Contacts of the strand formed by residues 14 - 22 (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 PHE 14 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G LYS 3.8 1.0 - - - +
10G ARG* 3.5 2.8 - - - -
11G LEU* 2.8 54.6 + - + +
12G GLY 3.0 3.4 - - - +
13G ASN* 1.3 79.8 - - - +
15G ARG* 1.3 66.1 + - - +
16G LEU* 4.0 20.2 - - + -
34G GLY 4.3 10.5 - - - -
35G ALA 4.0 5.2 - - - -
36G GLY* 3.5 25.1 - - - -
39G VAL* 4.1 11.9 - - + -
202G ASN* 3.8 13.5 - - - -
203G GLY* 3.4 36.6 - - - -
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Residues in contact with ARG 15 (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 3.4 5.6 - - - +
10G ARG* 4.7 23.8 - - + +
12G GLY 5.6 1.6 + - - -
13G ASN* 4.1 8.9 + - - +
14G PHE* 1.3 83.3 - - - +
16G LEU* 1.3 60.5 + - - +
17G ASN* 3.9 7.4 + - + +
202G ASN 3.5 21.5 - - - +
203G GLY* 3.5 4.3 - - - -
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Residues in contact with LEU 16 (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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7G ALA 4.3 1.1 - - - +
8G GLU* 2.9 4.3 - - - -
9G LYS* 2.7 52.3 + - + +
11G LEU* 6.6 0.2 - - + -
14G PHE* 4.0 11.4 - - + -
15G ARG* 1.3 73.3 - - - +
17G ASN* 1.3 57.2 + - - +
18G VAL* 3.2 40.8 - - + -
39G VAL* 3.4 33.0 - - + -
40G PHE* 4.1 8.5 - - + +
43G LEU* 3.5 27.4 - - + -
200G MET* 4.5 7.6 - - + -
203G GLY* 3.6 7.9 - - - +
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Residues in contact with ASN 17 (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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7G ALA 3.2 5.2 - - - -
8G GLU* 3.7 26.7 - - + +
15G ARG* 4.8 6.7 + - + +
16G LEU* 1.3 72.6 - - - +
18G VAL* 1.3 62.2 + - - +
202G ASN 5.5 0.2 + - - -
203G GLY 3.4 7.8 + - - +
204G ARG* 3.8 40.5 + - - +
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Residues in contact with VAL 18 (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* 3.6 19.5 - - + +
6G ARG* 3.0 8.0 - - - +
7G ALA* 2.8 42.5 + - + +
16G LEU* 3.2 25.8 - - + -
17G ASN* 1.3 75.6 - - - +
19G ASP* 1.3 61.1 + - - +
40G PHE* 3.6 27.4 - - + -
43G LEU* 5.1 1.3 - - + -
200G MET* 4.8 1.6 - - + -
203G GLY 3.5 13.9 - - - +
205G ILE* 3.6 31.4 - - + +
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Residues in contact with ASP 19 (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 3.4 3.1 - - - -
6G ARG* 4.4 18.1 - - + +
18G VAL* 1.3 75.0 - - - +
20G PHE* 1.3 61.1 + - - +
21G GLU* 4.9 10.4 + - - +
205G ILE* 4.6 16.4 + - - +
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Residues in contact with PHE 20 (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* 4.2 5.2 - - + -
4G LYS* 3.3 3.6 - - - +
5G VAL* 2.7 51.1 + - + +
19G ASP* 1.3 77.0 + - - +
21G GLU* 1.3 71.9 + - - +
22G MET* 3.4 33.2 - - + -
27G CYS* 3.7 28.0 - - - -
29G LEU* 5.5 1.1 - - + -
40G PHE* 3.6 20.9 - + + -
181G LEU* 3.9 25.8 - - + -
198G ALA* 4.0 12.3 - - + -
205G ILE* 3.7 28.5 - - + -
208G LYS* 3.9 13.9 - - + -
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Residues in contact with GLU 21 (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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1G MET* 3.5 28.1 - - + +
3G LEU 3.5 4.0 - - - -
4G LYS* 3.4 31.8 + - + +
19G ASP* 4.9 9.0 - - - +
20G PHE* 1.3 80.2 - - - +
22G MET* 1.3 56.2 + - - +
208G LYS* 2.4 35.3 + - + +
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Residues in contact with MET 22 (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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1G MET* 3.6 8.9 - - - -
2G PHE* 3.0 21.2 + - + -
3G LEU* 2.8 27.8 + - + +
20G PHE* 3.4 26.0 - - + -
21G GLU* 1.3 75.9 - - - +
23G GLY* 1.3 73.6 + - - +
25G ASP* 3.9 13.7 - - - +
27G CYS* 3.3 23.1 - - + -
147G LEU* 3.6 28.3 - - + -
179G PRO* 4.0 7.2 - - + -
180G ILE 3.5 26.5 - - - +
181G LEU* 4.0 8.7 - - - +
208G LYS* 3.1 5.6 - - - +
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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