Contacts of the helix formed by residues 34 - 44 (chain D) in PDB entry 2ONK
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 ASN 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU 3.7 8.7 + - - +
31D GLN* 4.0 12.5 + - - +
32D LEU 2.9 0.6 - - - -
33D PHE* 1.3 92.4 + - - +
35D PHE* 1.3 56.6 + - - +
36D ASP* 2.9 16.4 + - - +
37D GLU* 3.0 41.3 + - + +
38D PHE* 3.1 10.9 + - - +
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Residues in contact with PHE 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 GLN 3.5 18.4 - - - -
32D LEU* 2.9 33.0 + - + +
33D PHE 3.7 0.4 - - - -
34D ASN* 1.3 75.0 - - - +
36D ASP* 1.3 59.1 + - - +
38D PHE* 3.8 24.9 - + - -
39D LEU* 2.9 70.4 + - + +
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Residues in contact with ASP 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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34D ASN* 2.9 5.1 + - - +
35D PHE* 1.3 76.6 + - - +
37D GLU* 1.3 70.9 + - + +
39D LEU* 3.2 10.4 + - - +
40D LYS* 2.9 31.2 + - + +
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Residues in contact with GLU 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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34D ASN* 3.0 34.0 + - + +
36D ASP* 1.3 78.6 - - + +
38D PHE* 1.3 55.4 + - - +
40D LYS* 2.9 12.3 + - + +
41D ALA* 2.7 37.1 + - - +
227D SER* 4.3 15.1 - - - +
231D PRO* 4.4 15.7 - - + +
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Residues in contact with PHE 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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28D VAL* 5.9 0.2 - - + -
31D GLN* 3.5 50.5 + - + +
34D ASN 3.1 4.5 + - - +
35D PHE* 3.7 35.9 - + - +
37D GLU* 1.3 79.7 - - - +
39D LEU* 1.3 57.4 + - + +
41D ALA* 3.3 6.8 + - - +
42D ALA* 2.8 43.2 + - + +
231D PRO* 4.4 3.4 - - - -
234D ALA* 4.3 4.0 - - + -
235D ILE* 3.7 33.8 - - + +
238D LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 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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35D PHE* 2.9 59.6 + - + +
36D ASP* 3.5 8.1 - - - +
38D PHE* 1.3 77.2 - - + +
40D LYS* 1.3 58.6 + - + +
42D ALA* 3.1 11.8 + - + +
43D SER* 2.4 33.3 + - - -
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Residues in contact with LYS 40 (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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36D ASP* 2.9 19.7 + - - +
37D GLU* 3.3 12.8 - - - +
39D LEU* 1.3 72.0 - - + +
41D ALA* 1.3 55.8 + - - +
43D SER* 2.8 10.7 + - - -
44D ASP* 2.7 35.1 + - - +
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Residues in contact with ALA 41 (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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37D GLU 2.7 15.0 + - - +
38D PHE 3.3 8.5 - - - +
40D LYS* 1.3 71.7 - - - +
42D ALA* 1.3 64.4 + - - +
44D ASP* 3.0 28.4 + - - +
47D VAL* 4.0 7.9 - - - +
220D ARG* 5.3 5.2 - - - +
231D PRO* 3.8 21.5 - - + -
232D VAL* 4.6 9.4 - - + +
235D ILE* 3.4 20.3 - - + +
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Residues in contact with ALA 42 (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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38D PHE* 2.8 23.3 + - + +
39D LEU* 3.1 20.9 - - + +
41D ALA* 1.3 77.3 - - - +
43D SER* 1.3 51.9 + - - +
48D TRP* 2.5 40.7 + - + +
235D ILE* 3.4 15.2 - - + +
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Residues in contact with SER 43 (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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39D LEU 2.4 29.3 + - - -
40D LYS* 2.8 12.2 + - - -
42D ALA* 1.3 75.8 - - - +
44D ASP* 1.3 53.3 + - - +
45D PRO* 2.7 27.9 - - - +
48D TRP* 4.1 4.5 - - - +
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Residues in contact with ASP 44 (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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40D LYS 2.7 11.8 + - - +
41D ALA* 3.0 18.2 + - - +
43D SER* 1.3 71.8 - - - +
45D PRO* 1.3 65.4 - - - +
46D ALA* 2.8 28.2 + - - +
47D VAL* 2.9 29.8 + - + +
48D TRP* 3.5 6.5 - - - -
220D ARG* 3.0 27.8 + - - -
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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