Contacts of the helix formed by residues 85 - 92 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B GLU* 4.1 9.2 - - - +
31B ALA* 3.6 6.6 - - + +
33B ASN 4.9 0.4 + - - +
34B GLU* 3.2 45.1 + - + +
35B ASP 3.3 22.9 + - - -
36B ASN* 3.5 10.6 + - - -
38B VAL 4.9 1.4 + - - -
84B MET* 1.3 78.4 - - - +
86B ARG* 1.3 64.2 + - - +
87B VAL* 3.0 18.9 + - - +
88B VAL* 3.2 16.3 + - - +
89B ARG* 3.1 24.3 + - - +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 5.0 6.5 + - - +
85B ASN* 1.3 75.8 - - - +
87B VAL* 1.3 55.7 - - + +
89B ARG* 3.3 30.0 + - - +
90B ASN* 2.7 44.8 + - - +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ASN* 3.7 37.0 - - + +
85B ASN* 3.0 10.6 + - - +
86B ARG* 1.3 79.2 - - + +
88B VAL* 1.3 57.8 + - - +
90B ASN* 3.5 5.3 + - - +
91B ASN* 3.1 36.9 + - - +
151B ILE 3.5 19.6 - - - +
152B PHE* 3.8 10.1 - - + -
153B LEU* 4.1 28.9 - - + +
162B GLU* 6.1 1.1 - - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 3.2 28.7 - - - +
38B VAL 4.6 4.7 - - - +
59B LEU* 4.0 4.0 - - + -
67B ALA* 4.3 6.5 - - + -
69B CYS* 4.0 26.0 - - - -
84B MET* 3.8 31.2 - - + -
85B ASN* 3.2 19.1 + - - +
87B VAL* 1.3 71.7 - - + +
89B ARG* 1.3 60.0 + - - +
91B ASN* 3.2 8.3 + - - +
92B LEU* 3.0 38.3 + - + +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 4.6 7.6 - - + -
29B ASP 4.9 2.4 + - - -
30B GLU* 2.7 40.0 + - - +
84B MET* 3.4 36.0 + - - +
85B ASN 3.1 14.3 + - - +
86B ARG* 3.6 33.6 - - - +
88B VAL* 1.3 75.5 - - - +
90B ASN* 1.3 57.0 + - - +
92B LEU 3.5 0.3 + - - -
93B ARG 3.0 6.4 + - - -
94B VAL* 2.9 57.4 + - + +
95B GLY* 4.4 2.7 - - - -
96B LEU* 3.4 44.5 - - - +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 2.7 32.0 + - - +
87B VAL* 3.6 6.7 - - - +
89B ARG* 1.3 70.3 - - - +
91B ASN* 1.3 60.1 + - - +
93B ARG* 2.7 45.8 + - - +
151B ILE* 5.8 4.1 - - + +
198B LEU* 3.7 37.8 - - - +
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 2.8 35.1 + - - +
66B GLU 4.2 8.3 - - - +
67B ALA* 4.7 5.9 - - + +
87B VAL* 3.1 19.8 + - - +
88B VAL* 3.2 7.7 + - - +
90B ASN* 1.3 81.2 - - - +
92B LEU* 1.3 56.5 + - - +
93B ARG* 3.3 3.1 - - - +
150B ASP* 3.5 28.9 - - - +
151B ILE* 3.0 57.9 + - - +
152B PHE* 5.4 0.5 - - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.5 37.5 - - + +
60B LYS 4.0 0.2 - - - -
61B GLY* 3.6 20.0 - - - +
62B LYS 3.2 23.9 + - - +
65B ARG* 4.0 4.9 - - - +
66B GLU* 3.8 4.9 - - - -
67B ALA* 3.6 20.0 - - + +
84B MET* 3.7 37.7 - - + -
88B VAL* 3.0 22.3 + - + +
91B ASN* 1.3 74.3 - - - +
93B ARG* 1.3 68.6 + - - +
94B VAL* 3.2 15.9 + - + +
100B ILE* 4.5 6.7 - - + -
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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