Contacts of the helix formed by residues 23 - 32 (chain F) in PDB entry 4I6U
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 THR 23 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ARG* 3.7 9.9 - - - +
21F GLY 5.3 2.5 - - - +
22F MET* 1.3 76.9 - - - +
24F GLN* 1.3 63.7 + - - +
25F GLU* 3.5 18.2 + - - +
26F ASP* 3.0 35.9 + - - +
27F LEU* 3.0 18.9 + - - +
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Residues in contact with GLN 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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17F ARG* 3.6 29.0 - - - +
23F THR* 1.3 72.1 - - - +
25F GLU* 1.3 60.2 + - - +
27F LEU* 3.2 1.9 + - - +
28F ALA* 2.9 29.8 + - - +
35F ARG* 2.9 45.0 + - + +
38F ILE* 4.0 15.3 - - + +
39F SER* 3.6 24.2 + - - +
42F GLU* 2.9 27.7 + - - +
43F ARG* 6.1 1.0 - - - +
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Residues in contact with GLU 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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23F THR* 3.6 19.5 - - - +
24F GLN* 1.3 76.7 + - - +
26F ASP* 1.3 60.0 + - - +
28F ALA* 3.3 3.6 + - - +
29F TYR* 2.8 31.9 + - - +
35F ARG* 4.0 39.9 + - + +
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Residues in contact with ASP 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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21F GLY 4.5 2.6 - - - +
22F MET* 3.7 15.2 - - + +
23F THR* 3.0 46.4 + - - +
25F GLU* 1.3 78.7 - - - +
27F LEU* 1.3 59.1 + - - +
29F TYR* 3.5 5.9 + - - +
30F LYS* 3.0 34.5 + - - +
101F GOL 3.1 32.1 + - - +
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Residues in contact with LEU 27 (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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13F ILE* 4.0 26.0 - - + -
17F ARG* 4.1 15.9 - - + -
22F MET* 3.6 9.0 - - + -
23F THR 3.0 13.3 + - - +
24F GLN 3.8 6.3 - - - +
26F ASP* 1.3 74.5 - - - +
28F ALA* 1.3 60.0 + - - +
30F LYS* 3.4 0.6 + - - -
31F SER* 2.9 50.5 + - - +
38F ILE* 4.0 29.8 - - + -
42F GLU* 4.7 0.2 - - - +
56F ILE* 4.1 6.3 - - + +
59F GLY 4.0 3.1 - - - -
60F LEU* 3.7 42.4 - - + +
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Residues in contact with ALA 28 (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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24F GLN 2.9 17.2 + - - +
25F GLU* 3.6 5.4 - - - +
27F LEU* 1.3 77.5 - - - +
29F TYR* 1.3 63.4 + - - +
32F ASN* 3.0 4.5 + - - -
33F LEU* 2.9 46.6 + - - +
34F ASP 3.7 2.2 - - - -
35F ARG* 3.6 27.1 - - + +
38F ILE* 3.8 12.0 - - + +
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Residues in contact with TYR 29 (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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25F GLU 2.8 20.9 + - - +
26F ASP* 3.7 4.7 - - - +
28F ALA* 1.3 75.0 - - - +
30F LYS* 1.3 89.0 + - + +
32F ASN* 3.3 12.5 + - - +
101F GOL 4.0 20.9 - - - -
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Residues in contact with LYS 30 (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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22F MET* 4.1 7.6 - - + -
26F ASP 3.0 25.0 + - - +
27F LEU 4.1 1.1 - - - +
29F TYR* 1.3 88.3 - - + +
31F SER* 1.3 59.0 + - - +
32F ASN* 3.4 0.9 + - - +
58F LYS* 4.9 2.5 - - - +
59F GLY* 3.4 34.7 + - - +
61F GLU* 3.6 30.2 + - - +
101F GOL 3.7 35.5 + - - +
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Residues in contact with SER 31 (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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27F LEU* 2.9 37.1 + - - +
28F ALA* 4.2 1.1 - - - -
30F LYS* 1.3 76.1 - - - +
32F ASN* 1.3 68.8 + - - +
33F LEU* 3.5 20.4 + - - +
38F ILE* 5.2 0.4 - - - -
55F LEU* 3.2 51.9 + - - +
56F ILE* 3.4 5.7 - - - -
58F LYS* 6.0 0.2 - - - -
59F GLY* 3.5 2.6 - - - -
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Residues in contact with ASN 32 (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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28F ALA 3.0 5.7 + - - -
29F TYR* 3.3 10.7 + - - +
30F LYS 3.4 1.7 - - - +
31F SER* 1.3 81.6 - - - +
33F LEU* 1.3 64.5 + - - +
55F LEU* 5.2 6.0 - - + +
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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