Contacts of the helix formed by residues 2 - 19 (chain S) in PDB entry 2WQT
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 THR 2 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0S LEU 4.8 2.8 + - - -
1S MET* 1.3 81.8 + - + +
3S LYS* 1.3 60.2 + - - +
4S HIS 3.3 2.0 - - - -
5S THR* 3.1 16.5 + - - +
6S LEU* 2.9 47.3 + - - +
29S LEU 6.1 0.9 - - - +
34S ASN* 5.6 7.6 + - - +
37S ALA* 5.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 3 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0S LEU* 3.6 38.3 - - + +
1S MET 3.2 3.0 - - - -
2S THR* 1.3 79.0 + - - +
4S HIS* 1.3 62.6 + - - +
6S LEU* 3.3 14.4 + - + +
7S GLU* 3.1 46.8 + - + +
44S ILE* 4.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 4 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0S LEU 5.5 0.6 + - - -
1S MET 4.4 5.7 + - - +
2S THR 3.3 0.6 - - - -
3S LYS* 1.3 78.0 - - - +
5S THR* 1.3 65.7 + - - +
7S GLU* 3.3 12.2 + - - +
8S GLN* 3.1 51.8 + - + +
1320S NA 4.3 15.5 - - - -
1413S K 4.5 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 5 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET 4.4 3.3 + - - -
2S THR* 3.1 22.5 + - - +
4S HIS* 1.3 79.9 - - - +
6S LEU* 1.3 61.8 + - + +
8S GLN* 3.2 19.6 + - - +
9S LEU* 2.9 47.0 + - + +
29S LEU* 4.9 20.0 - - + +
30S ILE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0S LEU 6.3 0.4 - - - +
2S THR* 2.9 34.7 + - + +
3S LYS* 3.5 17.3 - - + +
5S THR* 1.3 79.3 - - - +
7S GLU* 1.3 56.7 + - - +
9S LEU* 3.3 2.4 + - - +
10S ALA* 2.9 30.9 + - - +
30S ILE* 4.1 25.6 - - + -
37S ALA* 4.1 19.5 - - + +
40S ALA* 4.0 21.8 - - + -
41S ILE* 3.9 22.4 - - + +
44S ILE* 5.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S LYS* 3.1 46.3 + - + +
4S HIS* 3.3 12.1 + - - +
6S LEU* 1.3 74.3 - - - +
8S GLN* 1.3 57.6 + - - +
10S ALA* 3.5 5.8 + - - +
11S ALA* 3.0 29.1 + - - +
14S ARG* 5.2 3.3 + - - -
44S ILE* 3.6 30.4 - - + +
1413S K 4.6 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S HIS* 3.1 45.4 + - + +
5S THR* 3.2 23.4 + - + +
7S GLU* 1.3 78.0 - - - +
9S LEU* 1.3 59.6 + - + +
11S ALA* 3.2 7.5 + - - +
12S ASP* 3.0 36.3 + - - +
1413S K 4.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S THR* 2.9 28.1 + - + +
6S LEU 3.9 3.4 - - - +
8S GLN* 1.3 74.8 - - + +
10S ALA* 1.3 66.5 + - - +
12S ASP* 3.1 18.7 + - - +
13S LEU* 3.0 26.4 + - - +
23S ILE* 5.3 0.2 - - - +
26S LEU* 4.0 31.3 - - + +
29S LEU* 4.2 30.7 - - + -
30S ILE* 3.4 32.8 - - + -
41S ILE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S LEU 2.9 18.1 + - - +
7S GLU 3.6 4.7 - - - +
9S LEU* 1.3 76.3 - - - +
11S ALA* 1.3 56.6 + - - +
13S LEU* 3.3 1.8 + - - -
14S ARG* 3.0 24.7 + - - +
41S ILE* 3.8 17.4 - - + +
44S ILE* 3.8 26.9 - - + -
45S ASN* 3.3 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262H PO4 5.0 6.1 + - - +
