Contacts of the helix formed by residues 104 - 108 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24L ILE* 3.5 45.8 - - + -
27L ARG* 3.5 30.8 - - + +
28L PHE* 3.8 20.4 - - + -
90L MET* 3.0 19.8 + - + +
91L LEU* 4.1 11.4 - - + +
103L THR* 1.3 70.7 - - - +
105L ARG* 1.3 61.2 + - - +
108L PHE* 2.9 39.7 + - + +
116L ILE* 3.8 20.0 - - + -
117L ILE* 4.0 19.3 - - + -
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Residues in contact with ARG 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LYS* 4.9 0.6 - - - +
88L ARG* 5.7 4.4 - - - +
91L LEU* 3.0 33.1 + - - +
92L GLY 2.9 24.9 + - - -
93L GLU 2.9 19.1 + - - -
94L THR* 3.5 19.8 + - - +
96L PRO* 4.4 3.9 - - + +
99L SER* 3.4 12.8 - - - +
104L ILE* 1.3 76.5 - - - +
106L GLY* 1.3 62.8 + - - +
109L CYS* 3.0 44.1 + - - +
115L ASN* 3.3 47.8 + - - +
116L ILE* 4.5 0.9 - - + -
117L ILE* 2.8 37.8 + - + +
118L HIS* 4.3 6.1 - - - +
119L GLY 4.9 0.8 - - - +
31N LYS* 3.6 0.2 + - - -
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Residues in contact with GLY 106 (chain L).
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* 3.4 19.1 - - - +
100L LYS 3.7 9.6 - - - -
101L PRO* 4.4 8.7 - - - +
103L THR* 3.0 22.4 + - - -
105L ARG* 1.3 77.8 - - - +
107L ASP* 1.3 62.0 + - - +
31N LYS* 3.0 23.4 + - - +
90N MET* 5.2 4.9 - - - +
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Residues in contact with ASP 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ARG* 3.0 34.4 + - - +
101L PRO* 3.8 4.5 - - - +
102L GLY* 2.8 31.6 + - - -
103L THR 2.8 19.6 + - - +
104L ILE 3.9 2.5 - - - +
106L GLY* 1.3 80.7 - - - +
108L PHE* 1.3 68.1 + - + +
109L CYS 4.0 0.4 - - - -
27N ARG 4.5 0.7 - - - +
30N GLN* 3.4 18.9 - - - +
31N LYS* 3.4 22.1 + - - +
102N GLY 4.8 3.3 - - - +
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Residues in contact with PHE 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ARG* 2.7 36.4 + - - -
20L LEU* 3.5 39.3 - - + -
23L GLU* 4.1 28.5 - - + -
24L ILE* 5.3 2.9 - - + -
27L ARG* 3.1 43.5 - - - -
104L ILE* 2.9 37.8 + - + +
107L ASP* 1.3 85.0 - - + +
109L CYS* 1.3 56.5 + - - +
116L ILE* 3.6 5.4 - - + -
30N GLN* 3.3 41.7 - - + +
31N LYS 3.7 3.8 - - - -
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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