Contacts of the helix formed by residues 74 - 82 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D VAL* 4.1 3.9 - - - +
72D SER* 3.0 15.0 + - - +
73D THR* 1.3 75.0 + - - +
75D ILE* 1.3 62.1 + - - +
76D ASP* 3.7 6.1 + - - +
77D ASP* 2.8 44.8 + - + +
78D ALA* 3.4 18.0 + - - +
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Residues in contact with ILE 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.8 11.2 - - + -
35D VAL* 3.7 33.0 - - + -
36D ASP* 4.1 5.4 - - - +
37D VAL* 3.9 31.0 - - + +
73D THR 3.0 17.4 + - - +
74D ASN* 1.3 71.4 + - - +
76D ASP* 1.3 64.4 + - - +
78D ALA* 3.2 3.1 + - - +
79D ILE* 3.0 43.0 + - + +
115D ARG* 3.5 41.7 - - + +
502D UPG 5.2 3.6 - - - +
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Residues in contact with ASP 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASN* 3.4 6.6 + - - +
75D ILE* 1.3 77.8 - - - +
77D ASP* 1.3 61.3 + - - +
79D ILE* 3.5 3.7 + - - +
80D LYS* 3.0 28.0 + - - +
115D ARG* 3.0 32.7 + - - -
119D ASN* 3.1 42.2 + - - +
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Residues in contact with ASP 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASN* 2.8 34.2 + - - +
76D ASP* 1.3 77.8 - - - +
78D ALA* 1.3 66.5 + - - +
80D LYS* 3.5 18.2 + - - +
81D GLU* 3.1 33.2 + - + +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D CYS* 3.6 16.8 - - + +
33D THR* 3.9 17.7 - - + -
35D VAL* 3.6 32.3 - - + -
74D ASN 3.4 6.9 + - - +
75D ILE 3.2 5.7 + - - +
77D ASP* 1.3 78.9 - - - +
79D ILE* 1.3 63.5 + - - +
81D GLU* 3.5 3.8 + - - +
82D ALA* 3.3 23.0 + - - +
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D CYS* 3.7 16.8 - - - -
10D ILE* 4.0 18.2 - - + -
75D ILE* 3.0 30.2 + - + +
76D ASP 3.8 3.6 - - - +
78D ALA* 1.3 75.0 - - - +
80D LYS* 1.3 66.2 + - - +
82D ALA* 3.1 15.5 + - - +
85D VAL* 4.6 7.6 - - + -
115D ARG* 3.7 31.2 - - + +
116D ILE* 4.0 21.5 - - + +
119D ASN* 4.0 15.9 - - + +
120D SER* 3.5 22.7 - - - +
124D LYS* 3.2 16.1 - - - +
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Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ASP 3.0 17.8 + - - +
77D ASP* 3.5 21.3 + - - +
78D ALA 3.2 0.4 - - - -
79D ILE* 1.3 78.2 - - - +
81D GLU* 1.3 74.8 + - + +
119D ASN* 3.6 22.7 - - + +
121D ASN* 5.8 1.2 + - - +
124D LYS* 2.9 21.2 + - - +
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS* 3.6 44.5 + - + +
77D ASP* 3.1 20.2 + - + +
78D ALA* 4.2 3.6 - - - +
80D LYS* 1.3 99.8 + - + +
82D ALA* 1.3 62.0 + - - +
83D ASP* 3.8 3.8 + - - +
124D LYS* 4.2 0.7 - - - -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS* 3.8 8.5 - - + +
7D ILE 4.4 0.9 - - - -
8D CYS* 3.6 23.8 - - + +
78D ALA 3.3 17.1 + - - +
79D ILE 3.1 9.1 + - - +
81D GLU* 1.3 77.9 - - - +
83D ASP* 1.3 60.3 + - - +
84D LEU 3.7 12.8 - - - +
85D VAL* 4.0 7.2 - - + -
123D TYR 4.7 0.5 - - - +
124D LYS* 2.6 34.1 + - - +
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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