Contacts of the helix formed by residues 2 - 25 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SER* 1.3 77.9 - - - +
3A LEU* 1.3 63.9 + - + +
4A LEU 3.5 0.7 - - - -
5A GLU* 3.8 14.4 - - - +
6A LEU* 3.6 13.2 + - - +
16C LYS* 5.1 3.8 - - - +
20C LEU* 3.9 29.8 - - + +
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Residues in contact with LEU 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER 3.4 6.8 - - - +
2A LYS* 1.3 81.4 - - + +
4A LEU* 1.3 59.0 + - - +
5A GLU 3.3 2.0 - - - -
6A LEU* 3.4 9.5 - - - +
7A LEU* 2.9 25.9 + - - +
3B LEU* 4.4 18.7 - - + +
4B LEU* 3.5 33.2 - - + -
7B LEU* 4.0 18.2 - - + +
20C LEU* 3.8 32.5 - - + -
24C TRP* 3.8 21.8 - - + -
21D LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 4.1 27.6 + - - +
2A LYS 3.5 0.4 - - - -
3A LEU* 1.3 74.6 - - - +
5A GLU* 1.3 60.3 + - - +
7A LEU* 3.6 22.8 - - + +
8A ARG* 3.0 29.0 + - - +
3B LEU* 3.8 26.0 - - + -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 3.2 20.3 + - - +
2A LYS* 3.8 13.7 - - - +
4A LEU* 1.3 76.2 - - - +
6A LEU* 1.3 63.7 + - - +
8A ARG* 3.3 30.1 + - - +
9A LYS* 3.0 26.5 + - - +
16C LYS* 3.0 35.9 + - + -
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS 3.6 7.6 + - - +
3A LEU 3.4 10.7 + - - +
4A LEU 3.4 0.2 - - - -
5A GLU* 1.3 79.2 - - - +
7A LEU* 1.3 61.9 + - - +
9A LYS* 3.2 3.5 + - - +
10A LEU* 3.0 36.8 + - + +
7B LEU* 3.7 29.2 - - + -
13C ALA* 3.6 31.0 - - + +
16C LYS* 4.0 13.1 - - + +
17C ALA* 4.4 15.3 - - + +
20C LEU* 4.2 10.3 - - + -
14D LEU* 4.8 3.6 - - + -
18D ILE* 4.6 7.2 - - + -
21D LEU* 4.0 21.8 - - + -
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU 2.9 17.1 + - - +
4A LEU* 3.6 28.3 - - + +
6A LEU* 1.3 74.6 - - - +
8A ARG* 1.3 65.0 + - - +
10A LEU* 3.1 6.4 + - - +
11A GLY* 2.9 19.8 + - - -
3B LEU* 4.8 5.6 - - + -
6B LEU* 4.1 28.3 - - + -
7B LEU* 3.8 16.8 - - + +
10B LEU* 3.3 31.8 - - + +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU 3.0 17.6 + - - +
5A GLU* 3.3 36.1 + - - +
7A LEU* 1.3 76.3 - - - +
9A LYS* 1.3 85.6 + - - +
11A GLY* 3.1 4.2 + - - +
12A GLU* 2.8 50.0 + - + +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 3.0 16.5 + - - +
6A LEU 3.2 8.0 + - - +
8A ARG* 1.3 99.9 - - - +
10A LEU* 1.3 56.3 + - - +
12A GLU* 3.3 23.0 + - - +
13A ALA* 2.9 30.7 + - - +
9C LYS* 4.6 9.3 - - + +
12C GLU* 3.5 39.1 + - + +
13C ALA* 4.0 22.0 - - + +
16C LYS* 3.5 31.0 - - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.0 19.8 + - + +
7A LEU* 3.5 6.1 - - - +
9A LYS* 1.3 75.4 - - - +
11A GLY* 1.3 57.0 + - - +
13A ALA* 3.8 4.4 - - - +
14A LEU* 2.9 32.9 + - - +
7B LEU* 3.5 42.6 - - + +
10B LEU* 4.4 17.4 - - + +
11B GLY* 4.6 7.0 - - - -
14B LEU* 3.8 16.5 - - + +
13C ALA* 4.5 3.4 - - + -
14D LEU* 3.7 31.4 - - + -
18D ILE* 3.7 24.7 - - + -
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU 2.9 12.8 + - - -
8A ARG* 3.1 5.6 + - - -
10A LEU* 1.3 78.2 - - - +
12A GLU* 1.3 54.6 + - - +
14A LEU* 3.8 7.2 - - - +
15A HIS* 2.9 29.5 + - - +
10B LEU* 4.8 7.7 - - - +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 2.8 48.6 + - + +
9A LYS* 3.7 19.5 - - - +
11A GLY* 1.3 71.0 - - - +
13A ALA* 1.3 64.7 + - - +
15A HIS* 3.4 9.5 + - - +
16A LYS* 3.1 30.8 + - - +
9C LYS* 3.4 34.1 - - + +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS 2.9 17.2 + - - +
10A LEU* 3.8 4.0 - - - +
12A GLU* 1.3 75.4 - - - +
14A LEU* 1.3 57.9 + - - +
16A LYS* 3.2 5.7 + - - +
17A ALA* 3.0 28.9 + - - +
14B LEU* 3.9 24.0 - - + -
6C LEU* 3.8 14.0 - - + +
9C LYS* 4.1 24.3 - - + +
