Contacts of the helix formed by residues 10 - 35 (chain E) in PDB entry 2WCD
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 VAL 10 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E LYS* 5.8 1.6 - - - +
9E THR* 1.3 79.0 - - + +
11E GLU* 1.3 62.7 + - + +
12E VAL 3.0 6.1 - - - -
13E VAL* 2.8 38.4 + - + -
14E LYS* 3.3 9.9 + - + +
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 3.6 29.2 + - - +
8E LYS* 4.5 33.6 - - + +
9E THR 3.2 1.2 - - - +
10E VAL* 1.3 84.8 - - + +
12E VAL* 1.3 56.1 + - - +
13E VAL 3.4 0.2 - - - -
14E LYS* 3.7 27.9 - - + +
15E ASN* 2.9 32.5 + - + +
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Residues in contact with VAL 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 4.4 26.5 - - - +
10D VAL* 4.8 9.1 - - + +
8E LYS 5.7 2.4 + - - +
9E THR* 3.8 13.2 + - - +
10E VAL 2.9 0.8 + - - -
11E GLU* 1.3 76.5 - - - +
13E VAL* 1.3 65.7 + - + +
15E ASN* 3.4 5.4 + - - +
16E ALA* 2.8 33.0 + - + +
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Residues in contact with VAL 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E THR 5.2 1.1 - - - +
10E VAL* 2.8 28.0 + - + +
12E VAL* 1.3 81.6 - - + +
14E LYS* 1.3 51.2 + - - +
16E ALA* 3.1 7.3 + - - +
17E ILE* 2.7 52.7 + - + +
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Residues in contact with LYS 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 3.3 6.8 + - + +
11E GLU* 3.7 32.5 - - + +
13E VAL* 1.3 79.8 - - - +
15E ASN* 1.3 68.9 + - - +
17E ILE* 3.0 24.7 + - + +
18E GLU* 3.1 39.4 + - + +
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Residues in contact with ASN 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 5.0 14.7 - - - +
10D VAL* 4.4 11.1 - - + +
11D GLU* 4.0 30.3 - - - +
14D LYS* 4.2 18.2 - - - +
11E GLU* 2.9 25.5 + - + +
12E VAL* 3.8 5.2 - - - +
14E LYS* 1.3 82.4 + - + +
16E ALA* 1.3 57.4 + - - +
18E GLU* 3.4 11.0 + - - +
19E THR* 2.9 30.6 + - - -
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Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 4.2 20.1 - - + +
12E VAL* 2.8 20.9 + - + +
13E VAL* 3.5 6.7 - - + +
15E ASN* 1.3 73.3 - - - +
17E ILE* 1.3 63.3 + - + +
19E THR* 3.1 10.8 + - - +
20E ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E VAL* 2.7 31.6 + - + +
14E LYS* 3.1 18.8 - - + +
16E ALA* 1.3 72.8 - - + +
18E GLU* 1.3 69.9 + - + +
20E ALA* 3.2 9.6 + - + +
21E ASP* 3.0 25.6 + - - +
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Residues in contact with GLU 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LYS* 5.5 6.0 - - + -
14E LYS* 3.1 38.6 + - + +
15E ASN* 3.7 13.3 - - - +
17E ILE* 1.3 85.9 - - + +
19E THR* 1.3 66.7 + - - +
21E ASP* 3.2 16.4 + - - +
22E GLY* 3.3 11.6 + - - -
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Residues in contact with THR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 4.3 20.8 - - + +
13D VAL* 4.4 10.3 - - + -
14D LYS* 3.1 50.8 - - + +
17D ILE* 5.0 7.0 - - + +
15E ASN* 2.9 17.9 + - - -
16E ALA* 3.1 13.2 + - - +
18E GLU* 1.3 78.6 - - - +
20E ALA* 1.3 63.2 + - - +
22E GLY* 3.5 1.9 + - - -
23E ALA* 3.0 21.8 + - + +
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Residues in contact with ALA 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA 2.8 12.0 + - - +
17E ILE* 3.4 13.9 - - + +
19E THR* 1.3 75.7 - - - +
21E ASP* 1.3 68.6 + - - +
23E ALA* 3.0 21.4 - - - +
24E LEU* 3.2 9.4 + - - +
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Residues in contact with ASP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ILE 3.0 11.2 + - - +
18E GLU* 3.2 14.5 + - - +
20E ALA* 1.3 71.1 - - - +
22E GLY* 1.3 60.3 + - - +
23E ALA 2.8 9.4 + - - -
24E LEU* 2.9 22.7 + - - +
25E ASP* 3.2 22.2 + - - +
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Residues in contact with GLY 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.3 14.6 - - - +
18E GLU 3.3 8.9 + - - -
