Contacts of the helix formed by residues 85 - 92 (chain F) in PDB entry 3HU1
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 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F GLU* 4.0 5.2 - - - +
31F ALA* 3.6 7.2 - - + +
33F ASN 5.2 0.4 + - - -
34F GLU* 2.9 47.0 + - + +
35F ASP 3.3 14.9 + - - -
36F ASN* 3.2 18.8 + - - +
38F VAL 5.0 1.6 + - - -
84F MET* 1.3 78.4 - - - +
86F ARG* 1.3 63.8 + - - +
87F VAL* 3.3 6.4 + - - +
88F VAL* 3.2 28.3 + - - +
89F ARG* 3.2 27.9 + - - +
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Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLU* 5.2 6.6 + - - +
85F ASN* 1.3 76.1 - - - +
87F VAL* 1.3 58.5 + - + +
89F ARG* 3.3 28.1 + - - +
90F ASN* 2.7 46.8 + - - +
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ASN* 3.6 42.0 - - + +
85F ASN* 3.3 6.0 + - - +
86F ARG* 1.3 77.6 - - + +
88F VAL* 1.3 62.4 + - - +
90F ASN* 3.5 5.6 + - - +
91F ASN* 3.0 34.7 + - - +
151F ILE 3.5 19.6 - - - +
152F PHE* 3.9 9.2 - - + -
153F LEU* 4.0 29.6 - - + +
162F GLU* 6.2 0.2 - - - +
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ASN 3.3 27.8 - - - +
38F VAL 4.6 6.3 - - - +
39F VAL* 4.4 0.2 - - + -
59F LEU* 4.0 14.1 - - + -
67F ALA* 4.5 6.5 - - + -
69F CYS* 4.0 14.4 - - - -
84F MET* 3.7 33.2 - - + -
85F ASN* 3.2 16.5 + - - +
87F VAL* 1.3 72.2 - - + +
89F ARG* 1.3 60.2 + - - +
91F ASN* 3.0 10.4 + - - +
92F LEU* 3.0 38.1 + - + +
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Residues in contact with ARG 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 4.5 6.1 - - + -
29F ASP 4.9 2.4 + - - -
30F GLU* 2.9 37.8 + - - -
84F MET* 3.2 33.8 + - - -
85F ASN 3.2 28.0 + - - +
86F ARG* 3.3 27.4 + - - +
88F VAL* 1.3 77.6 - - - +
90F ASN* 1.3 60.6 + - - +
92F LEU 3.4 1.2 + - - -
93F ARG 3.0 3.8 + - - -
94F VAL* 3.0 56.7 + - + +
95F GLY* 4.3 2.3 - - - -
96F LEU* 3.5 44.1 - - - +
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Residues in contact with ASN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ARG* 2.7 29.9 + - - +
87F VAL* 3.7 6.7 - - - +
89F ARG* 1.3 71.7 - - - +
91F ASN* 1.3 58.4 - - - +
93F ARG* 2.8 45.2 + - - +
94F VAL 5.2 0.2 - - - -
151F ILE* 5.7 3.5 - - + +
198F LEU* 3.7 37.4 - - - +
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Residues in contact with ASN 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ARG* 2.9 36.6 + - - +
66F GLU 3.9 8.3 - - - +
67F ALA* 4.6 6.5 - - + +
87F VAL* 3.0 20.3 + - - +
88F VAL* 3.0 10.9 + - - +
90F ASN* 1.3 78.0 - - - +
92F LEU* 1.3 57.6 + - - +
93F ARG 3.3 0.2 - - - -
150F ASP* 3.7 26.7 - - - +
151F ILE* 3.0 57.9 + - - +
152F PHE* 5.4 0.3 - - - +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU* 3.4 39.3 - - + +
60F LYS 4.0 0.2 - - - -
61F GLY* 3.4 21.0 - - - +
62F LYS 3.0 29.6 + - - +
65F ARG* 4.0 4.7 - - - -
66F GLU* 3.8 3.4 - - - -
67F ALA* 3.6 19.5 - - + +
84F MET* 3.8 36.8 - - + -
88F VAL* 3.0 20.7 + - + +
89F ARG 3.4 0.2 + - - -
90F ASN 3.2 0.2 - - - -
91F ASN* 1.3 76.3 - - - +
93F ARG* 1.3 64.6 + - - +
94F VAL* 3.4 14.6 - - + +
100F ILE* 4.5 7.2 - - + -
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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