Contacts of the helix formed by residues 8 - 25 (chain G) in PDB entry 1DWK
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 ARG 8 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ASP* 4.3 21.9 + - + +
90C THR* 4.9 12.2 - - - +
5G GLN* 6.1 0.2 - - - -
7G ASN* 1.3 72.4 + - - +
9G ASN* 1.3 69.9 + - - +
10G ILE 3.2 0.6 + - - -
11G ARG* 3.3 7.2 + - - +
12G LEU* 2.9 47.8 + - + +
50G GLN* 6.0 0.7 - - - +
80G LEU* 3.5 40.7 - - + +
82G GLY* 2.9 30.6 + - - +
83G CYS 4.3 1.6 - - - -
84G ILE 2.9 21.6 + - - +
85G ASP* 2.9 32.6 + - - +
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Residues in contact with ASN 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 5.9 1.2 + - - -
7G ASN* 2.8 26.4 + - - +
8G ARG* 1.3 90.4 + - - +
10G ILE* 1.3 58.5 + - + +
12G LEU* 4.3 12.4 - - - +
13G ASP* 2.9 42.6 + - - +
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Residues in contact with ILE 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP* 3.7 38.8 - - + +
5G GLN* 3.3 27.4 - - - +
7G ASN* 3.4 6.7 + - - +
8G ARG 3.2 1.4 + - - -
9G ASN* 1.3 78.5 - - + +
11G ARG* 1.3 58.6 + - + +
13G ASP* 3.5 7.8 + - - +
14G LEU* 3.1 24.3 + - - +
74G LEU* 3.9 30.8 - - + +
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Residues in contact with ARG 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G GLN* 4.4 21.1 - - + +
7G ASN 4.6 0.6 + - - -
8G ARG* 3.3 7.8 + - - +
10G ILE* 1.3 79.3 - - + +
12G LEU* 1.4 63.2 + - + +
14G LEU* 3.4 15.5 + - - +
15G ALA* 2.9 26.2 + - - +
46G ALA 2.8 21.2 + - - -
47G LEU 4.8 1.5 + - - +
49G GLY* 3.8 27.8 - - - +
51G GLN 2.8 25.9 + - - -
74G LEU* 3.0 33.8 + - - -
75G LEU* 3.9 22.3 + - - +
77G MSE 3.0 29.1 + - - +
79G PRO* 4.3 11.0 - - + +
80G LEU 6.3 0.2 - - - +
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.6 13.8 - - + +
7F ASN* 6.4 1.6 - - + -
8G ARG* 2.9 54.9 + - + +
9G ASN* 4.1 12.8 - - - +
11G ARG* 1.4 77.4 - - + +
13G ASP* 1.3 63.2 + - - +
15G ALA* 3.2 5.3 + - - +
16G ASP* 3.2 26.7 + - - +
48G LEU 3.6 23.6 - - - +
49G GLY* 4.8 1.6 - - - +
50G GLN* 4.0 14.1 - - - +
82G GLY 4.7 4.5 - - - +
83G CYS* 5.3 8.7 - - + +
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Residues in contact with ASP 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASN* 5.4 1.7 + - - -
9G ASN* 2.9 30.9 + - - +
10G ILE* 3.7 9.0 - - - +
12G LEU* 1.3 73.4 - - - +
14G LEU* 1.3 66.5 - - - +
16G ASP* 3.2 16.2 + - - +
17G ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE 3.1 12.1 + - - +
11G ARG* 3.5 16.6 - - - +
13G ASP* 1.3 79.5 - - - +
15G ALA* 1.4 64.3 + - - +
17G ALA* 3.1 11.8 + - + +
18G ILE* 2.8 39.0 + - + +
47G LEU 5.6 0.2 - - - +
67G LEU* 5.0 3.1 - - + -
71G SER* 3.6 48.2 - - - +
74G LEU* 3.8 24.2 - - + -
75G LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.0 17.7 - - + -
11G ARG 2.9 14.2 + - - +
12G LEU* 3.2 11.6 + - - +
14G LEU* 1.4 76.7 - - - +
16G ASP* 1.3 57.3 + - - +
18G ILE* 3.3 4.6 + - - +
19G LEU* 2.8 36.2 + - - +
47G LEU 3.4 25.1 + - - +
48G LEU* 3.9 17.3 - - + -
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Residues in contact with ASP 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLN* 5.0 4.5 + - - +
6F ILE* 4.2 11.1 - - - +
7F ASN* 2.9 45.6 + - - +
10F ILE* 4.0 23.4 - - + +
12G LEU* 3.2 15.1 + - - +
13G ASP* 3.2 17.1 + - - +
15G ALA* 1.3 75.1 - - - +
17G ALA* 1.3 59.0 + - - +
19G LEU* 3.3 9.9 + - - +
20G LEU* 3.0 26.3 + - - +
