Contacts of the strand formed by residues 3 - 11 (chain F) 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 LEU 3 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET 4.4 0.2 - - - -
2F PHE* 1.3 83.8 - - + +
4F LYS* 1.3 63.6 + - - +
5F VAL* 3.6 19.7 - - + -
20F PHE* 3.6 17.2 - - + +
21F GLU* 3.5 1.9 - - - -
22F MET* 2.8 48.0 + - + +
44F ILE* 4.0 22.0 - - + -
55F VAL* 4.2 11.2 - - + -
56F ARG 3.3 16.8 - - - +
57F LEU* 4.1 18.4 - - + -
147F LEU* 3.5 24.9 - - + -
181F LEU* 4.5 7.2 - - + -
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Residues in contact with LYS 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.5 33.0 - - + +
3F LEU* 1.3 76.9 - - - +
5F VAL* 1.3 67.8 + - - +
6F ARG 4.3 0.2 - - - -
20F PHE 3.3 4.0 - - - +
21F GLU* 3.4 29.1 + - + +
54F GLU 4.3 0.4 - - - +
56F ARG* 2.9 64.3 + - + +
59F GLY* 6.5 1.3 - - - -
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Residues in contact with VAL 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F LEU* 3.6 16.8 - - + -
4F LYS* 1.3 82.6 - - - +
6F ARG* 1.3 62.5 + - - +
7F ALA* 4.7 3.8 - - + +
18F VAL* 3.3 25.4 - - + +
20F PHE* 2.7 49.0 + - + +
40F PHE* 4.0 9.0 - - + -
43F LEU* 5.2 4.5 - - + -
44F ILE* 3.2 28.9 - - + -
54F GLU 3.9 3.8 - - - +
55F VAL* 4.1 21.1 - - + -
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Residues in contact with ARG 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LYS 4.3 0.2 - - - -
5F VAL* 1.3 71.5 - - - +
7F ALA* 1.3 62.7 + - - +
18F VAL 3.0 8.7 - - - +
19F ASP* 4.6 18.2 - - + +
52F ARG* 3.6 28.6 - - - +
53F GLY* 3.3 5.5 - - - -
54F GLU* 2.9 32.7 + - + +
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Residues in contact with ALA 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F VAL* 4.0 6.6 - - + -
6F ARG* 1.3 78.9 - - - +
8F GLU* 1.3 65.4 + - - +
16F LEU* 3.2 3.7 - - - +
17F ASN* 3.2 1.4 - - - -
18F VAL* 2.8 36.4 + - + +
43F LEU* 4.7 14.8 - - + -
50F PRO* 3.8 17.9 - - + -
52F ARG 3.2 14.6 - - - +
53F GLY* 4.0 4.3 - - - -
54F GLU 4.1 7.4 - - - +
55F VAL* 5.4 0.2 - - + -
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Residues in contact with GLU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ALA* 1.3 76.5 - - - +
9F LYS* 1.3 61.6 + - - +
16F LEU 2.9 6.7 - - - +
17F ASN* 3.7 21.9 - - + +
50F PRO* 3.7 3.4 - - - +
51F ASP* 3.0 27.5 + - + +
52F ARG* 2.9 57.6 + - + +
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Residues in contact with LYS 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F GLU* 1.3 76.9 - - - +
10F ARG* 1.3 59.9 + - - +
11F LEU* 3.9 36.2 - - + +
14F PHE* 3.8 1.0 - - - +
15F ARG* 3.4 3.3 - - - +
16F LEU* 2.7 61.3 + - + +
39F VAL* 6.1 1.1 - - + -
43F LEU* 4.8 6.1 - - + -
48F VAL* 3.5 23.8 - - + +
49F LYS* 2.5 34.5 + - - +
50F PRO* 4.0 2.0 - - + -
51F ASP* 3.0 29.3 + - - +
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Residues in contact with ARG 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LYS* 1.3 76.6 - - - +
11F LEU* 1.3 80.8 + - - +
12F GLY 4.1 15.0 - - - +
14F PHE 3.5 5.6 - - - +
15F ARG* 4.7 21.8 - - + +
51F ASP* 2.5 20.7 + - - +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LYS* 3.9 31.4 - - + -
10F ARG* 1.3 87.0 - - - +
12F GLY* 1.3 59.9 + - - +
13F ASN 3.5 0.3 + - - -
14F PHE* 2.8 45.0 + - + +
16F LEU* 6.6 0.2 - - + -
39F VAL* 4.0 27.8 - - + -
48F VAL* 5.7 4.5 - - + -
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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