Contacts of the helix formed by residues 83 - 90 (chain A) in PDB entry 1HK8
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 ASP 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU 3.4 1.8 + - - -
82A VAL* 1.3 71.7 - - - +
84A LEU* 1.3 62.2 + - - +
85A LYS* 3.8 6.2 + - - +
86A GLY* 3.3 24.6 + - - -
87A MET* 3.2 21.2 + - - +
307A ASP* 3.7 21.7 - - - +
308A GLY 3.8 9.6 - - - +
374A GLY 3.4 16.5 - - - +
375A ALA 3.0 12.7 + - - +
377A GLY* 3.4 22.4 - - - +
379A ARG* 5.6 1.4 + - - -
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Residues in contact with LEU 84 (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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82A VAL* 3.0 13.1 + - + +
83A ASP* 1.3 73.3 - - - +
85A LYS* 1.3 57.6 + - - +
87A MET* 3.7 3.8 - - + -
88A LEU* 2.9 48.2 + - + +
112A MET* 3.7 35.9 - - + -
115A ILE* 3.6 31.0 - - + -
129A PHE* 3.8 29.4 - - + -
132A VAL* 5.1 2.7 - - + -
135A VAL* 4.0 20.4 - - + -
136A LEU* 4.3 11.7 - - + -
307A ASP* 5.4 0.2 - - - +
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Residues in contact with LYS 85 (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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83A ASP* 3.2 7.3 - - - +
84A LEU* 1.3 78.9 - - - +
86A GLY* 1.3 58.1 + - - +
88A LEU* 3.9 2.4 - - - +
89A GLU* 2.8 71.2 + - + +
134A LYS 6.1 0.4 - - - -
135A VAL* 4.0 37.7 - - + +
139A TYR* 5.0 0.2 + - - -
307A ASP* 5.3 7.6 - - - +
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Residues in contact with GLY 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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83A ASP* 3.3 22.3 + - - -
85A LYS* 1.3 78.9 - - - +
87A MET* 1.3 63.4 + - - +
89A GLU* 4.6 4.9 - - - -
90A ASN* 2.6 37.4 + - - +
374A GLY 5.8 0.2 - - - -
379A ARG* 4.0 9.2 + - - -
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Residues in contact with MET 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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82A VAL* 4.0 14.1 - - - -
83A ASP 3.2 15.8 + - - +
84A LEU* 3.7 8.5 - - - +
85A LYS 3.2 1.0 - - - -
86A GLY* 1.3 77.6 - - - +
88A LEU* 1.3 56.8 - - - +
90A ASN 2.9 21.1 - - - +
91A GLY 3.5 2.6 - - - +
92A PHE* 3.3 55.4 - - + -
115A ILE* 3.9 20.2 - - + -
369A ILE* 3.8 19.5 - - + -
373A GLU 3.7 9.9 - - - +
374A GLY* 3.7 15.5 - - - -
375A ALA* 3.6 24.0 - - - +
379A ARG* 4.6 5.4 - - - +
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Residues in contact with LEU 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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84A LEU* 2.9 43.8 + - + +
85A LYS* 4.0 2.0 - - - +
87A MET* 1.3 74.9 - - - +
89A GLU* 1.3 54.7 + - - +
90A ASN 3.1 4.7 - - - +
92A PHE* 4.3 9.4 - - + -
100A GLU 4.7 0.3 - - - -
101A THR* 2.8 36.7 + - - -
102A PRO* 4.2 21.3 - - + -
108A ALA* 4.6 5.4 - - + +
111A ILE* 3.8 31.0 - - + -
135A VAL* 5.0 2.7 - - + -
136A LEU* 4.1 16.2 - - + -
139A TYR* 3.4 35.7 - - + +
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Residues in contact with GLU 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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85A LYS* 2.8 61.5 + - + +
86A GLY* 4.6 4.2 - - - -
88A LEU* 1.3 76.4 - - - +
90A ASN* 1.3 68.3 + - - +
101A THR* 2.7 20.5 + - - +
139A TYR* 4.2 11.2 - - - +
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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 GLY* 2.6 34.8 + - - +
87A MET 2.9 12.5 - - - +
88A LEU 3.1 9.9 - - - +
89A GLU* 1.3 85.6 + - - +
91A GLY* 1.3 68.3 + - - +
92A PHE* 4.9 0.3 - - - -
99A ILE 4.7 0.5 - - - +
100A GLU 4.8 0.3 - - - -
101A THR* 3.9 7.9 + - - -
379A ARG* 4.4 11.4 - - - +
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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