Contacts of the helix formed by residues 158 - 162 (chain N) in PDB entry 1N8R
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 ARG 158 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A G 4.3 0.6 + - - -
433A C 2.8 28.7 + - - -
113N ARG* 4.3 4.7 - - + -
114N VAL 2.9 28.6 + - - +
115N LEU 4.5 6.3 + - - -
149N TRP* 3.4 18.8 - - - -
150N ILE* 3.8 19.3 - - - -
155N HIS* 2.6 57.5 + - - +
156N ARG 4.5 0.4 - - - -
157N LEU* 1.3 69.9 - - - +
159N THR* 1.3 65.3 + - - +
161N ARG* 2.9 14.2 + - - +
163N LEU* 3.0 48.0 + - + +
164N THR* 4.2 18.2 + - - +
168N ARG* 4.4 0.4 - - - +
8518N CL 3.2 7.0 - - + +
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Residues in contact with THR 159 (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 ARG* 4.3 10.2 + - + +
102N GLU* 3.8 18.4 - - + +
103N GLU* 4.4 16.1 - - - +
106N ASN* 3.8 5.9 + - - +
114N VAL* 3.1 44.9 - - + +
158N ARG* 1.3 76.7 - - - +
160N PHE* 1.3 67.6 + - - +
162N GLY* 2.7 24.9 + - - +
164N THR* 3.8 15.9 - - - +
8518N CL 3.5 13.1 - - - +
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Residues in contact with PHE 160 (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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156A C 3.7 12.0 + - - +
181A G 2.9 40.3 + - - +
182A G 3.9 23.1 - - - +
103N GLU* 3.9 24.0 - - + -
106N ASN* 3.1 35.7 - - + -
107N ARG* 3.4 51.6 - - + -
157N LEU* 3.0 41.5 + - + +
159N THR* 1.3 77.8 - - - +
161N ARG* 1.3 59.0 + - - +
162N GLY 3.4 0.2 - - - -
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Residues in contact with ARG 161 (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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155A C 2.8 40.1 + - - +
156A C 3.2 16.3 - - - +
181A G 4.2 0.2 - - - +
182A G 3.6 27.7 + - - +
183A A 3.1 41.1 + - - -
187A A 3.6 9.9 + - - -
188A C 3.1 25.2 + - - -
154N ARG 2.6 30.1 + - - -
155N HIS* 3.9 3.0 - - - +
156N ARG 3.1 25.9 + - - +
157N LEU 3.9 2.9 + - - +
158N ARG 2.9 8.1 + - - +
159N THR 2.9 0.8 - - - -
160N PHE* 1.3 81.6 - - - +
162N GLY* 1.3 63.6 + - - +
163N LEU* 3.2 20.7 + - + +
171N ARG* 4.6 0.5 - - - -
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Residues in contact with GLY 162 (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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156A C 4.2 7.8 - - - -
99N ARG* 3.9 19.5 - - - +
159N THR* 2.7 15.1 + - - -
160N PHE 3.4 0.4 - - - -
161N ARG* 1.3 79.6 - - - +
163N LEU* 1.3 59.6 + - - +
164N THR* 3.0 9.1 + - - -
167N GLY* 3.6 4.7 - - - -
168N ARG* 3.5 18.5 + - - +
171N ARG* 3.7 13.9 + - - -
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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