Contacts of the helix formed by residues 36 - 46 (chain G) 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 GLY 36 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G PHE* 3.5 17.9 - - - -
34G GLY 3.4 2.6 - - - -
35G ALA* 1.3 79.5 - - - +
37G LYS* 1.3 58.1 + - - +
38G SER 3.3 0.7 - - - -
39G VAL* 2.9 12.9 - - - +
40G PHE* 2.9 25.1 + - - +
200G MET* 3.1 17.2 - - - +
804G PO4 3.1 11.1 + - - -
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Residues in contact with LYS 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G LEU* 4.4 7.9 - - + +
30G LEU 5.2 0.2 - - - -
31G GLY* 2.7 36.6 + - - +
32G PRO 3.7 7.6 + - - +
33G THR* 4.8 1.6 - - - +
35G ALA* 4.1 4.3 - - + -
36G GLY* 1.3 77.9 - - - +
38G SER* 1.3 62.4 + - - +
40G PHE* 3.2 5.6 - - - +
41G LEU* 3.1 25.8 + - - +
152G GLU* 3.4 18.5 + - - -
183G VAL* 3.0 36.0 - - + +
184G THR 3.2 25.6 + - - +
185G HIS* 3.6 3.0 - - - +
200G MET* 3.9 21.1 - - + -
804G PO4 2.7 26.4 + - - +
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Residues in contact with SER 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LYS* 1.3 73.9 - - - +
39G VAL* 1.3 67.2 + - - +
41G LEU* 3.4 7.9 + - - +
42G GLU* 3.1 30.4 + - - +
74G PHE* 5.5 0.5 - - - -
151G ASP* 3.0 18.5 + - - +
704G MG 1.9 33.4 - - - -
804G PO4 2.9 9.1 + - - -
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Residues in contact with VAL 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LYS* 6.0 1.1 - - + -
11G LEU* 4.0 26.7 - - + -
14G PHE* 4.1 10.3 - - + -
16G LEU* 3.4 24.9 - - + -
36G GLY* 2.9 34.5 - - - +
38G SER* 1.3 75.6 - - - +
40G PHE* 1.3 71.3 + - - +
42G GLU* 2.9 19.8 + - - +
43G LEU* 2.7 24.4 + - - +
48G VAL* 5.6 6.0 - - + +
804G PO4 4.4 1.1 + - - +
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Residues in contact with PHE 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 4.0 11.2 - - + -
16G LEU* 4.2 6.7 - - + -
18G VAL* 3.6 39.7 - - + -
20G PHE* 3.6 28.3 - + + -
29G LEU* 4.0 22.9 - - + -
36G GLY 2.9 14.5 + - - +
37G LYS* 3.2 12.6 - - - +
39G VAL* 1.3 78.3 - - + +
41G LEU* 1.3 69.0 + - + +
43G LEU* 2.9 28.8 - - + +
44G ILE* 3.1 22.4 + - + +
181G LEU* 3.7 24.5 - - + -
200G MET* 4.3 8.1 - - + -
205G ILE* 3.8 12.8 - - + -
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LYS 3.1 7.7 + - - +
38G SER* 3.7 9.0 - - - +
39G VAL 3.1 0.2 - - - -
40G PHE* 1.3 81.0 - - + +
42G GLU* 1.3 54.5 + - - +
43G LEU 3.0 1.8 - - - -
44G ILE* 3.3 2.8 + - + -
45G ALA* 2.7 36.5 + - - +
74G PHE* 4.1 13.0 - - + -
75G VAL 5.0 0.2 - - - +
149G LEU* 3.3 35.9 - - + +
150G LEU 3.3 41.7 - - - +
151G ASP* 3.9 12.3 - - + +
181G LEU* 3.9 14.8 - - + -
183G VAL* 3.6 22.9 - - + -
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Residues in contact with GLU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G SER* 3.1 17.6 + - - +
39G VAL* 2.9 25.1 + - - +
41G LEU* 1.3 76.5 - - - +
43G LEU* 1.3 57.4 + - - +
45G ALA* 3.7 7.6 - - - -
46G GLY 2.9 5.9 + - - -
47G ILE* 2.7 48.3 + - + +
48G VAL* 3.5 19.1 + - + +
74G PHE* 4.5 16.8 - - + -
160I HIS* 3.9 23.2 + - - -
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G VAL* 5.2 2.2 - - + -
7G ALA* 4.7 14.1 - - + +
9G LYS* 4.8 8.7 - - + -
16G LEU* 3.5 35.9 - - + -
18G VAL* 5.1 2.9 - - + -
39G VAL 2.7 7.8 + - - +
40G PHE* 2.9 20.2 - - + +
42G GLU* 1.3 74.2 - - - +
44G ILE* 1.3 67.2 + - + +
46G GLY* 3.0 11.1 + - - -
48G VAL* 3.8 16.1 - - + +
50G PRO* 3.4 44.0 - - + +
55G VAL* 4.6 15.6 - - + +
70G ARG* 3.1 9.2 + - - -
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Residues in contact with ILE 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G LEU* 4.0 15.9 - - + -
5G VAL* 3.3 37.9 - - + -
40G PHE* 3.1 36.8 + - + +
41G LEU* 4.0 9.9 - - + +
43G LEU* 1.3 74.2 - - + +
45G ALA* 1.3 56.1 + - - +
55G VAL* 4.9 9.5 - - + +
62G ILE* 6.2 0.2 - - - +
70G ARG* 2.8 22.4 + - - +
72G ILE* 3.0 28.6 - - + +
147G LEU* 3.8 19.3 - - + -
149G LEU* 3.5 18.4 - - + -
181G LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU 2.7 22.3 + - - +
42G GLU* 3.5 12.1 - - - +
44G ILE* 1.3 74.3 - - - +
46G GLY* 1.3 58.8 + - - +
47G ILE* 4.3 11.4 - - + -
67G PRO* 3.6 15.0 - - - +
70G ARG* 3.5 14.0 - - - +
72G ILE* 3.9 13.7 - - - +
74G PHE* 3.8 26.9 - - + -
149G LEU* 3.7 3.8 - - + +
164I THR* 4.9 2.6 + - - +
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Residues in contact with GLY 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G GLU 2.9 4.4 + - - -
43G LEU 3.0 7.3 + - - -
45G ALA* 1.3 79.7 - - - +
47G ILE* 1.3 62.0 + - - +
48G VAL 3.4 5.2 - - - -
49G LYS* 6.1 1.7 - - - +
65G LEU 4.9 0.9 - - - +
66G PRO* 4.4 0.7 - - - +
67G PRO* 3.0 26.3 - - - +
70G ARG* 2.8 33.9 + - - +
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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