Contacts of the helix formed by residues 44 - 51 (chain E) in PDB entry 4KZX
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 LEU 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LEU 3.2 3.7 + - - -
43E PRO* 1.3 70.5 - - - +
45E ILE* 1.3 51.9 - - - +
47E PHE* 2.6 39.2 + - + +
48E LEU* 2.6 56.5 + - + +
61E VAL* 5.2 1.3 - - + -
65E CYS* 4.8 13.0 - - + -
70E ILE* 4.0 26.5 - - + -
72E ILE* 5.2 14.1 - - + -
77E ARG* 4.7 12.6 - - + +
79E ASP 4.2 17.3 - - - +
80E ILE* 3.9 7.2 + - - +
82E TYR* 3.1 14.7 + - + +
84E ALA* 5.3 2.2 - - - +
90E ILE* 5.4 5.2 - - + -
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Residues in contact with ILE 45 (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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29E PRO* 3.6 36.1 - - + -
43E PRO* 3.9 6.5 - - + -
44E LEU* 1.3 73.1 - - - +
46E ILE* 1.3 74.5 + - + +
49E ARG* 2.9 45.1 + - + +
58E GLY* 4.3 21.1 - - - -
61E VAL* 3.7 25.4 - - + -
80E ILE* 3.1 44.1 + - + +
81E THR* 5.8 0.2 - - + -
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Residues in contact with ILE 46 (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 TRP* 2.8 65.5 - - + +
20E LEU* 4.6 2.2 - - + -
29E PRO* 4.0 13.2 - - + -
42E LEU* 5.2 6.7 - - + -
43E PRO* 2.8 35.9 + - + +
45E ILE* 1.3 80.9 - - - +
47E PHE* 1.3 56.4 + - - +
50E ASN* 2.8 56.7 + - + +
51E LYS* 3.0 20.2 + - + +
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Residues in contact with PHE 47 (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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42E LEU* 5.4 8.2 - - + +
43E PRO 3.3 2.5 + - - +
44E LEU* 2.6 31.2 + - + +
46E ILE* 1.3 76.2 - - - +
48E LEU* 1.3 71.9 + - + +
51E LYS* 4.4 11.9 - - + -
52E LEU* 2.5 81.3 + - + +
90E ILE* 3.5 34.1 - - + -
92E ILE* 5.2 3.4 - - + -
99E PHE* 4.0 21.5 - + + -
101E LEU* 4.3 26.2 - - + -
111E VAL* 5.1 9.9 - - + -
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Residues in contact with LEU 48 (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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44E LEU* 2.6 34.5 + - + +
45E ILE 4.1 1.6 - - - +
47E PHE* 1.3 95.4 - - + +
49E ARG* 1.3 56.8 + - - +
52E LEU* 3.8 9.0 - - + +
53E LYS 3.4 3.5 + - - -
54E TYR* 3.1 35.7 + - + +
55E ALA* 3.1 6.6 + - + -
61E VAL* 4.2 23.8 - - + +
64E ILE* 3.9 23.8 - - + -
65E CYS* 5.2 0.7 - - - -
70E ILE* 2.8 38.4 - - + -
92E ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 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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11E ARG* 5.4 5.5 - - - +
20E LEU* 4.4 5.7 - - - +
29E PRO* 5.4 5.1 - - - +
45E ILE* 2.9 29.6 + - + +
46E ILE* 5.2 0.6 - - - +
48E LEU* 1.3 74.3 - - - +
50E ASN* 1.3 104.1 + - - +
51E LYS 3.9 0.2 - - - -
53E LYS* 4.4 16.9 - - - +
55E ALA* 3.1 44.2 - - + +
56E LEU 4.1 11.7 + - - +
57E THR 4.1 7.6 - - - +
58E GLY* 6.1 0.9 - - - -
61E VAL* 3.4 13.7 - - + -
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Residues in contact with ASN 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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18E TRP 5.5 2.5 - - - +
19E MET 5.7 1.5 - - - +
20E LEU* 3.0 30.4 - - + +
46E ILE* 2.8 38.2 + - + +
49E ARG* 1.3 130.5 + - - +
51E LYS* 1.3 65.5 + - + +
53E LYS* 4.0 15.5 + - - +
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Residues in contact with LYS 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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17E HIS 4.4 7.3 + - - -
18E TRP* 3.6 27.3 + - - +
19E MET* 4.2 14.6 - - - +
42E LEU* 5.9 3.1 - - + -
46E ILE* 3.0 22.6 + - + +
47E PHE* 3.8 15.7 - - + +
50E ASN* 1.3 84.0 + - - +
52E LEU* 1.3 65.0 + - + +
53E LYS* 3.5 7.9 + - - +
108E ARG* 4.7 7.9 - - - +
109E PHE* 4.5 20.6 + - + +
111E VAL* 3.9 29.1 - - + +
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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