Contacts of the helix formed by residues 85 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 4.0 9.9 - - - +
31A ALA* 3.5 7.8 - - + +
33A ASN 5.1 0.4 + - - -
34A GLU* 2.9 45.6 + - + +
35A ASP 3.1 18.7 + - - -
36A ASN* 3.3 14.8 + - - +
38A VAL 5.1 1.4 + - - -
84A MET* 1.3 78.7 - - - +
86A ARG* 1.3 64.6 + - - +
87A VAL* 3.2 9.1 + - - +
88A VAL* 3.1 26.9 + - - +
89A ARG* 3.1 23.0 + - - -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 5.2 6.2 + - - +
85A ASN* 1.3 75.3 - - - +
87A VAL* 1.3 55.8 + - + +
89A ARG* 3.0 30.8 + - - +
90A ASN* 2.7 46.8 + - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASN* 3.7 37.7 - - + +
85A ASN* 3.2 10.0 + - - +
86A ARG* 1.3 77.7 - - + +
88A VAL* 1.3 63.0 + - + +
90A ASN* 3.4 6.4 - - - +
91A ASN* 3.0 34.2 + - - +
151A ILE 3.6 19.7 - - - +
152A PHE* 3.9 6.7 - - + -
153A LEU* 4.1 28.9 - - + +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASN* 3.3 28.0 - - - +
38A VAL 4.5 5.6 - - - +
59A LEU* 4.0 15.0 - - + -
67A ALA* 4.2 7.4 - - + -
69A CYS* 4.0 16.4 - - - -
84A MET* 3.8 33.0 - - + -
85A ASN* 3.1 15.9 + - - +
87A VAL* 1.3 71.3 - - + +
89A ARG* 1.3 66.2 + - - +
91A ASN* 3.1 9.6 + - - +
92A LEU* 3.0 34.4 + - + +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.6 7.4 - - + -
29A ASP 4.8 2.6 + - - -
30A GLU* 2.8 40.8 + - - +
84A MET* 3.3 33.7 + - - -
85A ASN 3.1 12.4 + - - +
86A ARG* 3.0 42.8 + - - +
88A VAL* 1.3 74.3 - - - +
90A ASN* 1.3 56.0 + - - +
92A LEU 3.3 2.8 + - - -
93A ARG 3.0 23.0 + - - -
94A VAL* 3.0 41.6 + - + +
95A GLY* 4.3 2.7 - - - -
96A LEU* 3.6 43.3 - - - +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 2.7 30.1 + - - +
87A VAL* 3.4 8.7 - - - +
89A ARG* 1.3 71.2 - - - +
91A ASN* 1.3 57.2 + - - +
93A ARG* 2.8 45.3 + - - +
151A ILE* 5.6 5.3 - - + +
198A LEU* 3.6 38.4 - - - +
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Residues in contact with ASN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 2.9 34.8 + - - +
66A GLU 4.0 9.7 - - - +
67A ALA* 4.7 4.9 - - + -
87A VAL* 3.0 21.8 + - - +
88A VAL* 3.1 11.6 + - - +
90A ASN* 1.3 78.0 - - - +
92A LEU* 1.3 57.2 + - - +
93A ARG* 3.7 3.5 + - - +
150A ASP* 3.7 29.3 - - - +
151A ILE* 3.0 53.7 + - - +
152A PHE* 5.4 0.5 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.5 38.6 - - + +
60A LYS 4.0 0.4 - - - -
61A GLY* 3.5 19.8 - - - +
62A LYS 3.1 24.6 + - - +
65A ARG* 4.0 4.0 - - - -
66A GLU* 3.7 4.5 - - - -
67A ALA* 3.6 20.2 - - + +
84A MET* 3.8 37.5 - - + -
88A VAL* 3.0 22.3 + - + +
91A ASN* 1.3 75.0 - - - +
93A ARG* 1.3 67.6 + - - +
94A VAL* 3.4 15.7 + - + +
100A ILE* 4.6 6.1 - - + -
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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