Contacts of the helix formed by residues 150 - 158 (chain F) in PDB entry 1NF4
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 GLY 150 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145F HIS 3.4 1.2 + - - -
146F ILE* 2.8 27.2 + - - -
147F LYS 4.6 0.8 + - - -
148F ASN 3.8 0.4 - - - -
149F LEU* 1.3 76.4 - - - +
151F ASP* 1.3 59.4 + - - -
153F TYR* 3.0 20.3 + - - +
154F LEU* 3.3 15.9 + - - +
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Residues in contact with ASP 151 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149F LEU 3.4 1.0 + - - -
150F GLY* 1.3 69.0 - - - -
152F THR* 1.3 62.0 + - - +
154F LEU* 3.7 18.7 - - - +
155F ALA* 2.8 30.1 + - - +
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Residues in contact with THR 152 (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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149F LEU* 3.4 14.3 + - - -
150F GLY 3.1 0.6 - - - -
151F ASP* 1.3 77.9 - - - +
153F TYR* 1.3 63.8 + - - +
155F ALA* 3.6 11.8 + - + +
156F LYS* 3.6 8.8 + - - +
151L ASP* 3.9 15.2 + - + +
152L THR* 3.6 43.7 - - + +
155L ALA* 3.8 14.2 - - + +
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Residues in contact with TYR 153 (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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44F GLU* 5.0 2.8 + - - -
45F LEU* 3.9 9.4 - - + +
142F ILE* 3.3 32.1 - - + +
145F HIS* 3.6 40.5 + + + +
146F ILE* 4.2 17.9 - - + +
149F LEU* 3.7 21.5 + - + +
150F GLY 3.0 9.4 + - - +
152F THR* 1.3 78.9 - - - +
154F LEU* 1.3 76.4 + - + +
156F LYS* 3.1 20.3 + - + +
157F ILE* 3.4 35.1 + - + +
155L ALA* 4.3 11.0 - - - -
158L ALA* 4.0 23.1 - - + -
159L GLY* 5.8 1.7 - - - -
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Residues in contact with LEU 154 (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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42F TYR* 3.6 42.9 - - + +
45F LEU* 4.0 26.9 - - + -
88F VAL* 4.5 23.6 - - + -
146F ILE* 5.0 5.8 - - + -
150F GLY 3.3 11.9 + - - +
151F ASP* 3.4 20.8 + - - +
153F TYR* 1.3 86.6 - - + +
155F ALA* 1.3 65.4 + - - +
157F ILE* 3.0 4.1 + - + +
158F ALA* 2.9 24.6 + - - +
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Residues in contact with ALA 155 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151F ASP 2.8 21.7 + - - +
152F THR* 3.9 9.6 - - + +
153F TYR 3.3 0.4 - - - -
154F LEU* 1.3 72.9 - - - +
156F LYS* 1.3 62.3 + - - +
158F ALA* 3.6 19.3 + - - +
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Residues in contact with LYS 156 (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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152F THR 3.6 8.1 + - - +
153F TYR* 3.1 12.5 + - + +
154F LEU 3.0 0.4 - - - -
155F ALA* 1.3 81.4 - - - +
157F ILE* 1.3 74.1 + - + +
158F ALA 4.3 2.3 - - - +
160F THR* 3.6 13.2 - - - +
155L ALA* 3.4 22.4 - - + +
156L LYS* 3.1 40.2 + - + +
158L ALA 4.0 12.4 + - - -
160L THR* 4.8 6.5 - - - +
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Residues in contact with ILE 157 (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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42F TYR* 3.7 34.9 - - + -
44F GLU* 3.4 28.0 - - + +
45F LEU* 4.0 15.7 - - + +
153F TYR* 3.7 42.4 - - + +
154F LEU* 3.0 8.1 + - - +
156F LYS* 1.3 96.1 - - + +
158F ALA* 1.3 63.7 - - - +
159F GLY 3.4 0.9 + - - -
160F THR* 2.6 37.7 + - + +
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Residues in contact with ALA 158 (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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40F MET 6.0 0.2 - - - +
41F ASP* 3.6 9.0 - - - +
42F TYR* 3.8 14.1 - - + -
154F LEU 2.9 15.3 + - - +
155F ALA* 3.8 16.1 - - - +
156F LYS 3.4 4.5 - - - +
157F ILE* 1.3 75.9 - - - +
159F GLY* 1.3 60.2 + - - +
160F THR* 3.3 2.1 + - - +
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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