Contacts of the helix formed by residues 27 - 39 (chain C) 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 GLU 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C ILE* 1.3 67.1 + - + +
29C ASP* 3.5 11.2 + - - +
30C LYS* 3.8 41.6 + - - +
31C LYS* 3.7 20.6 + - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU* 1.3 77.1 - - + +
29C ASP* 1.3 64.7 + - - +
30C LYS 3.2 0.2 - - - -
31C LYS* 3.2 34.9 - - - +
32C ILE* 3.1 34.1 + - + +
51C THR* 5.6 0.2 - - - +
53C LEU* 4.0 30.5 - - + -
58C ILE* 6.0 0.4 - - + -
61C ARG* 3.4 42.1 - - - +
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU 4.1 6.0 + - - +
28C ILE* 1.3 78.5 - - - +
30C LYS* 1.3 53.2 + - + +
32C ILE* 3.2 7.1 + - - +
33C ILE* 2.8 43.9 + - + +
61C ARG* 3.4 32.9 + - - +
64C LYS* 2.8 33.9 + - - -
65C LEU* 4.1 16.3 - - + +
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU* 3.8 43.5 + - - +
28C ILE 3.2 0.6 - - - -
29C ASP* 1.3 78.8 - - + +
31C LYS* 1.3 56.5 + - - +
33C ILE* 3.6 5.5 + - + +
34C LYS* 2.9 28.5 + - - +
170C ILE* 3.7 36.5 - - + +
83D LEU* 5.7 7.6 - - + -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLU 3.7 8.6 + - - +
28C ILE* 3.2 45.9 + - - +
30C LYS* 1.3 76.7 - - - +
32C ILE* 1.3 61.4 + - + +
34C LYS* 3.7 10.6 - - + +
35C ILE* 2.8 35.8 + - + +
51C THR* 3.2 37.1 + - - +
53C LEU* 6.0 2.7 - - - +
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ILE* 3.1 28.6 + - + +
29C ASP* 3.5 8.1 - - - +
31C LYS* 1.3 75.4 - - + +
33C ILE* 1.3 59.2 + - - +
35C ILE* 3.1 8.7 + - - +
36C LEU* 2.8 39.7 + - + +
47C ILE* 4.8 18.8 - - + -
51C THR* 5.8 2.5 - - + +
58C ILE* 4.5 15.3 - - + -
61C ARG* 3.6 36.3 - - + -
62C ILE* 4.0 26.5 - - + -
65C LEU* 4.6 8.7 - - + -
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Residues in contact with ILE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 2.8 30.8 + - + +
30C LYS* 3.8 7.0 - - + +
32C ILE* 1.3 72.0 - - - +
34C LYS* 1.3 57.4 + - - +
36C LEU* 3.4 5.0 + - - +
37C GLN* 2.9 32.0 + - - +
65C LEU* 4.0 22.4 - - + -
70C VAL* 3.8 27.1 - - + -
71C ILE* 4.9 3.6 - - + -
170C ILE* 3.5 27.4 - - + -
78D ILE* 3.8 34.9 - - + +
83D LEU* 4.8 9.9 - - + -
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS 2.9 18.4 + - - +
31C LYS* 3.7 11.9 - - + +
32C ILE 3.3 0.2 - - - -
33C ILE* 1.3 77.6 - - - +
35C ILE* 1.3 62.7 + - + +
37C GLN* 4.0 5.0 - - - +
38C ASN* 3.4 30.2 + - - +
167C GLU* 5.1 1.0 - - - +
170C ILE* 4.2 29.1 - - + +
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 2.8 29.0 + - + +
32C ILE* 3.1 9.6 + - - +
34C LYS* 1.3 78.6 - - + +
36C LEU* 1.3 57.2 + - - +
38C ASN* 3.2 7.9 + - - +
39C ASP* 2.9 28.1 + - + +
42C ALA* 3.8 25.1 - - + -
46C GLU* 6.1 1.8 - - + -
47C ILE* 4.0 25.4 - - + -
50C ILE* 3.8 35.2 - - + -
51C THR* 6.1 2.5 - - - -
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 2.8 29.1 + - + +
33C ILE* 4.2 3.1 - - - +
35C ILE* 1.3 70.0 - - - +
37C GLN* 1.3 61.2 + - - +
39C ASP 3.5 8.3 - - - +
40C GLY* 3.0 34.7 + - - +
42C ALA* 4.4 8.7 - - + +
47C ILE* 4.3 20.6 - - + -
62C ILE* 3.9 28.3 - - + -
71C ILE* 3.8 26.0 - - + -
74C PHE* 4.1 12.3 - - + -
41D LYS* 5.2 3.6 - - - +
76D ALA* 2.9 32.9 + - + -
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE 2.9 19.7 + - - +
34C LYS* 4.0 5.3 - - - +
36C LEU* 1.3 75.7 - - - +
38C ASN* 1.3 64.0 + - - +
166C THR 4.2 2.6 + - - -
167C GLU* 3.6 21.4 - - + +
168C LEU* 3.0 55.4 + - - +
170C ILE* 3.6 15.4 - - - +
73D LYS* 3.2 12.1 + - - -
75D THR* 2.6 24.3 + - - -
76D ALA* 3.6 15.7 + - - +
78D ILE* 3.2 29.4 - - + +
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Residues in contact with ASN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LYS* 3.4 21.0 + - - +
35C ILE* 3.2 11.4 + - - +
37C GLN* 1.3 81.2 - - - +
39C ASP* 1.3 62.4 - - + +
167C GLU* 3.9 18.4 + - - +
73D LYS* 3.6 19.6 + - - +
74D PHE 4.5 0.2 - - - -
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Residues in contact with ASP 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE 2.9 13.5 + - - +
36C LEU* 3.3 5.7 - - - -
38C ASN* 1.3 79.4 - - + +
40C GLY* 1.3 61.6 + - - +
41C LYS* 3.2 25.1 + - - +
42C ALA* 3.2 38.7 + - + +
43C PRO* 5.2 0.9 - - - +
66D ARG* 3.8 12.5 + - - -
73D LYS* 5.8 0.9 - - - +
74D PHE* 3.6 11.4 + - - +
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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