Contacts of the helix formed by residues 2 - 19 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0H LEU* 4.6 0.4 - - - +
1H MET* 1.3 81.6 + - + +
3H LYS* 1.3 59.4 + - - +
4H HIS 3.3 2.0 - - - -
5H THR* 3.1 15.6 + - - +
6H LEU* 2.8 48.4 + - - +
29H LEU 6.0 1.3 - - - +
30H ILE* 6.6 0.4 - - - -
34H ASN* 5.6 7.9 + - - +
37H ALA* 5.7 2.0 - - - +
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Residues in contact with LYS 3 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H LEU* 3.7 49.2 + - + +
1H MET 3.2 2.6 - - - -
2H THR* 1.3 77.6 + - - +
4H HIS* 1.3 62.3 + - - +
6H LEU* 3.3 14.1 + - + +
7H GLU* 3.1 44.0 + - + +
44H ILE* 4.8 10.3 - - + -
52S GLN* 3.1 29.8 + - - +
53S GLY* 5.0 2.0 - - - -
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Residues in contact with HIS 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H LEU 4.8 1.4 + - - -
1H MET 4.4 1.7 + - - +
2H THR 3.3 0.6 - - - -
3H LYS* 1.3 78.4 - - - +
5H THR* 1.3 65.3 + - - +
7H GLU* 3.3 9.5 + - + +
8H GLN* 3.1 52.2 + - + +
49S ASP* 3.6 28.3 - - - -
52S GLN* 4.2 14.4 + - - +
54S ARG* 3.7 47.0 + - + +
85S ASP* 4.1 13.5 - - - +
98S ARG* 5.5 3.8 - - - -
1308S NA 4.2 9.0 - - - -
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Residues in contact with THR 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET 4.5 2.4 + - - -
2H THR* 3.1 23.1 + - - +
4H HIS* 1.3 80.9 - - - +
6H LEU* 1.3 61.6 + - + +
8H GLN* 3.2 18.6 + - + +
9H LEU* 2.9 46.9 + - + +
29H LEU* 4.9 20.6 - - + +
30H ILE* 5.7 0.9 - - + -
98S ARG* 5.6 9.1 + - - -
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Residues in contact with LEU 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H THR* 2.8 38.5 + - - +
3H LYS* 3.5 13.2 - - + +
5H THR* 1.3 79.0 - - - +
7H GLU* 1.3 56.1 + - - +
9H LEU* 3.3 3.0 + - - +
10H ALA* 2.9 31.5 + - - +
30H ILE* 4.2 18.8 - - + -
37H ALA* 4.1 26.5 - - + +
40H ALA* 4.1 21.1 - - + -
41H ILE* 4.0 22.6 - - + +
44H ILE* 5.1 11.7 - - + -
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Residues in contact with GLU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H LYS* 3.1 46.3 + - + +
4H HIS* 3.5 8.5 - - - +
6H LEU* 1.3 76.6 - - - +
8H GLN* 1.3 62.4 + - + +
10H ALA* 3.5 5.5 + - - +
11H ALA* 3.0 23.9 + - - +
14H ARG* 5.2 2.9 + - - -
44H ILE* 3.7 30.0 - - + +
18S GLU* 5.6 0.2 - - - -
52S GLN* 3.5 46.6 - - + +
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Residues in contact with GLN 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H HIS* 3.1 46.0 + - + +
5H THR* 3.2 24.3 + - + +
7H GLU* 1.3 76.6 - - + +
9H LEU* 1.3 59.8 + - + +
11H ALA* 3.2 5.1 + - - +
12H ASP* 2.9 33.9 + - - +
14S ARG 5.1 0.2 + - - -
17S ALA* 4.1 15.5 + - - +
18S GLU* 3.8 47.2 - - + +
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Residues in contact with LEU 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H THR* 2.9 27.5 + - + +
6H LEU* 3.8 3.1 - - - +
8H GLN* 1.3 74.2 - - + +
10H ALA* 1.3 66.0 + - - +
12H ASP* 3.1 18.2 + - - +
13H LEU* 3.0 26.0 + - - +
26H LEU* 4.0 31.7 - - + +
29H LEU* 4.2 30.7 - - + -
30H ILE* 3.4 32.8 - - + -
41H ILE* 4.0 19.1 - - + -
18S GLU 5.8 0.2 - - - +
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Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU 2.9 17.7 + - - +
7H GLU 3.7 4.9 - - - +
9H LEU* 1.3 76.9 - - - +
11H ALA* 1.3 56.8 + - - +
13H LEU 3.3 1.9 + - - -
14H ARG* 3.0 23.6 + - - +
41H ILE* 3.8 18.3 - - + +
