Contacts of the helix formed by residues 104 - 108 (chain F) in PDB entry 1NUE
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F ILE* 4.2 18.8 - - + -
27F ARG* 3.9 33.2 - - + +
28F PHE* 3.8 29.4 - - + -
90F MET* 2.9 25.1 + - + +
91F LEU* 4.1 16.4 - - + +
103F THR* 1.3 70.2 - - - +
105F ARG* 1.3 63.2 + - - +
108F PHE* 3.1 38.8 + - + +
116F ILE* 3.5 24.7 - - + -
117F ILE* 4.1 16.4 - - + -
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Residues in contact with ARG 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LYS* 3.5 0.7 + - - -
88F ARG* 5.4 2.0 - - - +
91F LEU* 2.9 32.0 + - - +
92F GLY 3.9 8.5 + - - -
93F GLU 3.2 28.2 + - - -
94F THR* 3.5 16.7 - - - +
96F PRO* 4.0 6.1 - - + +
99F SER* 3.8 12.1 - - - +
104F ILE* 1.3 76.5 - - - +
106F GLY* 1.3 63.1 + - - +
109F CYS* 3.2 44.4 + - - +
115F ASN* 3.2 45.0 + - - +
116F ILE* 4.7 0.7 - - + -
117F ILE* 2.7 38.7 + - + +
118F HIS* 4.4 1.0 - - - +
119F GLY 5.1 0.4 - - - +
160F GDP 3.7 20.4 + - - -
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Residues in contact with GLY 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LYS* 3.0 25.7 + - - +
90E MET* 5.4 4.0 - - - +
99F SER* 3.5 16.4 - - - -
100F LYS 3.5 10.5 - - - -
101F PRO* 4.4 7.8 - - - +
103F THR* 3.0 21.6 + - - -
105F ARG* 1.3 79.9 - - - +
107F ASP* 1.3 60.7 + - - +
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Residues in contact with ASP 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG 4.6 1.9 - - - +
30E GLN* 3.8 9.4 + - - +
31E LYS* 3.4 25.5 + - - +
90E MET* 6.0 0.2 - - - +
102E GLY 5.0 1.7 - - - +
27F ARG* 2.8 38.7 + - - +
101F PRO* 3.6 7.4 - - - +
102F GLY* 2.8 27.5 + - - -
103F THR 3.0 14.8 + - - +
104F ILE 4.1 1.8 - - - +
106F GLY* 1.3 79.0 - - - +
108F PHE* 1.3 68.8 + - + +
109F CYS 3.9 0.4 - - - -
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Residues in contact with PHE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLN* 3.5 46.2 - - + +
31E LYS 3.8 3.4 - - - -
18F ARG* 2.7 32.7 + - - -
20F LEU* 3.9 28.7 - - + -
23F GLU* 3.4 29.4 - - + -
24F ILE* 5.0 6.1 - - + -
27F ARG* 3.4 38.4 - - - -
104F ILE* 3.1 35.0 + - + +
107F ASP* 1.3 85.4 - - + +
109F CYS* 1.3 59.1 + - - +
116F ILE* 3.9 15.3 - - + -
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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