3 75.7 - - - +
22M GLU* 1.3 52.4 + - - +
24M TRP* 4.8 1.3 - - - -
25M GLY* 2.8 32.2 + - - -
17N ALA* 4.8 6.5 - - + +
20N LEU* 3.9 27.8 - - + -
21N LEU* 3.6 23.0 - - + +
24N TRP* 3.4 37.8 - - + -
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Residues in contact with GLU 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 3.6 32.6 - - + +
5K GLU* 4.7 2.8 - - - +
7K LEU* 5.7 2.6 - - + +
8K ARG* 3.2 31.5 - - - +
18M ILE* 2.8 15.4 + - + +
19M GLU* 3.4 24.7 - - - +
21M LEU* 1.3 73.5 - - - +
23M LYS* 1.3 64.3 + - - +
25M GLY 3.0 18.9 - - - +
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M GLU 3.1 9.4 + - - +
20M LEU* 3.1 13.3 + - + +
22M GLU* 1.3 80.9 - - - +
24M TRP* 1.3 70.0 + - + +
25M GLY 3.8 3.6 - - - +
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Residues in contact with TRP 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 2.9 35.5 + - + +
21M LEU* 4.2 2.7 - - - +
23M LYS* 1.3 81.9 - - + +
25M GLY* 1.3 65.5 + - - +
26M NH2 3.9 0.5 + - - -
21N LEU* 3.4 31.9 - - + -
24N TRP* 4.5 14.4 - - + +
25N GLY* 3.4 36.1 - - - -
3O LEU* 3.8 40.4 - - + -
4P LEU* 4.5 6.1 - - + -
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Residues in contact with GLY 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 3.5 14.9 - - - +
21M LEU 2.8 23.3 + - - -
22M GLU 3.0 13.9 - - - +
23M LYS 3.8 3.6 - - - +
24M TRP* 1.3 76.9 - - - +
26M NH2 1.3 47.5 + - - -
24N TRP* 3.4 23.2 - - - -
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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