Contacts of the helix formed by residues 104 - 108 (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 ILE 104 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24N ILE* 3.8 43.5 - - + +
27N ARG* 3.5 28.8 - - + +
28N PHE* 3.8 20.6 - - + -
90N MET* 3.0 20.7 + - + +
91N LEU* 4.0 16.4 - - + +
103N THR* 1.3 69.9 - - - +
105N ARG* 1.3 60.5 + - - +
108N PHE* 2.9 41.0 + - + +
116N ILE* 3.6 20.2 - - + -
117N ILE* 4.0 15.0 - - + -
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Residues in contact with ARG 105 (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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12N LYS* 4.9 0.6 - - - +
88N ARG* 5.8 4.2 - - - +
91N LEU* 3.0 39.9 + - - +
92N GLY 3.2 23.0 + - - -
93N GLU 2.9 16.9 + - - -
94N THR* 3.6 25.7 + - - +
96N PRO* 4.3 4.2 - - + +
99N SER* 3.4 13.0 - - - +
104N ILE* 1.3 75.9 - - - +
106N GLY* 1.3 63.5 + - - +
109N CYS* 3.0 42.1 + - - +
115N ASN* 3.3 42.5 + - - +
116N ILE* 4.4 1.1 - - + -
117N ILE* 2.6 38.8 + - + +
118N HIS* 4.2 6.1 - - - +
119N GLY 4.8 1.2 - - - +
31O LYS* 3.8 0.2 + - - -
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Residues in contact with GLY 106 (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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99N SER* 3.4 20.5 - - - +
100N LYS 3.6 9.0 - - - -
101N PRO* 4.4 8.3 - - - +
103N THR* 3.0 21.4 + - - -
105N ARG* 1.3 78.5 - - - +
107N ASP* 1.3 61.9 + - - +
31O LYS* 3.0 23.5 + - - +
90O MET* 5.3 4.3 - - - +
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Residues in contact with ASP 107 (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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27N ARG* 2.8 40.8 + - - +
101N PRO* 3.9 4.5 - - - +
102N GLY* 2.9 28.0 + - - -
103N THR 2.8 14.4 + - - +
104N ILE 3.9 2.0 - - - +
106N GLY* 1.3 80.4 - - - +
108N PHE* 1.3 69.1 + - + +
109N CYS 3.9 0.4 - - - -
27O ARG 4.6 0.7 - - - +
30O GLN* 3.4 18.5 - - - +
31O LYS* 3.4 23.0 + - - +
102O GLY 5.0 2.6 - - - +
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Residues in contact with PHE 108 (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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18N ARG* 2.7 35.2 + - - -
20N LEU* 3.5 41.3 - - + -
23N GLU* 3.9 30.1 - - + -
24N ILE* 5.3 2.2 - - + -
27N ARG* 3.2 42.2 - - - -
104N ILE* 2.9 36.7 + - + +
107N ASP* 1.3 84.8 - - + +
109N CYS* 1.3 56.9 + - - +
116N ILE* 3.7 4.7 - - + -
30O GLN* 3.2 43.2 - - + +
31O LYS 3.4 3.7 - - - +
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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