Contacts of the helix formed by residues 26 - 39 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D LEU* 1.3 77.7 - - - +
27D GLU* 1.3 63.6 + - - +
28D ILE* 3.0 30.4 + - + +
29D ASP* 3.2 11.4 + - - +
30D LYS* 3.5 23.1 + - - +
61D ARG* 3.0 33.8 + - - -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 1.3 76.1 - - - +
28D ILE* 1.3 65.9 + - + +
30D LYS* 3.3 35.4 + - - +
31D LYS* 3.2 46.0 + - - +
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 3.0 17.8 + - + +
27D GLU* 1.3 83.6 - - + +
29D ASP* 1.3 64.3 + - - +
30D LYS 3.1 1.1 - - - -
31D LYS* 3.3 20.3 + - + +
32D ILE* 3.2 29.3 + - + +
51D THR* 5.1 2.0 - - - -
53D LEU* 3.7 33.0 - - + -
61D ARG* 3.2 41.3 - - - +
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.6 21.3 - - + -
26D ASP* 3.2 29.2 + - - +
28D ILE* 1.3 75.6 - - - +
30D LYS* 1.3 57.2 + - - +
32D ILE* 3.3 5.9 + - - +
33D ILE* 2.9 35.8 + - + +
61D ARG* 2.9 30.4 + - - +
65D LEU* 3.8 33.0 - - + +
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LEU* 4.7 8.5 - - + -
25D LEU* 3.7 22.7 - - + -
26D ASP 3.5 19.5 + - - +
27D GLU* 3.3 37.5 + - - +
28D ILE 3.1 0.6 - - - -
29D ASP* 1.3 79.3 - - - +
31D LYS* 1.3 59.7 + - + +
33D ILE* 4.0 4.9 - - - +
34D LYS* 3.2 19.1 + - - +
170D ILE* 3.2 38.7 + - + +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 3.2 39.5 + - + +
28D ILE* 3.7 19.5 - - + +
29D ASP 3.3 0.4 - - - -
30D LYS* 1.3 75.4 - - - +
32D ILE* 1.3 64.5 + - - +
34D LYS* 3.5 7.6 - - - +
35D ILE* 3.3 29.1 + - + +
51D THR* 4.0 37.8 + - + +
53D LEU* 5.8 1.6 - - + +
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 3.2 20.3 + - + +
29D ASP* 3.7 8.1 - - - +
31D LYS* 1.3 74.1 - - - +
33D ILE* 1.3 59.9 + - - +
35D ILE* 3.1 10.2 + - - +
36D LEU* 2.9 51.3 + - + +
47D ILE* 4.1 19.7 - - + -
51D THR* 4.6 6.1 - - + -
58D ILE* 4.3 17.3 - - + -
61D ARG* 3.6 39.3 - - + -
62D ILE* 3.8 17.5 - - + -
65D LEU* 4.8 7.2 - - + -
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Residues in contact with ILE 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE* 3.7 35.2 - - + +
83C LEU* 4.4 8.3 - - + -
25D LEU* 4.3 11.9 - - + -
29D ASP 2.9 27.8 + - - +
30D LYS* 4.0 4.3 - - - +
32D ILE* 1.3 75.6 - - - +
34D LYS* 1.3 56.2 + - - +
36D LEU* 3.3 5.9 + - - +
37D GLN* 2.8 32.4 + - - +
65D LEU* 4.0 20.0 - - + -
70D VAL* 3.8 27.8 - - + -
71D ILE* 4.9 3.4 - - + -
170D ILE* 3.4 24.5 - - + -
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS 3.2 14.9 + - - +
31D LYS* 3.5 9.6 - - - +
32D ILE 3.3 0.2 - - - -
33D ILE* 1.3 79.3 - - - +
35D ILE* 1.3 63.6 + - + +
37D GLN* 3.9 5.6 + - - +
38D ASN* 3.3 21.8 + - - +
167D GLU* 4.7 1.7 - - - +
170D ILE* 4.0 35.0 - - + +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 3.3 15.9 + - + +
32D ILE* 3.1 6.8 + - - +
34D LYS* 1.3 77.2 - - + +
36D LEU* 1.3 59.8 + - - +
38D ASN* 3.1 8.1 + - - +
39D ASP* 2.8 29.0 + - + +
42D ALA* 3.7 25.8 - - + -
46D GLU* 5.5 2.7 - - - +
47D ILE* 3.8 35.9 - - + -
50D ILE* 3.9 42.8 - - + -
51D THR* 4.3 5.6 - - + -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 4.9 3.4 - - - +
76C ALA* 3.0 33.2 + - + -
32D ILE* 2.9 39.2 + - + +
33D ILE* 4.0 4.7 - - - +
35D ILE* 1.3 71.7 - - - +
37D GLN* 1.3 63.5 + - - +
39D ASP 3.5 12.6 - - - +
40D GLY* 3.2 28.1 + - - +
42D ALA* 4.5 6.5 - - + +
47D ILE* 4.0 22.0 - - + -
62D ILE* 3.9 20.4 - - + -
71D ILE* 4.0 20.4 - - + -
74D PHE* 4.2 12.1 - - + -
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Residues in contact with GLN 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 2.6 30.8 + - - -
75C THR* 2.7 13.8 + - - +
76C ALA 3.6 16.9 - - - +
78C ILE* 3.4 24.7 + - + +
33D ILE* 2.8 18.9 + - - +
34D LYS* 3.9 5.2 + - - +
36D LEU* 1.3 75.8 - - - +
38D ASN* 1.3 54.5 + - - +
39D ASP 3.6 0.2 + - - -
166D THR 4.2 2.1 - - - +
167D GLU* 3.4 21.7 + - + +
168D LEU* 2.8 55.3 + - - +
170D ILE* 3.5 18.9 - - - +
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Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LYS* 3.3 22.1 + - - +
74C PHE 4.1 1.4 - - - +
34D LYS 3.3 11.6 + - - +
35D ILE* 3.1 11.3 + - - +
37D GLN* 1.3 79.4 - - - +
39D ASP* 1.3 65.5 + - - +
167D GLU* 3.6 17.9 + - - +
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Residues in contact with ASP 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ARG* 4.5 9.4 + - - -
74C PHE* 3.5 10.9 + - - +
35D ILE 2.8 16.0 + - - +
36D LEU* 3.4 6.6 - - - -
37D GLN 3.4 0.4 - - - -
38D ASN* 1.3 87.5 - - - +
40D GLY* 1.3 62.1 + - - +
41D LYS* 3.0 28.7 + - - +
42D ALA* 3.3 28.6 + - + +
43D PRO* 5.5 1.0 - - - +
46D GLU* 5.7 0.5 - - - +
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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