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Residues in contact with ALA 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ASP 3.1 11.3 + - - +
14G LEU* 3.1 17.4 + - + +
16G ASP* 1.3 73.8 - - - +
18G ILE* 1.3 65.0 + - - +
20G LEU* 3.1 8.4 + - - +
21G SER* 2.9 24.0 + - - -
67G LEU* 5.6 4.3 - - + -
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Residues in contact with ILE 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 2.8 34.3 + - + +
15G ALA 3.5 4.9 - - - +
17G ALA* 1.3 76.7 - - - +
19G LEU* 1.4 66.6 + - + +
21G SER* 3.3 5.9 + - - -
22G LYS* 2.9 31.7 + - + +
47G LEU* 3.9 45.8 - - + +
48G LEU* 6.0 0.2 - - + -
65G LEU* 4.0 18.8 - - + +
67G LEU* 4.1 30.3 - - + -
75G LEU* 4.0 18.4 - - + -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLN* 4.8 0.9 - - - +
4F SER 3.6 24.9 - - - +
5F GLN* 4.3 11.9 - - - +
6F ILE* 3.9 38.6 - - + +
77F MSE 4.5 6.1 - - + +
15G ALA 2.8 24.5 + - - +
16G ASP* 3.7 9.2 - - - +
18G ILE* 1.4 78.8 - - + +
20G LEU* 1.3 58.8 + - - +
22G LYS* 3.7 10.7 - - + +
23G ALA* 3.0 28.2 + - - +
29G PHE* 3.8 31.6 - - + -
48G LEU* 4.1 12.6 - - + -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F GLN* 5.6 1.1 + - - -
70F ASP* 4.1 17.5 - - + +
73F LEU* 4.6 11.4 - - + -
74F LEU* 4.5 22.4 - - + -
77F MSE 5.4 2.5 - - - -
16G ASP 3.0 12.6 + - - +
17G ALA* 3.1 10.5 + - - +
19G LEU* 1.3 74.8 - - - +
21G SER* 1.3 60.1 + - - +
23G ALA* 3.2 4.3 + - + +
24G LYS* 2.9 62.9 + - + +
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Residues in contact with SER 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ALA 2.9 16.0 + - - -
18G ILE* 3.7 5.4 - - - -
20G LEU* 1.3 77.4 - - - +
22G LYS* 1.4 60.8 + - - +
24G LYS* 3.2 8.8 + - - +
25G LYS* 2.9 37.1 + - - +
65G LEU* 2.6 39.4 + - - -
66G ASP* 4.8 0.2 - - - +
67G LEU* 5.2 3.1 - - - -
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Residues in contact with LYS 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLU* 4.4 2.6 + - - -
2F ILE 4.1 7.5 + - - -
3F GLN* 2.9 29.2 + - - +
4F SER 5.1 1.2 - - - +
18G ILE* 2.9 23.8 + - + +
19G LEU* 3.7 13.6 - - + +
21G SER* 1.4 72.7 - - - +
23G ALA* 1.3 57.0 + - - +
25G LYS* 3.4 1.2 + - - -
26G ASP 3.0 21.0 + - - -
27G LEU* 3.0 36.8 + - + +
28G SER 3.8 1.8 - - - -
29G PHE* 3.5 62.1 - - + +
32G ILE* 3.8 17.0 - - + -
65G LEU* 3.7 15.3 - - + +
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Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLN* 3.5 30.3 + - + +
73F LEU* 4.0 23.9 - - + +
77F MSE 3.9 20.6 - - + -
19G LEU 3.0 19.5 + - - +
20G LEU* 3.2 4.5 + - - +
22G LYS* 1.3 72.2 - - - +
24G LYS* 1.3 67.3 + - - +
26G ASP* 3.1 14.6 + - - +
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Residues in contact with LYS 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ASP* 3.1 38.4 + - - +
73F LEU* 3.9 17.3 - - + -
20G LEU* 2.9 40.9 + - + +
21G SER* 3.7 7.9 - - - +
23G ALA* 1.3 77.7 - - - +
25G LYS* 1.3 63.3 + - + +
26G ASP* 3.6 1.6 + - - +
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Residues in contact with LYS 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G SER* 2.9 36.3 + - - +
22G LYS 4.1 1.3 - - - +
24G LYS* 1.3 78.1 - - + +
26G ASP* 1.3 68.8 + - - +
27G LEU* 3.1 27.9 - - + +
64G LYS 3.4 22.9 + - - +
65G LEU* 3.9 1.6 - - - -
66G ASP* 2.6 40.9 + - - -
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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