Contacts of the helix formed by residues 2 - 19 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R LEU* 4.5 0.4 - - - +
1R MET* 1.3 82.3 + - + +
3R LYS* 1.3 59.8 + - - +
4R HIS 3.3 1.8 - - - -
5R THR* 3.1 16.0 + - - +
6R LEU* 2.8 48.3 + - + +
29R LEU 6.1 0.9 - - - +
34R ASN* 5.6 7.6 + - - +
37R ALA* 5.7 2.3 - - - +
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Residues in contact with LYS 3 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I GLN* 3.2 29.1 + - - +
53I GLY* 5.1 3.8 - - - -
0R LEU* 3.8 31.4 - - + +
1R MET 3.2 2.0 - - - -
2R THR* 1.3 78.5 + - - +
4R HIS* 1.3 63.2 + - - +
6R LEU* 3.3 14.5 + - + +
7R GLU* 3.0 45.4 + - + +
44R ILE* 4.8 10.3 - - + -
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Residues in contact with HIS 4 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I ASP* 3.8 15.9 - - - -
52I GLN* 4.3 11.3 + - - +
54I ARG* 3.8 57.0 + - + +
85I ASP* 4.1 13.2 - - - +
98I ARG* 5.4 5.8 - - - -
1263I K 4.2 12.6 - - - -
1306I NA 4.5 4.7 - - - -
0R LEU 4.9 1.4 + - - +
1R MET 4.4 3.4 + - - +
2R THR 3.3 0.6 - - - -
3R LYS* 1.3 78.4 - - - +
5R THR* 1.3 65.2 + - - +
7R GLU* 3.3 8.9 + - - +
8R GLN* 3.1 48.2 + - + +
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Residues in contact with THR 5 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I ARG* 5.7 7.8 + - - -
1R MET 4.5 2.6 + - - -
2R THR* 3.1 24.1 + - - +
4R HIS* 1.3 79.7 - - - +
6R LEU* 1.3 62.5 + - + +
8R GLN* 3.2 19.7 + - + +
9R LEU* 2.9 47.3 + - + +
29R LEU* 4.9 20.0 - - + +
30R ILE* 5.7 0.7 - - + -
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Residues in contact with LEU 6 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R THR* 2.8 33.6 + - - +
3R LYS* 3.4 17.0 - - + +
5R THR* 1.3 80.3 - - - +
7R GLU* 1.3 56.9 + - - +
9R LEU* 3.3 3.0 + - - +
10R ALA* 2.9 31.9 + - - +
30R ILE* 4.1 19.1 - - + -
37R ALA* 4.1 25.6 - - + +
40R ALA* 4.1 21.1 - - + -
41R ILE* 4.0 21.7 - - + +
44R ILE* 5.1 11.4 - - + -
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Residues in contact with GLU 7 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 5.6 0.2 - - - -
52I GLN* 3.5 46.4 - - + +
3R LYS* 3.0 46.4 + - + +
4R HIS* 3.3 8.9 + - + +
6R LEU* 1.3 74.2 - - - +
8R GLN* 1.3 58.4 + - + +
10R ALA* 3.4 5.7 + - - +
11R ALA* 3.0 28.9 + - - +
14R ARG* 5.2 3.5 + - - -
44R ILE* 3.7 29.6 - - + +
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Residues in contact with GLN 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ALA* 4.0 15.9 + - - +
18I GLU* 3.8 46.4 - - + +
1263I K 4.5 4.5 - - - -
4R HIS* 3.1 45.5 + - + +
5R THR* 3.2 24.1 + - + +
7R GLU* 1.3 77.0 - - - +
9R LEU* 1.3 59.7 + - + +
11R ALA* 3.3 5.1 + - - +
12R ASP* 3.0 34.3 + - - +
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Residues in contact with LEU 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R THR* 2.9 27.8 + - + +
6R LEU* 3.8 3.8 - - - +
8R GLN* 1.3 73.7 - - + +
10R ALA* 1.3 66.2 + - - +
12R ASP* 3.1 18.3 + - - +
13R LEU* 3.0 26.0 + - - +
23R ILE* 5.3 0.2 - - - +
26R LEU* 3.9 30.3 - - + +
29R LEU* 4.2 30.7 - - + -
30R ILE* 3.4 32.3 - - + -
41R ILE* 3.9 18.6 - - + -
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Residues in contact with ALA 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R LEU 2.9 18.1 + - - +
7R GLU 3.6 5.2 - - - +
9R LEU* 1.3 76.1 - - - +
11R ALA* 1.3 56.2 + - - +
13R LEU* 3.3 1.8 + - - -
14R ARG* 3.0 24.0 + - - +
41R ILE* 3.8 19.6 - - + +
44R ILE* 3.8 26.5 - - + -
45R ASN* 3.3 31.5 + - - +
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Residues in contact with ALA 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 3.9 25.1 - - - +
1262K PO4 5.0 4.8 + - - +
