Contacts of the helix formed by residues 26 - 39 (chain G) in PDB entry 2ZNZ
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 ASP 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G LEU* 1.3 81.5 - - - +
27G GLU* 1.3 60.1 + - - +
28G ILE* 3.8 8.6 + - - +
29G ASP* 3.6 15.3 + - + +
30G LYS* 3.3 25.7 + - - +
61G ARG* 2.8 45.4 + - - +
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Residues in contact with GLU 27 (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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26G ASP* 1.3 73.3 - - - +
28G ILE* 1.3 88.5 + - + +
29G ASP 3.3 0.2 - - - -
30G LYS* 3.6 13.9 + - + +
31G LYS* 3.2 42.4 + - - +
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Residues in contact with ILE 28 (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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26G ASP* 3.4 5.7 - - - +
27G GLU* 1.3 107.7 - - + +
29G ASP* 1.3 56.6 + - - +
31G LYS* 3.4 16.8 + - - +
32G ILE* 3.0 37.9 + - + +
51G THR* 4.4 13.9 - - - +
53G LEU* 3.8 34.5 - - + -
61G ARG* 3.5 32.1 - - - +
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Residues in contact with ASP 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.2 11.2 - - + +
26G ASP* 3.6 23.1 + - + +
27G GLU 3.3 0.4 - - - -
28G ILE* 1.3 76.6 - - - +
30G LYS* 1.3 57.7 + - - +
32G ILE* 3.4 5.9 + - - +
33G ILE* 2.9 36.4 + - - +
61G ARG* 2.9 45.3 + - - +
64G LYS* 3.6 24.3 + - - +
65G LEU* 3.6 20.3 - - + +
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Residues in contact with LYS 30 (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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25G LEU* 3.8 29.6 - - + -
26G ASP 3.3 15.6 + - - +
27G GLU* 3.6 14.6 - - + +
29G ASP* 1.3 76.7 - - - +
31G LYS* 1.3 58.6 + - + +
33G ILE* 3.7 7.3 - - - +
34G LYS* 2.8 31.6 + - - +
170G ILE* 3.5 35.6 + - + +
83H LEU* 5.1 7.0 - - + -
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Residues in contact with LYS 31 (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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27G GLU* 3.2 37.5 + - - +
28G ILE* 3.6 17.9 - - - +
29G ASP 3.3 0.2 - - - -
30G LYS* 1.3 73.6 - - + +
32G ILE* 1.3 65.2 - - - +
34G LYS* 3.5 11.0 - - + +
35G ILE* 3.1 30.8 + - - +
50G ILE* 3.8 35.4 + - + +
51G THR* 4.2 17.4 + - + +
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Residues in contact with ILE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G ILE* 3.0 36.4 + - + +
29G ASP* 3.8 9.4 - - - +
30G LYS 3.3 0.2 - - - -
31G LYS* 1.3 73.1 - - - +
33G ILE* 1.3 60.6 + - - +
35G ILE* 3.1 8.5 + - - +
36G LEU* 2.9 51.9 + - + +
47G ILE* 3.9 22.2 - - + -
51G THR* 4.2 5.4 - - + -
58G ILE* 4.6 14.1 - - + -
61G ARG* 3.9 27.8 - - + -
62G ILE* 3.8 16.4 - - + -
65G LEU* 4.5 8.5 - - + -
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Residues in contact with ILE 33 (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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25G LEU* 4.0 18.2 - - + -
29G ASP 2.9 22.8 + - - +
30G LYS* 3.7 7.0 - - - +
32G ILE* 1.3 74.1 - - - +
34G LYS* 1.3 63.1 + - - +
36G LEU* 3.4 6.3 + - - +
37G GLN* 3.0 26.0 + - - +
65G LEU* 3.9 18.6 - - + -
70G VAL* 3.8 27.6 - - + -
71G ILE* 4.9 3.6 - - + -
170G ILE* 3.6 21.8 - - + -
78H ILE* 3.7 36.5 - - + +
83H LEU* 4.7 7.4 - - + -
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Residues in contact with LYS 34 (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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30G LYS 2.8 21.0 + - - +
31G LYS* 3.5 12.6 - - + +
33G ILE* 1.3 73.9 - - - +
35G ILE* 1.3 62.8 + - + +
37G GLN* 3.6 7.0 + - - +
38G ASN* 3.3 21.3 + - - +
167G GLU* 5.2 0.3 - - - +
170G ILE* 3.8 30.7 - - + +
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Residues in contact with ILE 35 (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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31G LYS 3.1 19.5 + - - +
32G ILE* 3.1 5.1 + - - +
34G LYS* 1.3 82.2 - - + +
36G LEU* 1.3 59.9 + - - +
38G ASN* 3.3 7.3 + - - +
39G ASP* 2.9 28.9 + - - +
42G ALA* 3.5 27.1 - - + -
46G GLU* 5.3 1.6 - - + +
47G ILE* 4.1 29.4 - - + -
50G ILE* 3.5 37.7 - - + -
51G THR* 5.0 0.4 - - + -
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Residues in contact with LEU 36 (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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32G ILE* 2.9 39.7 + - + +
33G ILE* 4.1 4.0 - - - +
35G ILE* 1.3 73.7 - - - +
37G GLN* 1.3 61.2 + - - +
39G ASP 3.5 10.8 - - - +
40G GLY* 3.1 33.2 + - - +
42G ALA* 4.9 4.3 - - + +
47G ILE* 4.3 20.9 - - + -
62G ILE* 3.9 20.2 - - + -
71G ILE* 3.9 25.6 - - + -
74G PHE* 4.3 8.5 - - + -
41H LYS* 5.7 1.6 - - - +
75H THR* 3.6 0.2 - - - -
76H ALA* 3.1 30.4 + - + -
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Residues in contact with GLN 37 (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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33G ILE* 3.0 18.6 + - - +
34G LYS* 3.7 5.3 - - - +
36G LEU* 1.3 76.9 - - - +
38G ASN* 1.3 51.6 + - - +
166G THR 4.0 3.4 + - - -
167G GLU* 3.2 21.5 - - + +
168G LEU* 2.9 54.1 - - - +
170G ILE* 3.7 14.4 - - - +
73H LYS* 2.7 20.8 + - - -
75H THR* 2.5 24.2 + - - +
76H ALA 3.5 16.9 + - - +
78H ILE* 3.3 29.5 - - + +
83H LEU* 4.9 0.2 - - - +
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Residues in contact with ASN 38 (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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34G LYS 3.3 10.1 + - - +
35G ILE* 3.3 10.4 + - - +
37G GLN* 1.3 79.1 - - - +
39G ASP* 1.3 68.2 + - - +
167G GLU* 3.7 19.2 + - - +
73H LYS* 3.6 18.3 - - - +
74H PHE 4.3 0.3 - - - +
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Residues in contact with ASP 39 (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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35G ILE 2.9 17.1 + - - +
36G LEU* 3.2 7.1 - - - +
37G GLN 3.3 0.6 - - - -
38G ASN* 1.3 89.4 - - - +
40G GLY* 1.3 59.0 + - - +
41G LYS* 2.8 37.2 + - - +
42G ALA* 3.2 25.8 + - + +
43G PRO* 5.9 0.2 - - - +
66H ARG* 4.7 7.4 + - - -
74H PHE* 3.5 8.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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