Contacts of the helix formed by residues 104 - 108 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24T ILE* 3.9 32.3 - - + -
27T ARG* 3.5 29.9 - - + +
28T PHE* 3.8 29.6 - - + -
90T MET* 3.0 20.5 + - + +
91T LEU* 4.0 18.4 - - + +
103T THR* 1.3 68.5 - - - +
105T ARG* 1.3 58.8 + - - +
108T PHE* 3.0 41.5 + - + +
116T ILE* 3.6 20.6 - - + -
117T ILE* 4.1 14.1 - - + -
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Residues in contact with ARG 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T LYS* 4.8 0.4 - - - +
88T ARG* 5.8 4.0 - - - +
91T LEU* 3.0 35.2 + - - +
92T GLY 3.1 24.0 + - - -
93T GLU 3.0 17.8 + - - -
94T THR* 3.6 25.5 + - - +
96T PRO* 4.2 4.1 - - + +
99T SER* 3.4 12.8 - - - +
104T ILE* 1.3 76.6 - - - +
106T GLY* 1.3 62.9 + - - +
109T CYS* 3.0 41.3 + - - +
115T ASN* 3.3 44.1 + - - +
116T ILE* 4.6 0.4 - - + -
117T ILE* 2.6 39.2 + - + +
118T HIS* 4.2 6.3 - - - +
119T GLY 4.8 1.0 - - - +
31U LYS* 3.7 0.5 + - - -
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Residues in contact with GLY 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99T SER* 3.5 23.1 - - - +
100T LYS 3.7 5.6 - - - -
101T PRO* 4.3 8.9 - - - +
103T THR* 3.0 21.8 + - - -
105T ARG* 1.3 78.2 - - - +
107T ASP* 1.3 61.5 + - - +
31U LYS* 3.1 23.9 + - - +
90U MET* 5.3 3.8 - - - +
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Residues in contact with ASP 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ARG* 2.7 34.7 + - - +
101T PRO* 3.9 3.8 - - - +
102T GLY* 2.9 29.4 + - - -
103T THR 2.7 15.6 + - - +
106T GLY* 1.3 76.7 - - - +
108T PHE* 1.3 79.5 + - + +
109T CYS 3.9 0.4 - - - -
27U ARG 4.5 0.3 - - - +
30U GLN* 3.3 18.4 - - - +
31U LYS* 3.3 24.1 + - - +
102U GLY 5.0 2.4 - - - +
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Residues in contact with PHE 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ARG* 2.7 34.1 + - - -
20T LEU* 3.5 37.9 - - + -
23T GLU* 4.0 29.2 - - + -
24T ILE* 5.4 2.9 - - + -
27T ARG* 3.3 41.5 - - - -
104T ILE* 3.0 37.1 + - + +
107T ASP* 1.3 84.9 - - + +
109T CYS* 1.3 58.0 + - - +
116T ILE* 3.7 4.5 - - + -
30U GLN* 3.2 43.3 - - + +
31U LYS 3.7 3.6 - - - -
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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