Contacts of the helix formed by residues 2 - 19 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0G LEU 5.5 1.4 + - - -
1G MET* 1.3 83.3 - - + +
3G LYS* 1.3 66.0 + - - +
4G HIS 3.3 1.8 - - - -
5G THR* 3.1 15.3 + - - +
6G LEU* 2.9 42.3 + - - +
29G LEU 6.1 0.9 - - - +
30G ILE* 6.6 0.2 - - - -
34G ASN* 5.6 8.0 + - - +
37G ALA* 5.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 3 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0G LEU* 3.5 47.7 + - + +
1G MET 3.2 2.8 - - - -
2G THR* 1.3 78.6 + - - +
4G HIS* 1.3 63.1 + - - +
6G LEU* 3.2 14.1 + - + +
7G GLU* 3.0 47.8 + - + +
44G ILE* 4.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 4 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0G LEU 4.5 2.5 + - - +
1G MET 4.4 5.9 + - - +
2G THR 3.3 0.4 - - - -
3G LYS* 1.3 78.3 - - - +
5G THR* 1.3 65.0 - - - +
7G GLU* 3.3 10.6 + - - +
8G GLN* 3.1 52.3 + - + +
1408G K 4.4 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 5 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET 4.4 3.1 + - - -
2G THR* 3.1 22.8 + - - +
4G HIS* 1.3 79.3 - - - +
6G LEU* 1.3 61.0 + - + +
8G GLN* 3.2 20.5 + - + +
9G LEU* 2.9 46.8 + - + +
29G LEU* 5.0 20.9 - - + +
30G ILE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 2.9 34.6 + - - +
3G LYS* 3.4 17.5 - - + +
5G THR* 1.3 79.8 - - - +
7G GLU* 1.3 57.2 + - - +
9G LEU* 3.3 2.3 + - - +
10G ALA* 2.9 32.0 + - - +
30G ILE* 4.2 18.8 - - + -
37G ALA* 4.2 24.9 - - + +
40G ALA* 4.0 22.0 - - + -
41G ILE* 3.9 23.1 - - + +
44G ILE* 5.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LYS* 3.0 47.0 + - + +
4G HIS* 3.3 13.2 + - + +
6G LEU* 1.3 75.5 - - - +
8G GLN* 1.3 57.3 + - + +
10G ALA* 3.5 5.3 + - - +
11G ALA* 3.0 29.3 + - - +
14G ARG* 5.2 2.8 + - - -
44G ILE* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G HIS* 3.1 43.6 + - + +
5G THR* 3.2 23.9 + - + +
7G GLU* 1.3 76.6 - - - +
9G LEU* 1.3 59.2 + - + +
11G ALA* 3.3 7.5 + - - +
12G ASP* 3.0 34.1 + - - +
1408G K 4.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G THR* 2.9 29.7 + - + +
6G LEU* 3.8 4.3 - - - +
8G GLN* 1.3 74.1 - - + +
10G ALA* 1.3 65.8 + - - +
12G ASP* 3.1 18.2 + - - +
13G LEU* 3.0 26.0 + - - +
23G ILE* 5.3 0.2 - - - +
26G LEU* 4.0 31.9 - - + +
29G LEU* 4.2 30.5 - - + -
30G ILE* 3.4 32.5 - - + -
41G ILE* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU 2.9 17.9 + - - +
7G GLU 3.6 4.7 - - - +
8G GLN 3.3 0.2 - - - -
9G LEU* 1.3 75.7 - - - +
11G ALA* 1.3 57.4 + - - +
13G LEU* 3.3 1.8 + - - -
14G ARG* 3.0 24.5 + - - +
41G ILE* 3.8 16.9 - - + +
44G ILE* 3.9 26.5 - - + -
45G ASN* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 11 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLU 3.0 17.0 + - - +
