Contacts of the helix formed by residues 26 - 39 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 1.3 81.3 - - - +
27E GLU* 1.3 60.3 + - - +
28E ILE* 3.6 9.9 - - - +
29E ASP* 3.4 25.3 + - - +
30E LYS* 3.2 27.0 + - - +
61E ARG* 3.1 35.3 + - - +
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASP* 1.3 74.8 + - - +
28E ILE* 1.3 69.2 + - + +
30E LYS* 3.8 26.7 + - - +
31E LYS* 3.3 22.5 + - - +
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Residues in contact with ILE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASP* 3.3 9.8 - - - +
27E GLU* 1.3 82.9 - - + +
29E ASP* 1.3 64.6 + - - +
31E LYS* 3.1 7.4 + - - +
32E ILE* 3.0 37.2 + - + +
51E THR* 5.2 4.7 - - - +
53E LEU* 4.2 35.0 - - + -
61E ARG* 3.4 43.5 - - + +
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 4.0 17.8 - - + +
26E ASP* 3.4 25.2 + - + +
28E ILE* 1.3 76.4 - - - +
30E LYS* 1.3 57.5 + - - +
32E ILE* 3.2 7.9 + - - +
33E ILE* 2.9 35.6 + - - +
61E ARG* 3.2 33.3 + - - +
64E LYS* 3.2 25.8 + - - -
65E LEU* 4.0 22.8 - - + +
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 4.1 33.9 + - + -
26E ASP 3.2 19.6 + - - +
27E GLU* 3.8 30.2 + - - +
28E ILE 3.3 0.2 - - - -
29E ASP* 1.3 78.5 - - - +
31E LYS* 1.3 57.3 + - - +
33E ILE* 4.5 4.7 - - - -
34E LYS* 3.0 30.1 + - - +
170E ILE* 3.7 35.6 - - + +
83F LEU* 5.4 3.4 - - + -
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Residues in contact with LYS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU 3.3 12.3 + - - +
28E ILE* 3.1 11.3 + - - +
30E LYS* 1.3 75.8 - - - +
32E ILE* 1.3 61.2 + - - +
34E LYS* 3.4 23.2 - - + +
35E ILE* 3.0 51.4 + - + +
50E ILE* 3.9 36.9 - - - +
51E THR* 4.6 16.8 - - - +
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Residues in contact with ILE 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ILE* 3.0 26.1 + - + +
29E ASP* 3.7 8.1 - - - +
31E LYS* 1.3 74.2 - - + +
33E ILE* 1.3 55.8 + - - +
35E ILE* 3.1 9.7 + - - +
36E LEU* 2.8 46.9 + - + +
47E ILE* 4.8 20.9 - - + -
51E THR* 5.3 4.5 - - - +
53E LEU* 6.0 0.2 - - + -
58E ILE* 4.6 14.6 - - + +
61E ARG* 3.5 36.6 - - + -
62E ILE* 3.7 24.7 - - + -
65E LEU* 4.8 7.2 - - + -
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Residues in contact with ILE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.8 22.0 - - + -
29E ASP 2.9 20.2 + - - +
30E LYS* 4.0 3.8 - - - +
32E ILE* 1.3 72.7 - - - +
34E LYS* 1.3 66.0 + - - +
36E LEU* 3.3 5.7 + - - +
37E GLN* 2.9 27.4 + - - +
65E LEU* 3.8 22.0 - - + -
70E VAL* 3.7 27.6 - - + -
71E ILE* 4.8 2.7 - - + -
170E ILE* 3.6 26.0 - - + -
78F ILE* 3.7 35.6 - - + +
83F LEU* 5.0 1.8 - - + -
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Residues in contact with LYS 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS 3.0 19.7 + - - +
31E LYS* 3.4 26.7 - - + +
33E ILE* 1.3 77.0 - - - +
35E ILE* 1.3 60.9 + - + +
37E GLN* 3.8 5.2 + - - +
38E ASN* 3.5 19.4 + - - +
167E GLU* 4.9 1.7 - - - +
170E ILE* 4.2 34.5 + - + +
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Residues in contact with ILE 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LYS* 3.0 44.0 + - + +
32E ILE* 3.1 8.9 + - - +
34E LYS* 1.3 76.0 - - + +
36E LEU* 1.3 59.9 + - - +
38E ASN* 3.3 7.1 + - - +
39E ASP* 2.9 27.1 + - + +
42E ALA* 3.9 24.2 - - + -
46E GLU* 6.3 1.1 - - + -
47E ILE* 4.0 31.2 - - + +
50E ILE* 3.7 29.6 - - + -
51E THR* 4.8 4.9 - - - -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ILE* 2.8 41.6 + - + +
33E ILE* 4.1 4.3 - - - +
35E ILE* 1.3 70.6 - - - +
37E GLN* 1.3 60.2 + - - +
39E ASP 3.5 7.0 - - - +
40E GLY* 3.1 37.7 + - - +
42E ALA* 4.4 7.9 - - + +
47E ILE* 4.3 20.9 - - + -
62E ILE* 4.2 12.6 - - + -
71E ILE* 3.9 26.0 - - + -
74E PHE* 4.0 14.6 - - + -
41F LYS* 5.2 3.4 - - - +
76F ALA* 3.1 31.0 + - + -
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Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE 2.9 16.6 + - - +
34E LYS* 3.9 4.0 - - - +
36E LEU* 1.3 75.6 - - - +
38E ASN* 1.3 63.0 + - - +
166E THR 4.1 3.4 + - - +
167E GLU* 3.5 24.1 - - + +
168E LEU* 3.0 54.6 + - - +
170E ILE* 3.4 16.1 - - - +
73F LYS* 3.2 12.3 + - - -
75F THR* 2.7 24.4 + - - -
76F ALA 3.7 15.5 + - - +
78F ILE* 3.4 28.6 - - + +
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Residues in contact with ASN 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LYS 3.5 10.6 + - - +
35E ILE* 3.3 10.1 + - - +
37E GLN* 1.3 80.9 - - - +
39E ASP* 1.3 65.3 + - - +
167E GLU* 3.8 19.1 + - - +
73F LYS* 3.7 19.6 - - - +
74F PHE 4.1 1.4 - - - +
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Residues in contact with ASP 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ILE* 2.9 14.7 + - + +
36E LEU* 3.3 6.3 - - - -
38E ASN* 1.3 86.3 - - - +
40E GLY* 1.3 64.7 + - - +
41E LYS* 3.1 23.6 + - - +
42E ALA* 3.2 30.6 + - + +
66F ARG* 4.6 12.4 + - - -
74F PHE* 3.7 9.2 + - - +
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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
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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