Contacts of the helix formed by residues 27 - 38 (chain E) 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 LYS 27 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E THR* 1.3 73.4 - - - +
28E GLU* 1.3 82.9 + - + +
30E LEU* 3.1 9.8 - - - +
31E ARG* 3.0 31.7 + - + +
52E ASP* 5.3 0.6 - - - +
55E MET* 3.5 40.2 - - + -
64E GLY* 4.0 15.8 + - - +
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Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E THR* 3.3 6.4 - - + +
27E LYS* 1.3 106.4 + - + +
29E ASP* 1.3 58.8 + - - +
30E LEU 3.0 4.5 - - - -
31E ARG* 3.0 51.2 + - - +
32E VAL* 3.0 14.3 + - - +
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Residues in contact with ASP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LYS 4.8 1.7 - - - +
18E PHE* 3.0 51.1 - - - +
20E GLY* 5.5 1.0 + - - -
22E LYS* 5.2 5.4 + - - +
25E LEU* 4.0 4.0 - - - -
26E THR* 3.3 14.6 + - - +
28E GLU* 1.3 75.1 - - - +
30E LEU* 1.3 59.0 + - - +
32E VAL* 3.2 19.1 - - - +
33E LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.6 27.5 - - + +
26E THR 3.0 22.5 + - - +
27E LYS* 3.1 15.9 - - - +
29E ASP* 1.3 75.1 - - - +
31E ARG* 1.3 64.7 + - + +
33E LEU* 3.2 4.7 + - + +
34E MET* 3.0 47.2 + - + +
51E VAL* 3.7 20.6 - - + +
54E ILE* 6.0 0.2 - - + -
55E MET* 3.7 34.1 - - + -
58E LEU* 5.3 8.1 - - + -
66E VAL* 4.9 17.0 - - + -
71E PHE* 6.3 1.1 - - + -
74E LEU* 6.2 2.0 - - + -
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LYS* 3.0 19.5 + - - +
28E GLU* 3.0 35.6 + - - +
30E LEU* 1.3 76.6 - - - +
32E VAL* 1.3 64.0 - - + +
34E MET* 4.0 1.7 - - - +
35E GLU* 3.1 23.3 + - - +
48E PRO 4.9 9.3 + - - -
49E LEU* 5.0 5.1 - - - +
51E VAL* 3.5 32.6 - - + +
52E ASP* 3.1 30.9 + - - +
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E PHE* 3.8 17.7 - - + -
28E GLU 3.0 13.9 + - - +
29E ASP* 3.2 25.1 - - - +
31E ARG* 1.3 77.0 - - + +
33E LEU* 1.3 57.0 + - - +
35E GLU* 3.1 14.4 + - - +
36E LYS* 2.9 40.6 + - + +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 4.4 12.6 - - + +
15E PHE* 4.5 12.8 - - + +
18E PHE* 3.4 40.4 - - + -
25E LEU* 3.7 31.2 - - + -
29E ASP 2.9 15.9 + - - +
30E LEU* 3.3 4.5 - - + +
32E VAL* 1.3 75.1 - - - +
34E MET* 1.3 77.5 + - + +
36E LYS* 2.9 16.3 + - - +
37E GLU* 3.1 26.7 + - + +
71E PHE* 4.4 22.2 - - + -
74E LEU* 5.8 2.2 - - + -
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Residues in contact with MET 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LEU* 3.0 31.1 + - + +
31E ARG 4.0 2.7 - - - +
33E LEU* 1.3 86.2 - - + +
35E GLU* 1.3 61.5 + - - +
37E GLU* 3.3 13.3 + - - +
38E PHE* 3.5 25.3 + - + -
41E PHE* 6.3 0.7 - - + -
42E LEU* 3.8 16.2 - - + +
51E VAL* 3.5 37.5 - - + -
54E ILE* 3.6 45.5 - - + -
74E LEU* 4.5 22.4 - - + -
78E LEU* 6.2 0.4 - - + -
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG 3.1 15.1 + - - +
32E VAL* 3.2 23.4 - - - +
33E LEU 3.1 0.2 - - - -
34E MET* 1.3 75.9 - - - +
36E LYS* 1.3 77.2 + - - +
37E GLU 3.2 0.5 + - - -
38E PHE 3.9 11.6 + - - +
42E LEU* 3.4 20.5 - - + +
43E GLU* 6.1 0.9 - - - +
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LYS* 5.8 1.6 - - - -
18E PHE* 3.3 31.2 - - + -
32E VAL* 2.9 29.2 + - + +
33E LEU 3.2 6.3 - - - +
35E GLU* 1.3 89.7 - - - +
37E GLU* 1.3 77.7 - - - +
2F SER* 5.0 1.2 + - - -
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Residues in contact with GLU 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 3.7 22.7 + - + +
18E PHE* 4.5 5.7 - - - -
33E LEU* 3.1 22.4 + - + +
34E MET* 3.3 7.8 + - - +
35E GLU 3.1 1.0 - - - -
36E LYS* 1.3 96.4 - - - +
38E PHE* 1.3 84.1 + - + +
39E PRO* 3.5 5.2 - - - +
2F SER* 3.0 50.1 + - - -
3F GLN* 6.1 0.5 - - - +
4F MET* 3.3 24.2 + - + +
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Residues in contact with PHE 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.3 11.4 - - + -
34E MET* 3.5 25.8 + - + +
35E GLU 3.9 8.2 + - - +
36E LYS 3.8 1.0 - - - -
37E GLU* 1.3 93.8 - - + +
39E PRO* 1.3 66.4 - - - +
40E GLY 3.6 0.2 - - - -
41E PHE* 3.8 32.0 + + + +
42E LEU* 4.6 13.3 + - + +
43E GLU* 5.0 4.0 - - - +
74E LEU* 5.2 10.5 - - + -
78E LEU* 3.9 29.4 - - + -
4F MET* 4.8 12.3 - - + -
5F GLU* 3.2 25.1 - - + +
8F MET* 3.7 29.6 - - + -
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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