Contacts of the helix formed by residues 11 - 28 (chain D) in PDB entry 2WTK
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 SER 11 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LYS* 1.3 72.6 - - - +
12D PRO* 1.4 75.3 - - - +
13D ALA* 3.5 9.0 + - - +
14D ASP* 2.9 35.1 + - - -
15D ILE* 2.8 26.5 + - - +
69D GLN* 5.2 4.7 - - - -
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Residues in contact with PRO 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LYS 4.6 1.1 - - - +
11D SER* 1.4 85.3 - - - +
13D ALA* 1.3 58.6 + - - +
15D ILE* 3.1 10.1 + - + +
16D VAL* 2.8 33.2 + - - +
53D ILE* 4.4 15.7 - - + -
66D ALA* 3.7 27.6 - - + +
69D GLN* 4.0 23.8 - - + +
70D LEU* 3.9 32.5 - - + +
73D GLU* 4.5 2.9 - - + -
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Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 3.3 8.3 + - - +
12D PRO* 1.3 78.1 - - - +
14D ASP* 1.3 59.9 + - - +
16D VAL* 4.1 0.9 - - - +
17D LYS* 3.1 30.0 + - - +
69D GLN* 5.7 1.0 - - - +
73D GLU* 3.5 38.3 - - + +
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Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LYS* 3.8 15.5 - - + +
11D SER* 2.9 39.3 + - - +
13D ALA* 1.3 76.1 - - - +
15D ILE* 1.3 65.7 + - - +
17D LYS* 3.3 8.7 + - - +
18D ASN* 3.0 36.2 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LYS* 4.4 25.6 - - + +
11D SER 2.8 22.8 + - - +
12D PRO* 3.6 5.8 - - + +
14D ASP* 1.3 73.2 - - - +
16D VAL* 1.3 57.4 + - - +
18D ASN* 3.8 3.4 - - - +
19D LEU* 2.9 30.1 + - - +
46D ASN* 3.6 44.7 - - + +
49D ALA* 3.6 23.8 - - + -
50D MET* 3.8 17.9 - - + -
53D ILE* 3.7 26.0 - - + -
70D LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PRO 2.8 17.0 + - - +
13D ALA 4.1 2.2 - - - +
15D ILE* 1.3 70.9 - - - +
17D LYS* 1.3 54.1 + - - +
19D LEU 3.2 0.3 + - - -
20D LYS* 2.8 33.9 + - + +
50D MET* 3.4 25.4 - - + -
70D LEU* 3.6 20.4 - - + -
73D GLU* 3.8 27.6 - - + +
74D LEU* 4.0 11.0 - - + -
77D SER* 3.4 34.8 - - - +
79D LEU* 3.5 6.6 - - + +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA 3.1 21.0 + - - +
14D ASP* 3.3 7.4 + - - +
16D VAL* 1.3 78.3 - - - +
18D ASN* 1.3 58.1 + - - +
20D LYS* 3.2 10.5 + - + +
21D GLU* 2.8 64.5 + - + +
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Residues in contact with ASN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LYS* 5.3 5.5 - - - +
14D ASP* 3.0 26.1 + - - +
15D ILE* 3.8 1.9 - - - +
17D LYS* 1.3 81.5 - - - +
19D LEU* 1.3 57.3 + - - +
21D GLU* 3.8 14.7 + - - +
22D SER* 2.7 38.5 + - - -
42D GLU* 4.3 11.4 + - - +
46D ASN* 3.6 26.0 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE 2.9 18.5 + - - +
16D VAL* 3.5 4.3 - - - +
18D ASN* 1.3 76.7 - - - +
20D LYS* 1.3 62.5 + - - +
22D SER* 4.7 1.1 - - - -
23D MET* 3.0 34.0 + - + +
43D VAL* 4.0 41.1 - - + +
46D ASN* 4.3 11.0 - - + +
47D LEU* 4.0 23.3 - - + +
