Contacts of the helix formed by residues 9 - 16 (chain F) in PDB entry 5FNA
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 ARG 9 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLU* 5.7 2.0 + - - -
30C GLN* 3.3 38.0 + - - +
31C THR* 6.3 1.0 - - - +
5F LEU 4.0 0.7 - - - -
6F LYS 3.4 6.3 - - - +
7F GLU* 3.5 19.3 + - - +
8F LYS* 1.3 79.4 + - - +
10F LYS* 1.3 65.3 + - - +
11F LEU* 2.9 35.6 + - + +
12F PHE* 3.2 38.2 + - + +
13F ILE* 4.9 0.3 - - - +
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Residues in contact with LYS 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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26C ASP* 5.5 3.3 - - - +
29C LEU* 6.3 2.5 - - + -
30C GLN* 3.3 11.9 + - - +
3F LYS* 6.5 0.4 - - - +
5F LEU* 3.8 24.4 + - - +
6F LYS* 3.7 22.4 + - + +
8F LYS* 5.7 3.6 - - - +
9F ARG* 1.3 77.1 - - - +
11F LEU* 1.3 59.4 + - - +
12F PHE 3.2 3.4 - - - -
13F ILE* 3.2 36.4 - - + +
57F ILE* 3.6 42.2 - - + +
60F VAL* 4.9 17.1 - - - +
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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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26C ASP* 4.1 18.2 - - + +
27C GLU* 2.8 30.1 - - - +
30C GLN* 2.5 48.0 - - + +
9F ARG* 2.9 21.8 + - + +
10F LYS* 1.3 79.0 - - - +
12F PHE* 1.3 59.1 + - + +
13F ILE* 3.3 4.9 + - - -
14F ARG* 2.7 51.4 + - - +
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Residues in contact with PHE 12 (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 LYS 4.2 6.7 - - - -
9F ARG* 3.2 51.4 + - + +
11F LEU* 1.3 83.5 - - + +
13F ILE* 1.3 57.0 + - - +
14F ARG* 3.0 15.0 - - + +
15F SER* 2.8 31.6 + - - +
16F MET* 4.9 0.7 - - - +
83F ALA* 5.2 21.1 - - + +
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Residues in contact with ILE 13 (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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26C ASP* 5.1 9.9 - - - +
9F ARG 4.9 0.2 - - - +
10F LYS* 3.2 46.4 - - + +
11F LEU 3.3 1.5 - - - -
12F PHE* 1.3 78.9 - - - +
14F ARG* 1.3 60.6 + - + +
15F SER 3.0 1.1 - - - -
16F MET* 2.9 42.3 + - - +
50F MET* 5.8 0.9 - - - +
53F THR* 3.3 41.6 + - + +
54F ARG* 4.4 13.0 - - + +
57F ILE* 3.8 22.0 - - + -
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Residues in contact with ARG 14 (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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11F LEU* 2.7 41.5 + - - +
12F PHE* 4.2 11.2 - - + +
13F ILE* 1.3 82.5 - - - +
15F SER* 1.3 63.7 + - - +
16F MET 3.7 1.1 + - - +
50F MET* 4.2 19.7 - - - +
35G ASN* 6.0 2.6 - - - +
37G GLU* 5.9 4.0 - - - +
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Residues in contact with SER 15 (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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12F PHE* 2.8 23.3 + - - +
14F ARG* 1.3 80.8 - - - +
16F MET* 1.3 62.1 + - - +
17F GLY 4.1 0.2 + - - -
82F LEU* 3.5 27.9 - - - +
83F ALA* 5.7 3.0 - - - +
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Residues in contact with MET 16 (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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12F PHE 4.9 0.2 - - - +
13F ILE* 2.9 30.8 + - - +
14F ARG 4.2 0.3 - - - +
15F SER* 1.3 86.3 - - - +
17F GLY* 1.3 59.3 + - - +
20F THR* 5.6 1.6 - - - +
21F ILE* 3.9 13.7 - - + -
24F LEU* 4.8 10.5 - - + -
50F MET* 4.1 24.1 - - - +
53F THR* 3.8 21.4 - - + +
56F LEU* 3.8 26.7 - - + -
75F ILE* 6.3 3.4 - - + -
78F GLU* 4.8 14.4 - - - +
82F LEU* 5.4 11.9 - - + -
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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