Contacts of the helix formed by residues 74 - 82 (chain E) in PDB entry 3KHU
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 ASN 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E VAL* 3.8 4.2 - - - +
72E SER* 2.8 15.0 + - - +
73E THR* 1.3 74.4 + - - +
75E ILE* 1.3 62.1 + - - +
76E ASP* 3.7 5.9 + - - +
77E ASP* 2.7 46.6 + - - +
78E ALA* 3.5 19.4 + - - +
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Residues in contact with ILE 75 (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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8E CYS* 5.0 0.2 - - - -
10E ILE* 4.9 7.4 - - + -
35E VAL* 3.9 31.9 - - + -
36E ASP* 4.1 3.8 - - - +
37E VAL* 3.8 33.0 - - + +
73E THR 2.9 18.0 + - - +
74E ASN* 1.3 70.1 - - - +
76E ASP* 1.3 67.5 + - - +
78E ALA* 3.3 2.9 + - - +
79E ILE* 3.0 41.9 + - + +
115E ARG* 3.6 41.1 - - + +
613E EDO 4.3 10.3 - - - +
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Residues in contact with ASP 76 (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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74E ASN* 3.5 6.1 + - - +
75E ILE* 1.3 77.2 - - - +
77E ASP* 1.3 62.5 + - - +
79E ILE* 3.2 5.1 + - - +
80E LYS* 2.9 31.2 + - - +
115E ARG* 2.9 31.4 + - - +
119E ASN* 3.1 41.8 + - - +
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Residues in contact with ASP 77 (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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74E ASN* 2.7 35.2 + - + +
76E ASP* 1.3 77.8 - - - +
78E ALA* 1.3 58.7 + - - +
80E LYS* 3.1 24.7 + - - +
81E GLU* 3.0 39.9 + - + +
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Residues in contact with ALA 78 (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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8E CYS* 3.3 16.2 - - + +
33E THR* 4.1 17.3 - - + -
35E VAL* 3.6 20.6 - - + -
74E ASN 3.5 18.5 + - - +
75E ILE 3.3 5.1 + - - +
76E ASP 3.2 0.4 - - - -
77E ASP* 1.3 78.9 - - - +
79E ILE* 1.3 60.3 + - - +
81E GLU* 3.7 3.2 + - - +
82E ALA* 3.2 24.9 + - - +
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Residues in contact with ILE 79 (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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8E CYS* 4.4 9.0 - - - -
10E ILE* 4.1 22.9 - - + -
75E ILE* 3.0 34.7 + - + +
76E ASP 3.5 5.8 - - - +
78E ALA* 1.3 73.6 - - - +
80E LYS* 1.3 67.0 + - - +
82E ALA* 3.2 14.6 + - - +
85E VAL* 4.5 8.0 - - + +
115E ARG* 3.7 23.1 - - + +
116E ILE* 4.0 21.5 - - + +
119E ASN* 4.0 16.4 - - + +
120E SER* 3.7 21.5 - - - +
124E LYS* 3.2 16.1 - - - +
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Residues in contact with LYS 80 (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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76E ASP* 2.9 14.5 + - - +
77E ASP* 3.1 31.6 + - - +
79E ILE* 1.3 75.0 - - - +
81E GLU* 1.3 69.6 + - + +
119E ASN* 3.5 45.0 + - - +
121E ASN* 6.2 2.0 - - - +
124E LYS* 2.8 21.1 + - - +
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Residues in contact with GLU 81 (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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6E LYS* 3.5 42.9 + - + +
77E ASP* 3.0 24.3 + - + +
78E ALA* 4.5 3.4 - - - +
80E LYS* 1.3 87.0 - - + +
82E ALA* 1.3 61.8 + - - +
83E ASP* 3.8 2.8 + - - +
124E LYS* 4.3 0.7 - - - -
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Residues in contact with ALA 82 (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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6E LYS* 3.8 7.6 - - + +
7E ILE 4.3 0.9 - - - -
8E CYS* 3.6 23.6 - - + +
78E ALA 3.2 18.7 + - - +
79E ILE 3.2 8.2 + - - +
80E LYS 3.3 0.2 - - - -
81E GLU* 1.3 78.5 - - - +
83E ASP* 1.3 61.3 + - - +
84E LEU 3.8 12.6 - - - +
85E VAL* 4.0 6.5 - - + -
123E TYR 4.7 0.2 - - - +
124E LYS* 2.6 35.2 + - - +
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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