10C LEU* 4.5 5.6 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU 2.9 18.2 + - - +
11A GLY* 3.8 6.5 - - - +
13A ALA* 1.3 73.7 - - - +
15A HIS* 1.3 65.2 + - - +
17A ALA* 3.4 2.1 + - - +
18A ILE* 3.0 48.7 + - + +
10B LEU* 4.0 31.2 - - + +
13B ALA* 4.2 20.0 - - + +
14B LEU* 3.8 33.1 - - + +
17B ALA* 4.3 11.7 - - + -
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Residues in contact with HIS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLY 2.9 19.1 + - - +
12A GLU* 3.5 9.6 - - - +
13A ALA 3.3 0.2 - - - -
14A LEU* 1.3 76.3 - - - +
16A LYS* 1.3 69.6 + - + +
18A ILE* 3.4 9.4 + - - +
19A GLU* 3.1 57.0 + - + +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 3.1 17.1 + - - +
13A ALA* 3.2 7.1 + - - +
15A HIS* 1.3 81.5 - - + +
17A ALA* 1.3 63.2 + - - +
19A GLU* 3.3 10.0 + - - +
20A LEU* 3.1 28.3 + - + +
2C LYS 5.3 2.2 - - - +
5C GLU* 3.8 32.5 + - + +
6C LEU* 4.3 29.4 - - + +
8C ARG* 4.5 1.8 - - - +
9C LYS* 3.5 41.1 - - + +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 3.0 17.2 + - - +
14A LEU* 3.6 8.1 - - - +
16A LYS* 1.3 76.5 - - - +
18A ILE* 1.3 56.2 + - - +
20A LEU* 3.4 5.4 + - - +
21A LEU* 3.0 32.2 + - - +
14B LEU* 4.4 8.5 - - + -
17B ALA* 4.1 20.9 - - + -
18B ILE* 5.1 1.6 - - + -
21B LEU* 3.9 22.8 - - + +
6C LEU* 4.6 10.2 - - + +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.0 47.3 + - + +
15A HIS* 3.8 7.2 - - - +
16A LYS 3.3 0.2 - - - -
17A ALA* 1.3 72.3 - - + +
19A GLU* 1.3 62.0 + - + +
21A LEU* 3.1 17.3 + - + +
22A GLU* 2.9 37.4 + - - +
17B ALA* 5.4 1.3 - - + -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.1 46.1 + - + +
16A LYS* 3.3 10.3 + - - +
18A ILE* 1.3 74.8 - - + +
20A LEU* 1.3 62.4 + - + +
22A GLU* 3.3 10.1 - - - +
23A LYS* 3.2 45.7 + - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.1 15.3 + - + +
17A ALA 3.5 3.6 - - - +
19A GLU* 1.3 76.4 - - + +
21A LEU* 1.3 66.2 + - - +
23A LYS* 3.0 17.1 + - + +
24A TRP* 2.9 52.3 + - + +
21B LEU* 3.5 23.3 - - + -
2C LYS* 4.4 31.2 - - + +
3C LEU* 4.2 24.7 - - + -
6C LEU* 4.2 19.3 - - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.0 19.3 + - - +
18A ILE* 3.1 18.6 + - + +
20A LEU* 1.3 74.9 - - - +
22A GLU* 1.3 54.2 + - - +
24A TRP* 4.7 1.1 - - - +
25A GLY* 2.8 32.6 + - - -
17B ALA* 4.0 27.6 - - + +
20B LEU* 3.6 38.8 - - + -
21B LEU* 3.7 27.5 - - + +
24B TRP* 3.5 22.7 - - + -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 2.9 20.4 + - + +
19A GLU* 3.3 14.4 - - - +
21A LEU* 1.3 74.4 - - - +
23A LYS* 1.3 66.8 + - + +
25A GLY* 3.0 17.7 - - - +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 3.5 31.1 + - - +
20A LEU* 3.0 20.7 + - + +
22A GLU* 1.3 84.0 - - + +
24A TRP* 1.3 72.0 + - + +
25A GLY 3.3 5.0 - - - +
2C LYS* 5.5 12.8 - - - +
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Residues in contact with TRP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 2.9 41.0 + - + +
21A LEU* 4.4 1.3 - - + +
23A LYS* 1.3 84.2 - - + +
25A GLY* 1.3 61.5 + - - +
26A NH2 3.9 0.3 + - - -
21B LEU* 3.3 55.9 - - + -
24B TRP* 4.4 18.3 - - + +
25B GLY* 3.9 20.2 - - - -
3C LEU* 4.2 31.4 - - + -
4D LEU* 4.3 7.0 - - + -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU 2.8 23.3 + - - -
22A GLU* 3.0 15.1 - - - +
23A LYS 3.3 5.2 - - - +
24A TRP* 1.3 77.3 - - - +
26A NH2 1.3 47.5 + - - -
24B TRP* 3.5 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
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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