8G GLN* 3.5 7.6 - - - +
10G ALA* 1.3 73.1 - - - +
12G ASP* 1.3 60.8 + - - +
14G ARG* 3.2 28.1 + - - +
15G ARG* 2.9 42.9 + - - +
1262G PO4 5.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLN* 3.0 22.2 + - - +
9G LEU* 3.1 25.8 + - + +
11G ALA* 1.3 75.2 - - - +
13G LEU* 1.3 57.2 + - - +
15G ARG* 2.6 36.7 + - - +
16G ALA* 2.9 28.4 + - - +
23G ILE* 4.0 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU 3.0 10.1 + - - +
10G ALA 3.5 9.0 - - - +
11G ALA 3.3 0.2 - - - -
12G ASP* 1.3 75.1 - - - +
14G ARG* 1.3 63.4 + - - +
16G ALA* 3.4 4.3 + - - +
17G ALA* 3.2 21.5 + - - +
23G ILE* 3.7 23.3 - - + -
26G LEU* 3.7 27.1 - - + -
41G ILE* 3.8 16.8 - - + -
45G ASN* 3.8 9.6 - - - +
143G ARG* 3.9 22.5 - - + +
144G ILE* 4.7 5.2 - - + -
156G ALA 3.6 25.8 - - - +
157G ASP* 4.0 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLU* 5.2 2.2 + - - -
10G ALA* 3.0 18.1 + - - +
11G ALA* 3.2 29.4 + - - +
13G LEU* 1.3 74.7 - - - +
15G ARG* 1.3 59.6 + - - +
17G ALA* 3.3 7.3 + - - +
18G GLU* 3.0 41.4 + - - +
44G ILE* 4.5 7.1 - - - +
45G ASN* 2.8 49.8 + - - +
48G HIS* 3.7 51.8 + - - +
49G ASP* 4.7 4.5 - - - -
1265G K 4.6 7.6 - - - -
1313G NA 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.7 17.3 - - - +
1262B PO4 3.9 21.8 + - - -
11G ALA* 2.9 21.3 + - - +
12G ASP* 2.6 38.3 + - - +
14G ARG* 1.3 74.5 - - - +
16G ALA* 1.3 64.7 + - - +
18G GLU* 3.3 9.5 + - - +
19G GLN* 3.0 43.5 + - - +
1262G PO4 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ASP 2.9 18.9 + - - +
13G LEU* 3.5 8.7 - - - +
15G ARG* 1.3 75.8 - - - +
17G ALA* 1.3 56.5 + - - +
19G GLN* 5.0 1.6 - - - -
20G GLY* 3.0 26.0 + - - -
21G GLU 3.2 31.2 + - - +
23G ILE* 4.1 10.1 - - + +
100G LEU* 4.2 1.9 - - - +
143G ARG* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.8 18.3 + - - +
13G LEU 3.2 10.0 + - - +
14G ARG* 3.6 9.4 - - - +
16G ALA* 1.3 78.5 - - - +
18G GLU* 1.3 62.5 + - - +
19G GLN 3.3 0.3 + - - -
20G GLY* 3.4 9.9 + - - -
100G LEU* 5.4 2.4 - - - +
143G ARG* 3.8 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU 5.1 0.2 - - - +
8B GLN* 3.6 36.2 - - + +
9B LEU* 5.7 0.3 - - - +
11B ALA* 3.7 23.1 - - - +
12B ASP* 3.0 31.5 - - - +
15B ARG* 3.4 24.6 + - - +
14G ARG* 3.0 28.6 + - - +
15G ARG* 3.3 8.0 + - - +
17G ALA* 1.3 76.2 - - - +
19G GLN* 1.3 58.8 + - - +
1262G PO4 4.0 3.5 + - - -
1265G K 3.2 19.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP* 4.2 3.1 - - - +
15B ARG* 3.1 39.2 - - - +
19B GLN* 5.5 0.6 + - - -
1262B PO4 2.5 32.9 + - - -
15G ARG* 3.0 28.6 + - - +
16G ALA* 5.2 0.9 - - - -
18G GLU* 1.3 76.3 - - - +
20G GLY* 1.3 64.0 + - - +
21G GLU* 3.4 34.7 + - + +
----------------------------------------------------------
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