Contacts of the helix formed by residues 105 - 112 (chain Q) in PDB entry 1HI0
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102Q LEU* 4.2 14.8 - - + -
104Q SER* 1.3 72.7 + - - +
106Q LEU* 1.3 74.7 + - - +
107Q LYS 3.3 2.9 - - - -
108Q LYS* 3.2 7.1 + - + +
109Q ARG* 2.8 35.8 + - + +
330Q THR 2.8 30.2 + - - +
331Q PHE 3.6 7.7 + - - -
332Q TRP 3.2 24.0 + - - -
334Q GLY 5.0 2.3 + - - +
388Q GLU* 2.8 24.4 + - - +
389Q VAL* 4.9 2.0 - - - -
390Q GLY* 3.7 8.1 - - - -
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Residues in contact with LEU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q SER* 3.4 19.0 + - - +
105Q ASN* 1.3 89.1 + - - +
107Q LYS* 1.3 57.9 + - - +
109Q ARG* 3.3 11.4 + - - +
110Q ALA* 2.9 28.7 + - - +
116Q ASP* 6.6 0.2 - - + -
334Q GLY* 5.5 4.7 - - - +
335Q TRP* 6.2 2.5 - - + +
388Q GLU* 4.3 23.8 - - + +
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Residues in contact with LYS 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q SER* 5.0 1.6 + - - -
105Q ASN 3.3 0.4 - - - -
106Q LEU* 1.3 74.2 - - - +
108Q LYS* 1.3 71.3 + - - +
110Q ALA* 3.0 6.3 + - - -
111Q ASP* 2.7 62.7 + - - +
236Q GLY* 3.7 18.8 - - - +
237Q GLY* 3.7 27.1 - - - -
238Q GLU* 3.7 34.9 + - + +
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Residues in contact with LYS 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q LEU* 4.0 26.7 - - + -
105Q ASN 3.2 12.2 + - - +
107Q LYS* 1.3 81.5 - - - +
109Q ARG* 1.3 61.4 + - - +
111Q ASP* 4.1 6.1 - - - +
112Q ALA* 3.2 20.1 + - - +
232Q TYR* 6.1 1.1 - - + +
236Q GLY 4.2 5.9 + - - +
327Q ASP* 3.9 9.1 + - - +
330Q THR* 3.3 30.7 - - - +
331Q PHE* 3.3 40.8 - - + -
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Residues in contact with ARG 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Q ASN* 2.8 29.2 + - - +
106Q LEU* 3.5 11.4 - - - +
108Q LYS* 1.3 74.8 - - - +
110Q ALA* 1.3 65.4 + - - +
112Q ALA* 3.1 9.9 + - - +
113Q ASP 3.1 0.3 + - - -
114Q LEU* 3.1 40.4 + - + +
115Q ALA 3.1 27.3 + - - -
116Q ASP* 5.5 0.6 - - - +
331Q PHE* 2.7 53.9 + - + +
333Q PRO* 3.7 25.4 - - - +
335Q TRP* 3.9 10.9 - - - +
485Q TYR* 2.8 34.0 + - - +
486Q MET* 3.5 12.3 - - - -
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Residues in contact with ALA 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q LEU 2.9 17.4 + - - +
107Q LYS* 3.0 7.2 + - - +
109Q ARG* 1.3 73.3 - - - +
111Q ASP* 1.3 61.5 + - - +
112Q ALA 2.9 1.6 - - - -
113Q ASP* 2.6 29.3 + - - +
114Q LEU 4.5 7.9 - - - -
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Residues in contact with ASP 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Q LYS* 2.7 60.8 + - - +
108Q LYS* 4.1 5.1 - - - +
110Q ALA* 1.3 76.2 - - - +
112Q ALA* 1.3 58.9 + - - +
113Q ASP* 3.3 7.4 + - - +
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Residues in contact with ALA 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q LYS 3.2 17.7 + - - +
109Q ARG 3.1 6.7 + - - +
110Q ALA 2.9 1.2 + - - -
111Q ASP* 1.3 75.5 - - - +
113Q ASP* 1.3 69.6 - - - +
114Q LEU* 3.7 14.3 + - + +
331Q PHE* 3.9 20.6 - - + -
481Q ASN* 5.6 0.5 + - - -
487Q LYS* 3.9 30.1 + - - +
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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