Contacts of the helix formed by residues 48 - 52 (chain E) in PDB entry 5HK5
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 GLN 48 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TRP* 3.9 15.1 - - - +
98A ILE 4.1 0.9 - - - +
99A ASP* 3.5 7.3 - - - -
100A SER* 3.2 47.1 + - - +
30E ILE* 3.7 13.2 - - - +
47E HIS* 1.3 110.9 + - + +
49E ILE* 1.3 62.6 + - - +
50E LYS* 3.9 20.4 - - + +
51E GLU* 3.4 27.0 + - + +
52E VAL* 3.5 12.6 + - - +
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Residues in contact with ILE 49 (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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33A TRP* 4.3 10.5 - - + -
36A TRP* 3.4 24.3 - - + -
37A ILE* 3.6 33.0 - - + -
95A ILE* 5.8 0.9 - - + -
97A PHE* 4.1 23.5 - - + -
98A ILE 5.3 0.6 + - - -
109A TYR* 3.4 28.8 + - + +
30E ILE* 3.5 21.7 - - + +
48E GLN* 1.3 72.7 + - - +
50E LYS* 1.3 64.7 + - - +
52E VAL* 3.7 7.6 - - + -
53E LEU* 3.2 38.0 + - + +
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Residues in contact with LYS 50 (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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97A PHE* 5.2 5.5 - - + -
99A ASP* 6.5 0.9 - - - -
100A SER* 5.3 9.9 - - - +
107A LYS* 6.1 2.5 - - - +
109A TYR* 4.9 3.9 + - - -
48E GLN* 3.9 15.9 - - + +
49E ILE* 1.3 77.4 - - - +
51E GLU* 1.3 64.9 + - + +
53E LEU 3.3 15.5 - - - +
54E ALA* 5.4 0.3 - - - -
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Residues in contact with GLU 51 (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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34E TYR* 3.7 20.6 - - - -
45E TRP* 2.5 50.1 + - - +
46E HIS 3.9 2.5 + - - -
47E HIS* 3.6 28.1 + - - -
48E GLN* 3.4 22.2 + - + +
49E ILE 3.2 1.0 - - - -
50E LYS* 1.3 90.5 - - + +
52E VAL* 1.3 59.9 + - - +
53E LEU 4.9 0.4 - - - -
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Residues in contact with VAL 52 (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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33A TRP* 4.5 13.2 - - + -
64C ASN* 4.8 0.3 - - - +
67C VAL* 3.7 21.4 - - + +
30E ILE* 3.9 23.3 - - + -
31E PRO 3.8 8.5 - - - +
32E SER* 3.6 39.9 - - - +
33E PRO* 4.4 4.7 - - + -
34E TYR* 4.4 9.3 + - - -
45E TRP 4.5 0.7 - - - +
48E GLN 3.5 15.7 - - - +
49E ILE* 3.6 18.4 - - + +
51E GLU* 1.3 77.9 - - - +
53E LEU* 1.3 74.5 + - + +
54E ALA 4.4 0.2 + - - -
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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