Contacts of the helix formed by residues 43 - 51 (chain E) in PDB entry 1KYZ
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 ASP 43 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ALA 3.0 0.2 + - - -
40E LEU* 2.9 18.8 + - - +
41E GLU 3.1 2.2 - - - +
42E LEU* 1.3 81.3 - - - +
44E LEU* 1.3 65.0 + - - +
45E LEU 3.4 2.2 - - - -
46E GLU* 3.2 33.4 + - - +
47E ILE* 3.1 30.4 + - + +
50E LYS* 5.2 5.5 - - - -
117E LYS* 4.8 9.0 + - - -
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Residues in contact with LEU 44 (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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39E ALA* 2.9 37.4 + - + +
42E LEU* 3.2 18.8 - - + +
43E ASP* 1.3 78.1 - - - +
45E LEU* 1.3 63.7 + - + +
47E ILE* 3.4 6.5 + - + +
48E ILE* 3.1 28.2 + - + +
62E ILE* 3.7 25.1 - - + +
66E LEU* 4.1 8.7 - - + -
77E LEU* 3.7 30.1 - - + -
80E MET* 4.5 10.5 - - + -
81E LEU* 3.9 30.7 - - + -
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Residues in contact with LEU 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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36E LEU* 4.3 11.0 - - + -
39E ALA* 4.6 3.3 + - + -
40E LEU* 4.0 25.9 - - + +
43E ASP 3.4 0.6 - - - -
44E LEU* 1.3 79.3 - - + +
46E GLU* 1.3 63.3 + - + +
48E ILE* 3.3 6.7 + - + +
49E ALA* 2.9 29.5 + - - +
81E LEU* 5.6 0.4 - - + -
84E LEU* 4.6 15.9 - - + -
89E ILE* 4.8 4.0 - - + -
90E LEU* 3.7 29.8 - - + -
108E LEU* 3.9 16.3 - - + +
115E LEU* 3.8 44.0 - - + +
116E VAL* 4.8 4.3 - - + -
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Residues in contact with GLU 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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43E ASP* 3.2 34.9 + - - +
44E LEU 3.3 0.2 - - - -
45E LEU* 1.3 75.5 - - + +
47E ILE* 1.3 59.9 + - - +
49E ALA* 3.2 6.5 + - - +
50E LYS* 2.9 50.3 + - - +
115E LEU 4.3 2.8 - - - +
116E VAL* 3.5 16.7 - - - +
117E LYS* 2.7 60.2 + - + +
118E ASN* 5.3 2.1 - - - +
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Residues in contact with ILE 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 4.0 2.9 - - - +
43E ASP* 3.1 24.9 + - + +
44E LEU* 3.5 7.4 - - - +
45E LEU 3.2 0.2 - - - -
46E GLU* 1.3 75.9 - - - +
48E ILE* 1.3 62.5 + - - +
50E LYS* 3.3 21.8 + - + +
51E ALA* 3.7 6.2 + - - +
57E ILE* 4.2 8.0 - - + +
62E ILE* 3.9 36.8 - - + +
65E GLN* 3.8 37.7 - - + +
66E LEU* 3.7 29.6 - - + -
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Residues in contact with ILE 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 3.1 17.1 + - - +
45E LEU* 3.7 8.3 - - + +
47E ILE* 1.3 76.0 - - - +
49E ALA* 1.3 64.1 + - - +
51E ALA* 3.1 18.7 + - - +
52E GLY 4.1 4.5 + - - +
55E ALA* 4.8 4.9 - - - +
57E ILE* 4.0 11.9 - - + -
62E ILE* 3.7 31.6 - - + -
81E LEU* 4.6 6.1 - - + -
90E LEU* 4.2 26.9 - - + -
106E TYR* 4.0 16.8 - - + +
107E GLY* 3.8 20.6 - - - -
108E LEU* 3.7 20.9 - - + +
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Residues in contact with ALA 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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45E LEU 2.9 17.7 + - - +
46E GLU* 3.2 10.5 + - - +
48E ILE* 1.3 78.4 - - - +
50E LYS* 1.3 61.9 + - + +
52E GLY* 3.2 17.6 + - - -
108E LEU* 3.6 18.8 - - + -
116E VAL* 3.8 21.5 - - + -
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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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43E ASP* 5.2 5.4 - - - -
46E GLU* 2.9 40.9 + - - +
47E ILE* 3.7 13.0 - - + +
48E ILE 3.2 0.6 - - - -
49E ALA* 1.3 76.1 - - + +
51E ALA* 1.3 61.1 + - - +
52E GLY* 3.1 1.4 + - - -
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Residues in contact with ALA 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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47E ILE 3.7 2.6 + - - +
48E ILE* 3.1 14.9 + - + +
49E ALA 3.1 0.6 - - - -
50E LYS* 1.3 77.6 - - - +
52E GLY* 1.3 58.0 + - - +
55E ALA* 3.6 23.7 - - + +
57E ILE* 4.0 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