Contacts of the helix formed by residues 2 - 19 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0I LEU 5.2 2.4 + - - -
1I MET* 1.3 82.7 - - + +
3I LYS* 1.3 65.6 + - - +
4I HIS 3.3 2.0 - - - -
5I THR* 3.1 16.8 + - + +
6I LEU* 2.9 41.8 + - - +
29I LEU 6.0 1.3 - - - +
30I ILE* 6.6 0.4 - - - -
34I ASN* 5.6 8.6 + - - +
37I ALA* 5.7 2.0 - - - +
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Residues in contact with LYS 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0I LEU* 4.1 35.3 - - + +
1I MET 3.2 3.8 - - - +
2I THR* 1.3 78.3 + - - +
4I HIS* 1.3 62.8 + - - +
6I LEU* 3.3 14.0 + - + +
7I GLU* 3.0 42.3 + - + +
44I ILE* 4.8 10.3 - - + -
52K GLN* 2.7 32.5 + - - +
53K GLY* 4.6 6.2 - - - -
54K ARG* 6.5 0.2 - - - -
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Residues in contact with HIS 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0I LEU 5.5 0.6 + - - -
1I MET 4.5 1.4 + - - +
2I THR 3.3 0.8 - - - -
3I LYS* 1.3 77.6 - - - +
5I THR* 1.3 65.8 + - - +
7I GLU* 3.3 9.2 + - - +
8I GLN* 3.1 54.1 + - + +
49K ASP* 3.5 19.5 + - - -
52K GLN* 4.6 7.4 + - - +
54K ARG* 3.4 62.9 + - + +
85K ASP* 3.8 15.1 + - - +
98K ARG* 5.2 6.3 - - - -
1265K K 4.3 6.5 - - - -
1305K NA 4.1 9.8 - - - -
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Residues in contact with THR 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET 4.4 3.3 + - - -
2I THR* 3.1 23.2 + - + +
4I HIS* 1.3 79.9 - - - +
6I LEU* 1.3 61.7 + - + +
8I GLN* 3.2 20.3 + - + +
9I LEU* 2.9 46.6 + - + +
29I LEU* 5.0 20.4 - - + +
30I ILE* 5.7 0.7 - - + -
98K ARG* 5.1 17.7 + - - -
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Residues in contact with LEU 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 2.9 34.3 + - - +
3I LYS* 3.4 17.0 - - + +
5I THR* 1.3 77.0 - - - +
7I GLU* 1.3 59.9 + - - +
9I LEU* 3.3 1.9 + - - +
10I ALA* 2.9 31.1 + - - +
30I ILE* 4.1 25.8 - - + -
37I ALA* 4.1 20.0 - - + +
40I ALA* 4.0 22.9 - - + -
41I ILE* 3.9 23.7 - - + +
44I ILE* 4.9 12.1 - - + +
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Residues in contact with GLU 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LYS* 3.0 45.1 + - + +
4I HIS* 3.3 9.4 + - - +
6I LEU* 1.3 75.6 - - - +
8I GLN* 1.3 57.5 + - - +
10I ALA* 3.5 5.0 + - - +
11I ALA* 3.0 28.6 + - - +
14I ARG* 5.2 2.3 + - - -
44I ILE* 3.6 31.3 - - + +
18K GLU* 5.5 0.4 - - - -
52K GLN* 3.2 49.9 - - + +
1265K K 4.6 2.7 - - - -
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Residues in contact with GLN 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I HIS* 3.1 45.6 + - + +
5I THR* 3.2 24.0 + - + +
7I GLU* 1.3 77.2 - - - +
9I LEU* 1.3 59.9 + - + +
11I ALA* 3.3 4.7 + - - +
12I ASP* 3.0 34.4 + - - +
17K ALA* 3.8 34.5 + - - +
18K GLU* 3.9 27.6 - - + +
1265K K 4.5 4.7 - - - -
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Residues in contact with LEU 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 2.9 28.2 + - + +
6I LEU* 3.9 3.1 - - - +
8I GLN* 1.3 73.7 - - + +
10I ALA* 1.3 65.2 + - - +
12I ASP* 3.2 18.9 + - - +
13I LEU* 3.0 26.4 + - - +
26I LEU* 3.9 32.0 - - + +
29I LEU* 4.2 29.8 - - + -
30I ILE* 3.4 33.0 - - + -
41I ILE* 3.9 18.2 - - + -
18K GLU 5.7 0.2 - - - +
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Residues in contact with ALA 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU 2.9 17.9 + - - +
7I GLU 3.6 5.4 - - - +
9I LEU* 1.3 76.3 - - - +
11I ALA* 1.3 57.1 + - - +
13I LEU* 3.3 2.0 + - - -
14I ARG* 3.0 24.0 + - - +
41I ILE* 3.8 17.2 - - + +
44I ILE* 3.8 26.9 - - + -
45I ASN* 3.2 33.6 + - - +
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I GLU 3.0 17.0 + - - +
8I GLN 3.5 3.6 - - - +
9I LEU 3.2 0.2 - - - -