50D MET* 3.3 34.3 - - + -
79D LEU* 3.7 18.8 - - + -
83D LEU* 4.2 10.1 - - + -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL 2.8 20.6 + - - +
17D LYS* 3.5 8.7 - - + +
19D LEU* 1.3 71.8 - - - +
21D GLU* 1.3 65.2 + - + +
23D MET* 3.6 3.4 + - - +
24D ALA* 3.1 22.0 + - - +
76D ASN 5.7 0.2 + - - -
77D SER* 3.5 37.3 + - - +
79D LEU* 4.0 19.7 - - + +
82D THR* 5.9 3.4 - - + +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 2.8 52.6 + - + +
18D ASN* 3.8 13.7 + - - +
20D LYS* 1.3 79.5 - - + +
22D SER* 1.3 64.4 + - - +
24D ALA* 3.1 17.8 + - - +
25D VAL* 3.1 17.0 + - - +
42D GLU* 5.9 0.2 - - - +
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASN 2.7 23.7 + - - -
19D LEU* 4.1 2.2 - - - -
21D GLU* 1.3 73.9 - - - +
23D MET* 1.3 63.0 + - - +
25D VAL* 3.3 13.1 - - - +
26D LEU* 3.2 17.7 + - - +
39D ALA* 3.7 19.9 - - - +
42D GLU* 2.5 48.4 + - - +
43D VAL* 4.2 7.4 - - - -
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.0 24.7 + - + +
20D LYS* 3.7 5.2 - - - +
22D SER* 1.3 74.0 - - - +
24D ALA* 1.3 66.4 + - - +
26D LEU* 2.9 21.5 + - - +
27D GLU* 3.0 14.6 + - - +
43D VAL* 3.9 19.0 - - + +
79D LEU* 4.6 3.4 - - + -
82D THR* 4.1 23.6 - - + +
83D LEU* 3.9 22.4 - - + -
86D ASP* 3.9 32.3 - - + +
89D LEU* 5.2 3.5 - - + +
90D ILE* 3.9 36.1 - - + -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LYS 3.1 14.3 + - - +
21D GLU* 3.1 14.1 + - - +
23D MET* 1.3 75.5 - - - +
25D VAL* 1.3 56.6 + - + +
27D GLU* 3.2 7.7 + - - +
28D LYS* 2.9 29.4 + - - +
82D THR* 5.9 0.2 - - - +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLU 3.1 12.2 + - - +
22D SER* 3.3 12.6 - - - +
24D ALA* 1.3 77.1 - - + +
26D LEU* 1.3 63.0 + - - +
28D LYS* 3.2 12.5 - - - +
31D ILE* 3.1 39.9 - - + +
35D LYS* 4.1 19.3 - - + +
36D ALA* 5.1 1.3 - - - +
39D ALA* 3.7 21.3 - - + -
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D SER 3.2 12.1 + - - +
23D MET* 2.9 21.3 + - - +
25D VAL* 1.3 73.2 - - - +
27D GLU* 1.3 61.1 + - - +
28D LYS 4.1 3.6 - - - +
31D ILE* 5.3 0.2 - - - -
36D ALA* 3.9 19.1 - - + +
39D ALA* 4.0 12.1 - - + +
40D THR* 3.5 25.4 - - - +
43D VAL* 3.6 31.6 - - + -
89D LEU* 3.7 46.7 - - + +
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D MET 3.0 10.9 + - - +
24D ALA* 3.4 11.9 - - - +
26D LEU* 1.3 77.0 - - - +
28D LYS* 1.3 69.6 + - - +
29D GLN* 3.2 5.4 + - - +
86D ASP* 3.7 28.7 - - - +
89D LEU* 3.9 12.2 - - + +
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA 2.9 13.4 + - - +
25D VAL* 3.2 18.3 + - - +
26D LEU 4.1 5.0 - - - +
27D GLU* 1.3 80.8 + - - +
29D GLN* 1.3 91.7 + - - +
30D ASP* 2.9 9.1 + - - +
31D ILE* 3.8 30.5 - - + +
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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
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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