7R GLU 3.0 18.0 + - - +
8R GLN 3.5 5.6 - - - +
9R LEU 3.2 0.2 - - - -
10R ALA* 1.3 73.7 - - - +
12R ASP* 1.3 59.7 + - - +
14R ARG* 3.2 27.5 + - - +
15R ARG* 3.0 35.3 + - - +
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Residues in contact with ASP 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU* 3.2 27.2 - - - +
19I GLN* 4.5 2.5 - - - +
8R GLN* 3.0 19.9 + - - +
9R LEU* 3.3 25.9 - - + +
11R ALA* 1.3 75.6 - - - +
13R LEU* 1.3 56.4 + - - +
15R ARG* 2.6 36.2 + - - +
16R ALA* 2.9 28.8 + - - +
23R ILE* 3.9 25.8 - - + +
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Residues in contact with LEU 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R LEU 3.0 9.7 + - - +
10R ALA 3.5 7.9 - - - +
11R ALA 3.3 0.2 - - - -
12R ASP* 1.3 74.7 - - - +
14R ARG* 1.3 65.0 + - - +
16R ALA* 3.5 3.9 + - - +
17R ALA* 3.2 21.0 + - - +
23R ILE* 3.7 23.3 - - + -
26R LEU* 3.7 27.4 - - + -
41R ILE* 3.8 17.9 - - + -
45R ASN* 3.8 9.4 - - - +
143R ARG* 3.9 23.7 - - + +
144R ILE* 4.7 4.7 - - + -
156R ALA 3.7 24.7 - - - +
157R ASP* 4.0 18.6 - - - +
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Residues in contact with ARG 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLN* 5.0 0.3 + - - -
7R GLU* 5.2 2.2 + - - -
10R ALA* 3.0 16.7 + - - +
11R ALA* 3.2 30.7 + - - +
13R LEU* 1.3 76.0 - - - +
15R ARG* 1.3 59.5 + - - +
17R ALA* 3.2 7.5 + - - +
18R GLU* 3.0 41.1 + - - +
44R ILE* 4.5 7.5 - - - +
45R ASN* 2.8 47.7 + - - +
48R HIS* 3.7 53.8 + - - +
49R ASP* 4.7 4.5 - - - -
1263R K 4.5 7.4 - - - -
1318R NA 4.6 7.6 - - - -
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Residues in contact with ARG 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ARG* 3.8 6.1 - - - +
18I GLU* 3.3 17.4 + - - +
19I GLN* 3.3 29.9 - - - +
15K ARG* 3.7 17.3 - - - +
1262K PO4 2.8 51.8 + - - +
1263K PO4 3.3 20.2 - - - -
11R ALA 3.0 14.7 + - - +
12R ASP* 2.6 36.9 + - - +
14R ARG* 1.3 74.9 - - - +
16R ALA* 1.3 65.3 + - - +
18R GLU* 3.2 9.5 + - - +
19R GLN* 2.9 43.3 + - - +
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Residues in contact with ALA 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ASP 2.9 18.0 + - - +
13R LEU* 3.5 9.0 - - - +
15R ARG* 1.3 76.0 - - - +
17R ALA* 1.3 57.3 + - - +
19R GLN* 5.0 1.6 - - - -
20R GLY* 3.0 25.1 + - - -
21R GLU 3.2 30.2 + - - +
23R ILE* 4.1 10.5 - - + +
100R LEU* 4.1 2.1 - - - +
143R ARG* 3.8 27.8 - - + +
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Residues in contact with ALA 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLN* 3.9 18.8 + - - +
13R LEU 3.2 9.3 + - - +
14R ARG* 3.2 10.0 + - - +
15R ARG 3.2 0.6 - - - -
16R ALA* 1.3 75.9 - - - +
18R GLU* 1.3 66.2 + - - +
19R GLN 3.3 0.7 + - - -
20R GLY* 3.5 9.9 + - - -
100R LEU* 5.3 2.9 - - - +
143R ARG* 3.8 19.4 - - + +
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Residues in contact with GLU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K GLN* 3.7 34.4 - - + +
9K LEU* 5.6 0.5 - - - +
11K ALA* 3.7 23.3 - - - +
12K ASP* 3.0 31.8 - - - +
15K ARG* 3.2 28.6 + - - +
1262K PO4 4.2 3.6 + - - -
14R ARG* 3.0 29.8 + - - +
15R ARG* 3.2 8.1 + - - +
17R ALA* 1.3 75.8 - - - +
19R GLN* 1.3 58.2 + - - +
20R GLY 3.9 0.2 + - - -
1263R K 3.7 16.1 - - - -
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Residues in contact with GLN 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLN* 5.5 0.2 + - - -
12K ASP* 4.4 3.4 - - - +
15K ARG* 3.3 31.9 - - - +
1263K PO4 2.9 35.7 + - - -
15R ARG* 2.9 30.9 + - - +
16R ALA* 4.8 1.1 + - - -
18R GLU* 1.3 77.8 - - - +
20R GLY* 1.3 62.7 + - - +
21R GLU* 3.9 38.7 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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