Contacts of the helix formed by residues 26 - 38 (chain F) in PDB entry 4HRE
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 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22F LYS* 6.2 2.5 - - + -
24F TYR* 3.8 17.8 + - + +
25F LEU* 1.3 77.4 - - - +
27F LYS* 1.3 59.8 + - - +
28F GLU* 3.0 12.6 + - - +
29F ASP* 2.8 36.7 + - - +
30F LEU* 2.8 27.5 + - - +
55F MET* 3.8 3.8 - - - -
64F GLY 4.3 6.1 - - - +
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Residues in contact with LYS 27 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F THR* 1.3 73.0 - - - +
28F GLU* 1.3 76.5 + - + +
30F LEU* 3.5 4.9 - - - +
31F ARG* 2.9 32.1 + - - +
51F VAL* 3.7 4.6 - - - +
52F ASP* 3.2 43.2 - - - +
55F MET* 3.3 36.6 - - + +
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Residues in contact with GLU 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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26F THR* 3.0 10.7 + - - +
27F LYS* 1.3 93.4 + - + +
29F ASP* 1.3 68.1 + - - +
30F LEU 3.1 1.6 - - - -
31F ARG* 3.1 26.2 + - - +
32F VAL* 2.9 38.1 + - + +
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Residues in contact with ASP 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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18F PHE* 2.7 31.1 - - + +
19F ALA* 4.9 2.0 - - - -
22F LYS* 3.0 22.4 + - - +
24F TYR 5.1 1.7 - - - +
25F LEU* 3.6 23.6 - - + -
26F THR* 2.8 39.3 + - - +
28F GLU* 1.3 78.2 - - - +
30F LEU* 1.3 56.8 + - - +
32F VAL* 3.2 13.2 - - - +
33F LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 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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25F LEU* 4.2 21.0 - - + +
26F THR 2.8 18.2 + - - +
27F LYS* 3.5 3.1 - - - +
29F ASP* 1.3 76.9 - - - +
31F ARG* 1.3 59.4 + - - +
33F LEU* 3.0 10.6 + - + +
34F MET* 2.9 57.8 + - + +
51F VAL* 3.7 28.0 - - + +
54F ILE* 4.6 12.1 - - + -
55F MET* 3.6 27.8 - - + -
58F LEU* 5.3 5.6 - - + -
66F VAL* 5.6 2.0 - - + -
71F PHE* 6.4 0.2 - - + -
74F LEU* 4.6 13.2 - - + -
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Residues in contact with ARG 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 LYS* 2.9 23.9 + - - +
28F GLU* 3.1 27.7 + - - +
30F LEU* 1.3 76.8 - - - +
32F VAL* 1.3 64.3 + - - +
34F MET* 3.5 2.3 + - - -
35F GLU* 2.9 37.3 + - + +
42F LEU* 4.2 9.7 - - + +
51F VAL* 3.8 23.3 - - + -
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Residues in contact with VAL 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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18F PHE* 3.9 24.9 - - + -
28F GLU* 2.9 26.5 + - + +
29F ASP* 3.2 25.6 - - - +
31F ARG* 1.3 81.5 - - - +
33F LEU* 1.3 62.1 + - - +
35F GLU* 3.8 6.8 - - + +
36F LYS* 2.9 26.3 + - + +
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Residues in contact with LEU 33 (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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4E MET* 5.7 2.5 - - + -
14F THR* 5.2 11.2 - - - +
15F PHE* 5.5 2.0 - - - -
18F PHE* 3.7 32.8 - - + -
25F LEU* 3.7 29.2 - - + -
29F ASP 2.9 15.1 + - - +
30F LEU* 3.0 15.6 + - + +
32F VAL* 1.3 78.2 - - - +
34F MET* 1.3 66.4 + - + +
36F LYS* 3.7 1.2 - - - +
37F GLU* 2.9 43.0 + - + +
38F PHE* 5.6 3.6 - - + -
71F PHE* 4.0 26.2 - - + -
74F LEU* 6.0 2.0 - - + -
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Residues in contact with MET 34 (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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30F LEU* 2.9 36.1 + - + +
31F ARG* 4.3 3.6 - - - +
33F LEU* 1.3 74.2 - - + +
35F GLU* 1.3 55.6 + - - +
38F PHE* 2.8 65.5 + - + +
41F PHE* 4.9 10.8 - - + -
42F LEU* 4.1 18.4 - - + -
51F VAL* 3.9 24.5 - - - -
54F ILE* 5.4 7.4 - - + -
74F LEU* 3.6 41.1 - - + -
78F LEU* 5.0 5.6 - - + -
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Residues in contact with GLU 35 (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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31F ARG* 2.9 28.0 + - + +
32F VAL* 3.8 7.0 - - + +
34F MET* 1.3 77.6 - - - +
36F LYS* 1.3 61.0 + - - +
38F PHE 4.5 1.9 - - - +
39F PRO* 3.3 33.6 - - - +
40F GLY 4.7 0.5 + - - -
42F LEU* 4.2 13.0 - - + +
43F GLU* 2.8 32.1 - - - +
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E SER* 4.5 5.0 - - - -
18F PHE* 4.2 19.3 - - + -
32F VAL* 2.9 20.5 + - + +
33F LEU 3.8 2.2 - - - +
35F GLU* 1.3 76.6 - - - +
37F GLU* 1.3 69.6 + - + +
39F PRO* 3.4 11.4 - - - +
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Residues in contact with GLU 37 (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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2E SER* 2.6 49.5 + - - +
3E GLN* 4.2 5.5 + - - +
4E MET* 3.1 30.4 + - + +
5E GLU* 3.2 9.7 - - - +
14F THR* 4.1 12.5 - - - +
18F PHE* 4.5 10.2 - - + -
33F LEU* 2.9 37.4 + - + +
36F LYS* 1.3 82.4 - - - +
38F PHE* 1.3 78.4 + - + +
39F PRO* 3.4 4.8 - - - +
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Residues in contact with PHE 38 (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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5C HIS* 5.8 1.3 - - + -
8C LEU* 3.4 32.5 - - + -
4E MET* 4.7 10.5 - - + -
5E GLU* 4.1 13.9 - - + +
8E MET* 4.1 17.5 - - - -
33F LEU* 5.6 3.4 - - + -
34F MET* 2.8 61.0 + - + +
35F GLU* 4.5 1.9 - - - +
37F GLU* 1.3 92.7 - - + +
39F PRO* 1.3 66.6 - - - +
41F PHE* 3.2 35.7 + + + +
42F LEU* 4.4 2.1 + - - +
74F LEU* 5.6 0.7 - - + -
75F ILE* 4.4 22.4 - - + -
78F LEU* 4.5 10.8 - - + -
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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