10I ALA* 1.3 73.7 - - - +
12I ASP* 1.3 58.6 + - - +
14I ARG* 3.2 27.1 + - - +
15I ARG* 2.9 35.0 + - - +
18K GLU* 3.5 29.6 - - - +
1262K PO4 5.1 3.7 + - - +
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Residues in contact with ASP 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLN* 3.0 17.3 + - - +
9I LEU* 3.2 25.8 + - + +
11I ALA* 1.3 75.4 - - - +
13I LEU* 1.3 56.6 - - - +
15I ARG* 2.6 37.1 + - - +
16I ALA* 2.9 28.4 + - - +
23I ILE* 3.9 27.8 - - + +
18K GLU* 2.9 32.2 - - - +
19K GLN* 4.1 2.7 + - - +
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Residues in contact with LEU 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU 3.0 9.2 + - - +
10I ALA 3.4 8.3 - - - +
11I ALA 3.3 0.2 - - - -
12I ASP* 1.3 74.5 - - - +
14I ARG* 1.3 63.4 + - - +
16I ALA* 3.4 3.9 + - - +
17I ALA* 3.2 21.1 + - - +
23I ILE* 3.7 23.1 - - + -
26I LEU* 3.7 27.8 - - + -
41I ILE* 3.8 18.2 - - + -
45I ASN* 3.8 8.5 - - - +
143I ARG* 3.9 22.8 - - + +
144I ILE* 4.7 4.3 - - + -
156I ALA 3.6 25.6 - - - +
157I ASP* 4.0 18.8 - - + +
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Residues in contact with ARG 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I GLU* 5.2 2.8 + - - -
10I ALA* 3.0 17.9 + - - +
11I ALA* 3.2 29.2 + - - +
13I LEU* 1.3 75.2 - - - +
15I ARG* 1.3 59.5 + - - +
17I ALA* 3.2 7.1 + - - +
18I GLU* 3.0 39.6 + - - +
44I ILE* 4.5 7.3 - - - +
45I ASN* 2.8 51.6 + - - +
48I HIS* 3.7 53.4 + - - +
49I ASP* 4.8 4.3 - - - -
1263I K 4.4 7.9 - - - -
1306I NA 4.5 7.9 - - - -
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Residues in contact with ARG 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ALA 2.9 13.3 + - - +
12I ASP* 2.6 37.5 + - - +
14I ARG* 1.3 75.6 - - - +
16I ALA* 1.3 64.5 + - - +
18I GLU* 3.3 10.2 + - - +
19I GLN* 3.0 45.1 + - - +
15K ARG* 3.6 13.0 - - - +
18K GLU* 3.1 20.0 + - - +
19K GLN* 3.0 29.7 - - - +
1262K PO4 2.8 44.4 + - - +
1263K PO4 3.7 20.2 - - - -
15R ARG* 3.8 12.6 - - - +
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Residues in contact with ALA 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ASP 2.9 18.9 + - - +
13I LEU* 3.5 9.0 - - - +
14I ARG 3.3 0.4 - - - -
15I ARG* 1.3 75.8 - - - +
17I ALA* 1.3 57.1 + - - +
19I GLN* 5.0 1.3 - - - -
20I GLY* 3.0 24.8 + - - -
21I GLU 3.2 30.0 + - - +
23I ILE* 4.1 9.9 - - + -
100I LEU* 4.1 2.0 - - - +
143I ARG* 3.8 28.7 - - + +
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Residues in contact with ALA 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I LEU 3.2 9.8 + - - +
14I ARG* 3.6 9.6 - - - +
15I ARG 3.2 0.4 - - - -
16I ALA* 1.3 79.5 - - - +
18I GLU* 1.3 62.2 + - - +
19I GLN 3.2 0.9 + - - -
20I GLY* 3.4 9.6 + - - -
100I LEU* 5.3 2.4 - - - +
143I ARG* 3.8 19.9 - - + +
8R GLN* 4.0 16.7 + - - +
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Residues in contact with GLU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ARG* 3.0 28.5 + - - +
15I ARG* 3.7 7.8 - - - +
17I ALA* 1.3 76.3 - - - +
19I GLN* 1.3 58.5 + - - +
20I GLY 3.9 0.3 + - - -
1263I K 3.6 17.3 - - - -
1262K PO4 3.8 7.0 + - - -
8R GLN* 3.8 36.4 - - + +
11R ALA* 3.9 20.3 - - - +
12R ASP* 3.2 28.9 - - - +
15R ARG* 3.3 27.4 + - - +
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Residues in contact with GLN 19 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ARG* 3.0 31.8 + - - +
16I ALA* 5.2 1.0 - - - -
18I GLU* 1.3 76.5 - - - +
20I GLY* 1.3 63.0 + - - +
21I GLU* 3.8 37.0 + - + +
19K GLN* 5.2 0.2 + - - -
1263K PO4 2.9 43.1 + - - -
12R ASP* 4.5 2.5 - - - +
15R ARG* 3.3 28.5 - - - +
19R GLN* 5.5 0.2 + - - -
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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