19E THR 3.8 2.7 - - - -
21E ASP* 1.3 78.2 - - - +
23E ALA* 1.3 62.1 + - - +
25E ASP* 3.6 13.9 - - - +
26E LEU* 3.1 24.4 + - - +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.1 19.5 - - + -
19E THR* 3.0 15.2 + - + +
20E ALA* 3.0 17.9 - - - +
21E ASP 2.8 1.4 + - - -
22E GLY* 1.3 76.3 - - - +
24E LEU* 1.3 67.8 + - - +
26E LEU* 3.2 3.1 + - - +
27E TYR* 2.8 22.5 + - - +
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ALA 3.2 7.2 + - - +
21E ASP* 2.9 15.3 + - - +
23E ALA* 1.3 76.2 - - - +
25E ASP* 1.3 60.6 + - - +
27E TYR* 2.7 47.0 + - + +
28E ASN* 2.8 30.7 + - - +
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Residues in contact with ASP 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASP* 6.0 1.3 - - - +
21E ASP* 3.4 23.3 - - - +
22E GLY* 3.6 15.9 + - - +
23E ALA 3.2 0.4 - - - -
24E LEU* 1.3 78.4 - - - +
26E LEU* 1.3 58.1 + - - +
28E ASN* 3.3 6.0 + - - +
29E LYS* 2.8 32.7 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.0 28.0 - - + +
20D ALA* 4.0 24.9 - - + +
21D ASP* 3.5 43.8 + - + +
24D LEU* 4.5 15.3 - - + -
22E GLY 3.1 14.6 + - - +
23E ALA 3.7 3.1 - - - +
25E ASP* 1.3 77.3 - - - +
27E TYR* 1.3 64.2 + - - +
29E LYS* 3.4 8.1 - - + +
30E TYR* 2.9 26.3 + - + +
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Residues in contact with TYR 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ALA 2.8 13.5 + - - +
24E LEU* 2.7 35.3 + - + +
26E LEU* 1.3 73.4 - - - +
28E ASN* 1.3 71.3 + - - -
30E TYR* 3.3 6.5 + + - +
31E LEU* 2.7 67.4 + - + +
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Residues in contact with ASN 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 2.8 37.3 + - - +
25E ASP* 3.9 4.4 - - - +
27E TYR* 1.3 89.8 - - - +
29E LYS* 1.3 60.6 + - - +
31E LEU* 2.7 13.6 + - - +
32E ASP* 2.6 48.9 + - - +
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ASP* 2.7 38.1 + - - +
24D LEU* 4.3 15.9 - - + -
25D ASP* 3.0 30.2 + - - -
25E ASP 2.8 23.1 + - - +
26E LEU* 3.4 8.3 - - + +
28E ASN* 1.3 72.9 - - - +
30E TYR* 1.3 57.9 - - - +
32E ASP* 3.9 7.9 + - - +
33E GLN* 3.2 33.8 + - - +
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Residues in contact with TYR 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.1 33.0 - - + -
26E LEU* 2.9 19.5 + - + +
27E TYR* 3.7 5.8 - + - +
29E LYS* 1.3 72.3 - - - +
31E LEU* 1.3 66.1 + - + +
32E ASP 3.0 1.8 - - - -
33E GLN* 2.9 9.5 + - + +
34E VAL* 2.8 56.1 + - + +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E TYR* 2.7 62.6 + - + +
28E ASN* 2.7 15.7 + - - +
30E TYR* 1.3 74.8 - - + +
32E ASP* 1.3 54.2 + - - +
34E VAL* 3.3 12.3 + - + +
35E ILE* 2.7 56.1 + - + +
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Residues in contact with ASP 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ASN* 2.6 32.9 + - - +
29E LYS* 3.9 7.6 + - - +
31E LEU* 1.3 73.3 - - - +
33E GLN* 1.3 63.0 + - - +
34E VAL 2.9 5.5 + - - -
35E ILE 3.0 27.4 + - - +
36E PRO* 3.6 5.5 - - - +
37E TRP* 5.9 1.9 - - - +
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Residues in contact with GLN 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 3.4 34.8 - - - +
27D TYR* 5.0 1.0 - - - -
28D ASN* 2.9 41.2 + - - -
29E LYS* 3.2 23.7 + - - +
30E TYR* 2.9 15.5 + - + +
32E ASP* 1.3 79.8 - - + +
34E VAL* 1.3 59.7 + - - +
36E PRO* 4.9 6.4 - - - +
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 2.8 59.5 + - + +
31E LEU* 3.4 11.7 - - + +
33E GLN* 1.3 80.2 - - - +
35E ILE* 1.3 74.6 + - + +
36E PRO* 3.5 8.6 - - - +
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 2.7 33.2 + - + +
32E ASP* 3.0 18.5 - - - +
34E VAL* 1.3 91.9 - - + +
36E PRO* 1.3 56.6 - - + +
37E TRP* 2.7 45.0 + - + +
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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
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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