Contacts of the helix formed by residues 160 - 166 (chain C) in PDB entry 2NRA
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 LEU 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C VAL 5.2 1.3 - - - +
10C ASN 5.1 3.6 - - - +
13C THR* 3.1 30.0 + - - +
15C ILE* 4.0 14.8 - - + -
37C TYR* 3.7 35.0 - - + +
38C MET* 3.9 5.8 - - + -
41C ALA* 3.7 17.9 - - + -
65C LEU* 3.5 34.8 - - + -
158C GLN 3.6 3.2 + - - -
159C LEU* 1.3 70.0 - - - +
161C THR* 1.3 59.4 + - - +
163C SER* 3.1 8.5 + - - -
164C LEU* 2.9 53.2 + - + +
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Residues in contact with THR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LYS* 3.3 34.6 - - + +
13C THR 4.8 0.6 + - - +
65C LEU* 3.4 14.1 + - - -
159C LEU* 4.8 12.8 - - + -
160C LEU* 1.3 88.2 - - - +
162C ALA* 1.3 63.4 + - + +
164C LEU* 3.4 4.0 + - - +
165C ARG* 3.2 57.8 + - - +
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C LEU* 3.1 14.4 + - + +
161C THR* 1.3 77.8 - - + +
163C SER* 1.3 65.9 + - - +
164C LEU 3.0 2.4 + - - -
165C ARG* 3.0 11.8 + - - +
166C LEU* 3.4 19.1 + - - +
175C TYR* 3.7 19.1 - - + +
238C LYS 4.3 11.2 - - - +
239C THR* 3.9 28.3 - - + -
240C GLU* 4.4 3.6 - - + +
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.9 4.0 - - - +
33C LYS* 5.9 0.7 - - - +
34C ARG* 5.3 1.7 + - - +
37C TYR* 3.5 39.5 - - - -
158C GLN* 2.8 25.7 + - - +
159C LEU 2.9 16.3 + - - -
160C LEU* 3.3 12.6 - - - -
162C ALA* 1.3 75.9 - - - +
164C LEU* 1.3 61.2 + - - +
166C LEU* 3.8 12.4 + - - +
172C SER* 4.7 4.0 + - - -
175C TYR* 3.7 10.3 - - - -
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ARG* 2.8 72.9 + - + +
37C TYR* 4.3 12.1 - - + -
38C MET* 3.4 31.0 - - + -
62C LEU* 4.4 6.5 - - + -
65C LEU* 3.7 23.8 - - + +
66C ALA* 3.7 16.9 - - + +
160C LEU* 2.9 28.1 + - + +
161C THR 3.8 4.9 - - - +
162C ALA 3.0 0.4 - - - -
163C SER* 1.3 78.9 - - - +
165C ARG* 1.3 60.6 + - - +
166C LEU 3.2 0.2 - - - -
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A G 4.9 0.2 + - - -
11C LYS* 6.3 1.4 - - - +
34C ARG* 4.0 3.4 + - - +
64C ALA 4.8 2.2 + - - -
65C LEU 3.4 11.5 + - - -
66C ALA* 3.8 21.1 - - - +
67C LYS* 3.3 45.7 - - + +
161C THR* 3.2 38.3 + - - +
162C ALA 3.0 6.9 + - - +
164C LEU* 1.3 78.6 - - - +
166C LEU* 1.3 61.2 + - - +
167C SER* 3.5 3.0 + - - -
238C LYS* 2.8 55.4 + - + +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ALA 3.4 17.5 - - - +
163C SER* 3.8 5.3 + - - +
164C LEU 3.2 4.2 - - - -
165C ARG* 1.3 78.5 - - - +
167C SER* 1.3 64.4 + - - +
168C SER 3.1 1.4 + - - -
171C SER* 3.9 10.5 - - - +
172C SER* 3.6 28.9 - - - +
175C TYR* 3.6 38.8 - - + -
234C GLU* 2.4 61.6 - - + +
235C ILE* 4.7 2.7 - - + -
238C LYS* 4.1 17.9 - - + -
239C THR* 4.2 11.9 - - + -
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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