Contacts of the strand formed by residues 34 - 39 (chain E) 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 LYS 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210D PRO* 4.0 27.3 - - - +
32E ASN 4.0 6.1 - - - +
33E VAL* 1.3 76.9 - - - +
35E LEU* 1.3 60.2 + - - +
36E LYS* 3.8 7.7 + - + +
61E VAL* 4.8 0.4 - - - -
62E GLU* 3.4 20.0 - - + +
64E GLN* 2.9 37.9 + - + +
85E ASP* 3.6 3.3 - - - +
295E ASN* 3.4 19.6 - - - +
298E LEU* 6.0 0.4 - - - -
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Residues in contact with LEU 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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33E VAL 3.9 0.8 + - - -
34E LYS* 1.3 70.9 - - - +
36E LYS* 1.3 59.3 + - - +
37E VAL* 3.5 15.8 + - + +
54E PHE* 4.2 9.0 - - + -
61E VAL* 4.4 9.6 - - + -
62E GLU 2.8 14.9 + - - +
63E VAL* 3.5 17.3 - - + -
64E GLN* 2.7 27.6 + - - -
85E ASP* 3.4 26.5 - - + +
86E VAL* 4.6 0.4 - - + -
295E ASN* 4.8 2.9 - - + +
298E LEU* 4.1 24.0 - - + -
299E ALA* 4.2 7.6 - - - +
302E PHE* 3.7 41.3 - - + -
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 3.7 33.7 + - - +
209D TYR* 5.3 5.2 - - + -
34E LYS* 4.8 8.1 - - - +
35E LEU* 1.3 70.6 - - - +
37E VAL* 1.3 62.0 + - - +
38E PHE* 4.2 13.7 - - + -
64E GLN* 3.3 31.0 - - + +
82E ARG* 5.4 2.2 - - - +
83E LYS* 3.5 21.9 + - - +
84E ALA* 4.0 5.6 - - - -
85E ASP* 2.7 52.5 + - - +
86E VAL 2.9 7.3 + - - -
294E GLU* 5.0 17.1 + - - +
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Residues in contact with VAL 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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35E LEU* 3.8 23.6 - - + +
36E LYS* 1.3 81.0 - - - +
38E PHE* 1.3 67.4 + - - +
39E HIS* 3.6 4.0 - - + -
47E MET* 3.9 28.3 - - + -
63E VAL* 4.2 10.1 - - + -
64E GLN 2.9 16.1 + - - +
65E THR* 3.4 2.9 - - + -
66E GLU 3.2 21.0 + - - -
86E VAL* 3.4 39.5 - - + +
88E ALA* 5.6 0.7 - - + -
302E PHE* 4.2 8.1 - - + -
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Residues in contact with PHE 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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36E LYS* 4.3 15.3 - - + -
37E VAL* 1.3 77.4 - - - +
39E HIS* 1.3 63.1 + - - +
64E GLN 5.0 1.1 - - - -
66E GLU* 3.1 36.3 - - + +
73E THR* 3.9 18.8 - - + +
76E LYS* 3.5 42.0 - - + -
77E VAL* 4.3 5.2 - - + -
82E ARG* 3.4 28.5 - - + -
83E LYS 3.7 18.8 - - - -
84E ALA* 3.8 20.4 - - + -
86E VAL 3.1 5.7 + - - +
87E ILE* 3.2 19.3 - - + -
88E ALA 3.1 19.6 + - - -
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Residues in contact with HIS 39 (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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37E VAL* 3.6 9.0 - - + +
38E PHE* 1.3 75.6 - - - +
40E ALA* 1.3 95.2 + - - +
43E LEU* 3.9 12.1 - - + +
44E THR* 3.5 30.5 - - + -
47E MET* 3.7 25.4 - - + +
65E THR* 3.9 10.9 - - - -
66E GLU 3.2 43.0 + - - +
67E ALA* 3.7 10.0 + - + -
68E ALA 3.2 4.3 + - - -
73E THR* 3.2 14.1 + - - -
88E ALA* 3.2 24.2 - - + +
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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