Contacts of the helix formed by residues 20 - 32 (chain F) in PDB entry 3UNE
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 VAL 20 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F SER 4.8 0.4 - - - +
11F ALA* 3.8 31.0 - - - +
13F THR 4.4 12.3 - - - +
14F PHE* 3.9 27.4 - - + -
19F ARG* 1.3 74.5 - - - +
21F PHE* 1.3 63.6 + - - +
22F GLN 4.2 6.7 - - - +
23F VAL* 3.4 28.9 + - + +
24F GLU* 3.4 22.4 + - - +
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Residues in contact with PHE 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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1F SER* 3.7 22.2 - - - -
2F SER* 4.3 4.3 - - - -
3F ILE* 3.7 29.4 - - + -
7F TYR 4.6 8.5 + - - -
8F ASP* 3.7 25.1 - - + -
15F SER* 3.6 30.7 - - - -
17F ASP* 4.3 4.5 - - - -
19F ARG* 3.6 32.0 + - + -
20F VAL* 1.3 71.1 - - - +
22F GLN* 1.3 56.0 + - - +
24F GLU* 3.0 24.3 + - - +
25F TYR* 2.7 67.1 + + + -
28F LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 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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11E THR 2.8 29.1 + - - -
12E VAL* 3.8 0.9 - - - +
13E TRP* 2.8 52.3 + - + +
8F ASP* 2.9 24.6 - - - +
9F LEU 3.5 11.0 + - - +
10F SER 3.6 25.0 + - - +
11F ALA* 3.9 25.8 - - + +
20F VAL* 3.3 2.8 - - + +
21F PHE* 1.3 77.4 - - - +
23F VAL* 1.3 59.2 + - - +
25F TYR* 4.2 2.7 - - - -
26F ALA* 3.4 20.1 + - - +
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Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ALA* 5.6 4.5 - - + -
20F VAL* 3.4 29.3 + - + +
21F PHE 3.2 0.4 - - - -
22F GLN* 1.3 78.3 - - + +
24F GLU* 1.3 61.1 + - + +
26F ALA* 3.3 9.1 + - + +
27F MET* 3.0 48.1 + - + +
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Residues in contact with GLU 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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19F ARG* 2.8 55.3 + - - +
20F VAL 3.4 14.3 + - - +
21F PHE* 3.0 27.1 + - + +
23F VAL* 1.3 79.8 - - + +
25F TYR* 1.3 59.2 + - + +
27F MET* 3.3 18.3 + - - +
28F LYS* 3.1 31.4 + - - +
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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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13E TRP* 3.7 31.3 - - + -
14E SER 3.4 15.7 - - - +
15E PRO* 3.6 34.3 - - + +
17E GLY* 3.4 13.7 - - - -
2F SER* 5.2 1.7 - - - -
3F ILE 3.8 9.2 + - - -
8F ASP* 3.3 42.5 + - + +
21F PHE* 2.7 54.9 + + + +
22F GLN* 4.2 7.9 - - - +
24F GLU* 1.3 72.7 - - + +
26F ALA* 1.3 59.5 + - - +
27F MET 3.2 0.7 - - - -
28F LYS* 3.2 34.3 + - + +
29F ALA* 3.2 9.7 + - - +
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Residues in contact with ALA 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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13E TRP* 4.2 25.9 - - + +
22F GLN 3.4 13.7 + - - +
23F VAL* 3.3 12.8 + - + +
25F TYR* 1.3 77.6 - - - +
27F MET* 1.3 61.5 + - + +
29F ALA* 3.4 19.4 + - - +
30F VAL* 3.6 7.6 + - - +
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Residues in contact with MET 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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23F VAL* 3.0 35.2 + - + +
24F GLU* 3.4 21.3 - - - +
25F TYR 3.2 0.2 - - - -
26F ALA* 1.3 77.6 - - - +
28F LYS* 1.3 57.7 - - + +
29F ALA 3.3 0.9 - - - -
30F VAL* 3.1 28.2 - - + +
31F GLU* 3.2 14.8 - - - +
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Residues in contact with LYS 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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15E PRO* 3.4 27.3 + - - +
16E GLN* 4.2 5.1 - - - +
17E GLY* 4.2 9.6 - - - -
1F SER 5.2 7.9 + - - -
24F GLU* 3.1 16.1 + - - +
25F TYR* 3.2 35.8 + - + +
27F MET* 1.3 75.3 - - - +
29F ALA* 1.3 63.1 + - - +
30F VAL 3.3 0.4 - - - -
31F GLU* 3.5 9.7 + - + +
32F ASN* 3.0 31.6 + - - +
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Residues in contact with ALA 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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13E TRP* 3.8 23.6 - - + -
17E GLY 3.5 22.9 - - - +
25F TYR 3.2 4.5 + - - +
26F ALA 3.5 11.7 - - - +
27F MET 3.3 0.4 - - - -
28F LYS* 1.3 78.7 - - - +
30F VAL* 1.3 60.5 + - - +
32F ASN* 3.7 11.4 + - - +
33F SER* 3.8 8.0 + - - -
79F GLY* 4.1 10.5 - - - -
80F LEU* 5.5 8.5 - - + +
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Residues in contact with VAL 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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26F ALA 3.6 4.9 + - - +
27F MET* 3.1 30.5 - - + +
29F ALA* 1.3 75.2 - - - +
31F GLU* 1.3 71.4 + - - +
32F ASN 3.3 0.4 - - - -
33F SER* 3.6 16.6 + - - +
34F SER 5.3 0.2 - - - +
78F ALA* 3.3 41.8 - - + +
79F GLY* 3.9 8.0 + - - -
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Residues in contact with GLU 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 MET 3.2 17.7 + - - +
28F LYS* 3.7 13.5 - - + +
29F ALA 3.3 0.8 - - - -
30F VAL* 1.3 85.6 - - - +
32F ASN* 1.3 65.2 + - - +
33F SER 3.3 5.5 + - - +
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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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16E GLN* 3.8 17.5 + - - +
17E GLY 5.3 3.0 + - - -
18E ARG* 5.8 5.3 - - - +
28F LYS* 3.0 18.8 + - - +
29F ALA* 3.7 7.6 + - - +
30F VAL 3.3 0.4 - - - -
31F GLU* 1.3 81.5 - - - +
33F SER* 1.3 61.4 + - - +
34F SER 4.2 0.2 + - - -
52F LEU* 5.7 3.3 - - - +
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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