Contacts of the helix formed by residues 104 - 108 (chain U) 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 ILE 104 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24U ILE* 3.8 34.3 - - + -
27U ARG* 3.5 30.2 - - + +
28U PHE* 3.8 29.6 - - + -
90U MET* 3.0 20.3 + - + +
91U LEU* 4.0 16.8 - - + +
103U THR* 1.3 69.0 - - - +
105U ARG* 1.3 60.1 + - - +
108U PHE* 2.9 41.7 + - + +
116U ILE* 3.6 20.0 - - + -
117U ILE* 4.1 13.9 - - + -
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Residues in contact with ARG 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R LYS* 3.6 0.2 + - - -
12U LYS* 4.9 0.4 - - - +
88U ARG* 5.8 3.8 - - - +
91U LEU* 3.0 38.7 + - - +
92U GLY 3.2 23.8 + - - -
93U GLU 2.9 17.6 + - - -
94U THR* 3.6 25.0 + - - +
96U PRO* 4.4 3.9 - - + +
99U SER* 3.3 13.2 - - - +
104U ILE* 1.3 77.7 - - - +
106U GLY* 1.3 63.0 + - - +
109U CYS* 3.0 42.0 + - - +
115U ASN* 3.3 43.3 + - - +
116U ILE* 4.4 0.7 - - + -
117U ILE* 2.7 38.6 + - + +
118U HIS* 4.2 6.5 - - - +
119U GLY 4.8 1.0 - - - +
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Residues in contact with GLY 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R LYS* 3.0 23.5 + - - +
90R MET* 5.2 4.9 - - - +
99U SER* 3.4 20.6 - - - +
100U LYS 3.6 8.5 - - - -
101U PRO* 4.4 8.2 - - - +
103U THR* 3.0 21.6 + - - -
105U ARG* 1.3 78.2 - - - +
107U ASP* 1.3 62.2 + - - +
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Residues in contact with ASP 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R ARG 4.5 0.5 - - - +
30R GLN* 3.6 17.0 - - - +
31R LYS* 3.4 23.3 + - - +
102R GLY 4.9 2.9 - - - +
27U ARG* 2.9 39.8 + - - +
101U PRO* 3.9 4.5 - - - +
102U GLY* 2.9 29.4 + - - -
103U THR 2.7 18.0 + - - +
104U ILE 3.9 2.0 - - - +
106U GLY* 1.3 77.2 - - - +
108U PHE* 1.3 68.8 + - + +
109U CYS 3.9 0.2 - - - -
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Residues in contact with PHE 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R GLN* 3.3 41.5 - - + +
31R LYS 3.3 3.9 - - - +
18U ARG* 2.7 33.6 + - - -
20U LEU* 3.5 40.4 - - + -
23U GLU* 4.0 30.3 - - + -
24U ILE* 5.4 2.2 - - + -
27U ARG* 3.2 42.4 - - - -
104U ILE* 2.9 38.2 + - + +
107U ASP* 1.3 86.2 - - + +
109U CYS* 1.3 58.0 + - - +
116U ILE* 3.7 4.7 - - + -
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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