Contacts of the helix formed by residues 105 - 112 (chain B) in PDB entry 1HHS
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.4 4.7 - - + -
104B SER* 1.3 73.0 + - - +
106B LEU* 1.3 74.1 + - - +
107B LYS 3.4 2.0 - - - -
108B LYS* 3.8 16.6 - - + -
109B ARG* 3.0 30.2 + - + +
330B THR 2.9 29.0 + - - +
331B PHE 3.7 7.1 + - - -
332B TRP 2.9 27.1 + - - +
334B GLY 5.0 3.0 + - - +
388B GLU* 2.8 29.7 + - - +
389B VAL 4.8 2.2 - - - +
390B GLY* 3.5 6.8 - - - -
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Residues in contact with LEU 106 (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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104B SER* 3.4 17.4 + - - +
105B ASN* 1.3 86.9 - - - +
107B LYS* 1.3 57.1 + - - +
109B ARG* 3.4 9.8 + - + +
110B ALA* 3.0 27.8 + - - +
116B ASP* 6.4 1.8 - - + -
334B GLY* 5.8 3.8 - - - +
335B TRP* 6.3 3.6 - - + +
388B GLU* 4.3 25.1 - - + +
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Residues in contact with LYS 107 (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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104B SER* 5.0 1.6 + - - -
106B LEU* 1.3 75.7 - - - +
108B LYS* 1.3 62.8 + - - +
110B ALA* 4.4 6.3 - - - +
111B ASP* 2.7 63.4 + - - +
236B GLY* 3.6 22.2 - - - +
237B GLY* 3.8 23.3 - - - -
238B GLU* 3.6 37.0 + - + +
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Residues in contact with LYS 108 (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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102B LEU* 3.9 26.9 - - + +
105B ASN* 3.3 15.1 + - + +
107B LYS* 1.3 82.3 - - - +
109B ARG* 1.3 60.5 + - - +
111B ASP* 3.9 4.4 - - - +
112B ALA* 3.2 21.1 + - - +
236B GLY 4.6 4.6 + - - +
327B ASP* 4.9 5.9 + - - -
330B THR* 3.5 38.8 - - - +
331B PHE* 3.7 37.2 - - + -
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Residues in contact with ARG 109 (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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105B ASN* 3.0 31.5 + - + +
106B LEU* 3.7 9.2 - - - +
107B LYS 3.2 0.2 - - - -
108B LYS* 1.3 74.7 - - - +
110B ALA* 1.3 66.1 + - - +
112B ALA 3.1 7.4 + - - -
113B ASP 3.2 0.2 + - - -
114B LEU* 3.0 47.3 + - + +
115B ALA 2.8 29.3 + - - +
116B ASP* 5.4 0.6 - - - +
331B PHE* 2.7 53.0 + - + +
333B PRO* 3.6 25.4 - - - +
334B GLY 5.5 0.2 - - - +
335B TRP* 3.9 10.3 - - - +
485B TYR* 3.0 31.7 + - - +
486B MET* 3.5 9.1 - - - -
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Residues in contact with ALA 110 (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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106B LEU 3.0 17.4 + - - +
107B LYS* 3.3 6.5 + - - +
109B ARG* 1.3 76.4 - - - +
111B ASP* 1.3 62.0 + - - +
113B ASP* 2.9 21.8 + - - +
114B LEU 4.3 8.0 + - - -
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Residues in contact with ASP 111 (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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107B LYS* 2.7 61.9 + - - +
108B LYS* 4.0 4.8 - - - +
110B ALA* 1.3 77.0 - - - +
112B ALA* 1.3 57.1 + - - +
113B ASP* 3.1 6.9 + - - +
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Residues in contact with ALA 112 (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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108B LYS 3.2 16.0 + - - +
109B ARG 3.1 6.0 + - - +
111B ASP* 1.3 75.5 - - - +
113B ASP* 1.3 70.4 + - - +
114B LEU* 3.4 9.2 + - + +
331B PHE* 3.7 24.0 - - + -
481B ASN* 5.4 0.2 + - - -
487B LYS* 3.3 37.3 + - - +
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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