7S GLU 3.0 16.8 + - - +
8S GLN* 3.5 7.4 - - - +
9S LEU 3.2 0.2 - - - -
10S ALA* 1.3 72.9 - - - +
12S ASP* 1.3 66.8 + - - +
14S ARG* 3.2 26.9 + - - +
15S ARG* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S GLN* 3.0 22.5 + - - +
9S LEU* 3.1 26.5 + - + +
11S ALA* 1.3 76.3 - - - +
13S LEU* 1.3 57.9 + - - +
15S ARG* 2.7 36.3 + - - +
16S ALA* 2.9 28.2 + - - +
23S ILE* 3.9 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S LEU 3.0 9.8 + - - +
10S ALA 3.4 8.1 - - - +
12S ASP* 1.3 75.4 - - - +
14S ARG* 1.3 64.2 + - - +
16S ALA* 3.5 4.5 + - - +
17S ALA* 3.2 21.1 + - - +
23S ILE* 3.7 23.3 - - + -
26S LEU* 3.7 27.8 - - + -
41S ILE* 3.8 17.0 - - + -
45S ASN* 3.9 9.0 - - - +
143S ARG* 3.9 22.8 - - + +
144S ILE* 4.7 5.4 - - + -
156S ALA 3.7 25.1 - - - +
157S ASP* 4.0 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN* 5.1 0.2 + - - -
7S GLU* 5.2 2.8 + - - -
10S ALA* 3.0 17.5 + - - +
11S ALA* 3.2 29.6 + - - +
13S LEU* 1.3 74.8 - - - +
15S ARG* 1.3 59.5 + - - +
17S ALA* 3.3 6.6 + - - +
18S GLU* 3.0 43.3 + - - +
44S ILE* 4.5 7.3 - - - +
45S ASN* 2.8 47.2 + - - +
48S HIS* 3.7 53.5 + - - +
49S ASP* 4.8 5.6 - - - -
1308S NA 4.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ARG* 3.8 22.0 - - - +
1262H PO4 2.8 45.7 + - - +
11S ALA* 2.9 18.5 + - - +
12S ASP* 2.7 37.7 + - - +
14S ARG* 1.3 74.7 - - - +
16S ALA* 1.3 65.3 + - - +
18S GLU* 3.7 9.4 - - - +
19S GLN* 3.0 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ASP 2.9 18.2 + - - +
13S LEU* 3.5 8.7 - - - +
15S ARG* 1.3 77.1 - - - +
17S ALA* 1.3 57.9 + - - +
19S GLN* 5.0 1.8 - - - +
20S GLY* 3.0 25.1 + - - -
21S GLU 3.2 30.4 + - - +
23S ILE* 4.1 10.3 - - + +
100S LEU* 4.1 2.1 - - - +
143S ARG* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN* 4.1 18.3 + - - +
13S LEU 3.2 10.6 + - - +
14S ARG* 3.6 9.0 - - - +
15S ARG 3.2 0.4 - - - -
16S ALA* 1.3 76.4 - - - +
18S GLU* 1.3 65.5 + - - +
19S GLN 3.2 0.5 + - - -
20S GLY* 3.4 10.2 + - - -
100S LEU* 5.4 2.7 - - - -
143S ARG* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLU 5.1 0.2 - - - +
8H GLN* 3.8 37.3 - - + +
9H LEU* 5.8 0.5 - - - +
11H ALA* 3.8 22.7 - - - +
12H ASP* 3.2 29.8 - - - +
15H ARG* 3.3 27.6 + - - +
1262H PO4 4.1 3.2 + - - -
14S ARG* 3.0 32.2 + - - +
15S ARG* 3.3 8.4 + - - +
17S ALA* 1.3 75.9 - - - +
19S GLN* 1.3 58.3 + - - +
20S GLY 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASP* 4.5 2.5 - - - +
15H ARG* 3.4 35.9 + - - +
19H GLN* 5.6 1.0 + - - -
15S ARG* 3.0 36.8 + - - +
16S ALA* 5.3 1.0 - - - +
18S GLU* 1.3 76.3 - - - +
20S GLY* 1.3 62.6 + - - +
21S GLU* 3.4 40.4 + - + +
----------------------------------------------------------
Back to top of page
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