44H ILE* 3.8 27.6 - - + -
45H ASN* 3.3 31.4 + - - +
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Residues in contact with ALA 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLU 3.0 17.0 + - - +
8H GLN 3.5 4.9 - - - +
10H ALA* 1.3 74.4 - - - +
12H ASP* 1.3 59.6 + - - +
14H ARG* 3.2 27.7 + - - +
15H ARG* 2.9 35.2 + - - +
1262H PO4 4.9 5.5 + - - +
18S GLU* 3.8 24.9 - - - +
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Residues in contact with ASP 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H GLN* 2.9 20.3 + - - +
9H LEU* 3.3 25.9 - - + +
11H ALA* 1.3 76.2 - - - +
13H LEU* 1.3 56.1 + - - +
15H ARG* 2.6 36.6 + - - +
16H ALA* 2.9 28.4 + - - +
23H ILE* 4.0 26.8 - - + +
26H LEU* 5.7 0.2 - - - +
18S GLU* 3.2 27.9 - - - +
19S GLN* 4.5 2.4 - - - +
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Residues in contact with LEU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H LEU 3.0 9.6 + - - +
10H ALA 3.4 8.3 - - - +
12H ASP* 1.3 73.4 - - - +
14H ARG* 1.3 65.3 + - - +
16H ALA* 3.4 5.0 + - - +
17H ALA* 3.2 22.0 + - - +
23H ILE* 3.7 22.7 - - + -
26H LEU* 3.7 27.4 - - + -
41H ILE* 3.8 17.0 - - + -
45H ASN* 3.8 9.2 - - - +
143H ARG* 3.9 23.3 - - + +
144H ILE* 4.7 4.7 - - + -
156H ALA 3.6 26.5 - - - +
157H ASP* 4.0 19.1 - - - +
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLU* 5.2 3.0 + - - -
10H ALA* 3.0 17.3 + - - +
11H ALA* 3.2 29.6 + - - +
13H LEU* 1.3 75.3 - - - +
15H ARG* 1.3 58.7 + - - +
17H ALA* 3.2 7.7 + - - +
18H GLU* 3.0 43.4 + - - +
44H ILE* 4.5 7.5 - - - +
45H ASN* 2.8 48.5 + - + +
48H HIS* 3.7 52.2 + - - +
49H ASP* 4.8 5.8 - - - +
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Residues in contact with ARG 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ALA 2.9 14.6 + - - +
12H ASP* 2.6 36.5 + - - +
14H ARG* 1.3 75.1 - - - +
16H ALA* 1.3 64.8 + - - +
18H GLU* 3.7 14.3 + - - +
19H GLN* 2.9 53.1 + - + +
1262H PO4 2.7 48.6 + - - +
15S ARG* 3.8 18.7 - - - +
18S GLU* 3.3 18.8 + - - +
19S GLN* 3.4 29.7 + - - +
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASP 2.9 18.0 + - - +
13H LEU* 3.5 9.4 - - - +
15H ARG* 1.3 75.6 - - - +
17H ALA* 1.3 57.1 + - - +
19H GLN* 5.0 2.2 - - - +
20H GLY* 3.0 25.3 + - - -
21H GLU 3.2 29.5 + - - +
23H ILE* 4.1 10.1 - - + +
100H LEU* 4.2 1.8 - - - +
143H ARG* 3.8 27.4 - - + +
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Residues in contact with ALA 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU 3.2 10.6 + - - +
14H ARG* 3.6 9.0 - - - +
15H ARG 3.2 0.2 - - - -
16H ALA* 1.3 76.9 - - - +
18H GLU* 1.3 65.6 + - + +
19H GLN 3.3 0.3 + - - -
20H GLY* 3.4 9.8 + - - -
100H LEU* 5.4 2.2 - - - -
143H ARG* 3.8 20.5 - - + +
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ARG* 3.0 33.4 + - - +
15H ARG* 3.7 15.1 - - - +
17H ALA* 1.3 77.4 - - + +
19H GLN* 1.3 62.3 + - + +
20H GLY 3.9 0.2 + - - -
48H HIS* 6.0 0.3 + - - -
1262H PO4 4.2 13.1 + - - -
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Residues in contact with GLN 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ARG* 2.9 44.1 + - + +
16H ALA* 5.2 1.2 - - - +
18H GLU* 1.3 80.2 - - + +
20H GLY* 1.3 64.7 + - - +
21H GLU* 3.9 39.8 + - + +
19S GLN* 5.6 1.8 + - - -
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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
------------------------------------------------------------
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