Contacts of the helix formed by residues 83 - 91 (chain N) in PDB entry 1NSK
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 VAL 83 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5N GLU* 3.5 1.7 + - + -
6N ARG 3.4 23.3 - - - +
7N THR* 3.9 17.3 - - + +
28N PHE* 5.4 2.0 - - + -
33N PHE* 3.7 32.1 - - + -
78N TRP* 3.5 29.2 - - + +
80N GLY 2.8 33.3 + - - +
81N LEU 3.4 1.4 - - - -
82N ASN* 1.3 71.7 - - - +
84N VAL* 1.3 54.2 + - - +
86N THR* 3.9 5.8 - - - -
87N GLY* 2.7 32.6 + - - -
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Residues in contact with VAL 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N GLU* 3.0 19.0 + - - +
6N ARG 3.2 21.1 - - - +
7N THR* 3.3 16.2 - - - +
82N ASN 3.0 0.2 + - - -
83N VAL* 1.3 75.9 - - - +
85N LYS* 1.3 62.1 + - + +
87N GLY* 4.1 0.2 - - - -
88N ARG* 2.9 34.5 + - - +
120N SER 3.4 19.7 - - - +
121N ASP 4.0 3.1 - - - +
122N SER* 3.6 26.7 - - - +
123N VAL* 4.0 11.0 - - + +
126N ALA* 4.0 11.4 - - + -
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Residues in contact with LYS 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N GLU* 5.5 0.2 + - - -
82N ASN* 3.1 33.8 + - - +
84N VAL* 1.3 82.6 - - - +
86N THR* 1.3 66.4 + - + +
88N ARG* 3.3 6.0 + - - +
89N VAL* 3.2 29.0 + - + +
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Residues in contact with THR 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L PRO 5.7 0.9 - - - +
97L ALA* 4.9 21.8 - - + +
110L ILE* 5.9 3.8 - - + -
31N LYS* 4.9 11.9 - - - +
33N PHE* 3.0 31.8 - - + -
81N LEU 4.8 1.6 - - - +
82N ASN* 3.1 26.0 + - + +
85N LYS* 1.3 77.7 - - + +
87N GLY* 1.3 66.5 + - - +
89N VAL* 2.9 14.5 + - + +
90N MET* 2.9 27.1 + - - +
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Residues in contact with GLY 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ILE* 5.2 5.8 - - - -
28N PHE* 4.2 20.4 - - - -
33N PHE* 4.8 1.3 - - - -
83N VAL 2.7 26.8 + - - -
84N VAL 4.1 0.2 - - - -
86N THR* 1.3 76.6 + - - +
88N ARG* 1.3 60.5 + - - +
90N MET* 3.1 8.8 + - - +
91N LEU* 3.0 30.6 + - - +
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Residues in contact with ARG 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N VAL* 2.9 23.9 + - - +
85N LYS* 3.7 5.6 - - - +
86N THR 3.2 0.8 - - - -
87N GLY* 1.3 75.7 - - - +
89N VAL* 1.3 59.2 + - + +
91N LEU* 3.0 12.3 + - - +
92N GLY 2.9 34.0 + - - +
94N THR* 3.9 21.7 + - - +
105N ARG* 5.8 4.6 - - - +
118N HIS* 5.8 0.8 + - - -
119N GLY* 3.3 22.9 + - - +
120N SER 2.9 24.9 + - - +
121N ASP* 3.7 31.2 + - - +
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Residues in contact with VAL 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L SER 5.3 3.1 - - - +
100L LYS* 5.3 7.2 - - + -
101L PRO* 3.6 26.4 - - + +
85N LYS* 3.2 22.5 + - + +
86N THR* 2.9 16.6 + - + +
88N ARG* 1.3 75.2 - - + +
90N MET* 1.3 61.4 - - + +
92N GLY* 3.2 11.1 + - - +
103N THR* 3.3 14.6 - - - +
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Residues in contact with MET 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L PRO* 4.1 15.9 - - + -
106L GLY 5.2 4.3 - - - +
27N ARG* 3.9 36.3 + - + +
28N PHE* 4.0 27.1 - - + +
31N LYS* 3.9 20.2 - - + +
33N PHE* 3.6 30.3 - - - -
86N THR* 2.9 17.5 + - - +
87N GLY* 3.3 7.2 - - - +
89N VAL* 1.3 78.3 - - + +
91N LEU* 1.3 60.4 + - + +
103N THR* 3.4 6.4 - - - -
104N ILE* 3.0 30.8 + - + +
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Residues in contact with LEU 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N ILE* 4.4 2.7 - - + -
28N PHE* 3.6 26.0 - - + -
87N GLY 3.0 23.1 + - - +
88N ARG* 3.0 15.5 + - + +
90N MET* 1.3 78.5 - - - +
92N GLY* 1.3 57.4 + - - +
103N THR* 4.1 0.7 - - - -
104N ILE* 4.0 9.9 - - + -
105N ARG* 3.0 51.0 + - - +
117N ILE* 3.7 31.2 - - + -
118N HIS* 3.6 7.4 - - - +
119N GLY* 3.3 39.0 - - - +
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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