Contacts of the helix formed by residues 18 - 26 (chain F) in PDB entry 5X11
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 SER 18 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F LEU* 1.3 77.0 - - - +
19F GLY* 1.3 65.2 + - - +
20F TYR* 3.1 11.9 - - - -
21F ASP* 2.8 27.1 + - - +
22F ILE* 3.0 24.6 + - - +
67F LYS* 3.9 33.0 - - - -
68F LYS 3.7 9.2 - - - -
69F MET* 3.6 3.7 - - - -
7N A 5.3 0.7 - - - -
8N T 4.1 3.4 - - - -
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Residues in contact with GLY 19 (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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18F SER* 1.3 73.3 - - - +
20F TYR* 1.3 55.6 + - - +
22F ILE* 3.4 8.9 + - - +
23F THR* 3.0 28.4 + - - -
41F ILE* 4.4 3.1 - - - +
42F TYR* 3.9 13.4 - - - -
45F LEU* 3.9 27.6 - - - -
68F LYS 4.1 5.9 + - - -
70F TYR* 4.7 4.0 - - - -
8N T 3.6 9.0 + - - -
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Residues in contact with TYR 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F SER* 3.1 4.0 - - - -
19F GLY* 1.3 74.7 - - - +
21F ASP* 1.3 61.8 + - - +
23F THR* 3.2 14.5 + - + -
24F SER* 2.9 38.4 + - - -
42F TYR* 4.1 2.9 - - - +
5N T 3.8 2.3 - - - +
6N C 2.4 75.7 + + + -
7N A 3.3 51.8 - + + +
8N T 3.0 28.0 + - + +
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Residues in contact with ASP 21 (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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16F GLU 5.0 0.2 - - - +
17F LEU* 3.7 25.5 - - + +
18F SER* 2.8 37.8 + - - +
20F TYR* 1.3 77.8 - - - +
22F ILE* 1.3 62.5 + - - +
24F SER* 3.1 19.2 + - - -
25F TYR* 3.1 21.6 + - + -
67F LYS* 5.4 2.7 + - - -
69F MET* 4.2 9.4 - - - +
7N A 4.1 13.2 + - - -
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Residues in contact with ILE 22 (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 ILE* 3.8 30.1 - - + -
11F LEU* 4.1 16.4 - - + -
12F LEU* 4.5 12.8 - - + -
17F LEU* 4.6 15.5 - - + +
18F SER 3.0 20.3 + - - +
19F GLY* 3.5 10.8 - - - +
21F ASP* 1.3 75.2 - - - +
23F THR* 1.3 61.8 + - - +
25F TYR* 3.2 16.8 + - - +
26F PHE* 3.4 35.7 + - + -
41F ILE* 3.8 17.3 - - + -
45F LEU* 3.9 20.6 - - + -
70F TYR* 5.3 0.4 - - + -
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Residues in contact with THR 23 (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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19F GLY 3.0 15.6 + - - -
20F TYR* 3.2 18.8 + - + -
22F ILE* 1.3 76.2 - - - +
24F SER* 1.3 62.1 + - - +
26F PHE* 3.5 13.1 + - - +
27F LYS* 3.6 33.8 + - - +
36F ALA 5.0 3.8 - - - +
37F LYS* 5.5 0.7 - - - -
38F HIS* 3.7 32.3 - - + +
41F ILE* 3.5 21.3 - - + +
42F TYR* 5.3 0.5 + - - -
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Residues in contact with SER 24 (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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20F TYR* 2.9 30.7 + - - -
21F ASP* 3.1 12.9 + - - -
23F THR* 1.3 77.9 - - - +
25F TYR* 1.3 62.8 + - - +
27F LYS* 3.1 22.1 + - - +
28F GLU* 3.4 17.1 + - - +
6N C 5.1 2.4 + - - -
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Residues in contact with TYR 25 (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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103E TYR* 4.0 21.5 - + - -
11F LEU* 3.8 27.8 - - + -
17F LEU* 4.0 35.9 - - + +
21F ASP* 3.1 27.7 + - + -
22F ILE* 3.2 8.2 + - - +
24F SER* 1.3 76.3 - - - +
26F PHE* 1.3 57.9 + - - +
27F LYS 3.1 0.2 - - - -
28F GLU* 3.1 26.7 + - + +
29F GLU* 5.0 4.7 - - - -
30F LEU* 3.7 18.7 - - + +
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Residues in contact with PHE 26 (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 LEU* 4.4 10.5 - - + -
7F ALA* 3.8 24.9 - - + -
8F ILE* 5.0 0.4 - - + -
11F LEU* 3.9 8.7 - - + -
22F ILE* 3.4 37.3 + - + -
23F THR 3.8 6.7 - - - +
24F SER 3.3 0.8 - - - -
25F TYR* 1.3 76.4 - - - +
27F LYS* 1.3 59.8 + - + +
28F GLU 3.4 0.2 - - - -
30F LEU* 4.1 20.4 - - + -
31F GLY* 3.1 23.9 - - - +
34F TRP* 3.3 37.2 - + + -
35F SER* 3.6 15.9 - - - -
36F ALA* 3.9 21.1 - - + +
41F ILE* 3.8 21.5 - - + -
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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