Contacts of the helix formed by residues 21 - 28 (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 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C HIS* 4.0 14.1 - - + -
18C ARG 2.8 13.3 + - - +
19C ASN 2.7 2.0 + - - -
20C GLU* 1.3 78.1 - - - +
22C ASN* 1.3 64.4 + - - +
23C HIS 3.3 2.7 - - - -
24C THR* 3.1 35.4 + - + +
25C LEU* 3.2 31.1 + - + +
36C MET* 4.9 7.9 - - + -
40C LEU* 5.5 2.0 - - + -
89C ILE* 4.1 9.4 - - + -
141C ILE* 3.9 32.5 - - + -
144C TYR* 4.0 32.5 - - + +
145C ILE* 5.5 1.8 - - + -
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Residues in contact with ASN 22 (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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17C HIS* 2.8 27.0 + - - -
18C ARG 3.6 0.7 - - - +
19C ASN* 2.9 17.1 + - - +
20C GLU 3.5 0.2 - - - -
21C LEU* 1.3 76.4 - - - +
23C HIS* 1.3 64.1 + - - +
25C LEU* 3.1 4.2 + - - +
26C ALA* 3.0 20.1 + - - +
156C THR* 3.3 21.4 + - - -
176C GLN* 3.1 40.6 - - - +
177C LEU* 5.6 1.0 - - - +
180C LYS* 4.0 20.7 - - - +
201C GLU* 5.4 8.1 + - - +
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Residues in contact with HIS 23 (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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19C ASN 4.8 0.2 + - - -
20C GLU 4.8 3.8 + - - +
21C LEU 3.3 0.6 - - - -
22C ASN* 1.3 78.3 - - - +
24C THR* 1.3 61.4 + - - +
26C ALA* 3.3 5.5 + - + +
27C GLN* 2.8 52.3 + - - +
90C SER* 2.8 33.0 + - - +
92C ARG* 3.4 41.2 + - + +
200C GLU* 4.2 7.8 + - - +
201C GLU* 5.4 2.9 - - - -
203C ILE* 3.4 17.5 - - + +
205C TYR* 3.1 26.2 + - - -
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Residues in contact with THR 24 (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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20C GLU 4.9 1.0 + - - -
21C LEU* 3.1 27.4 + - + +
23C HIS* 1.3 80.4 + - - +
25C LEU* 1.3 67.0 + - + +
27C GLN* 3.3 16.1 + - + +
28C LEU* 3.5 10.1 + - + +
88C LYS 3.4 24.2 - - - +
89C ILE* 3.7 14.5 - - - +
90C SER* 2.9 31.2 + - - -
120C ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 25 (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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17C HIS* 3.5 38.6 - - + +
21C LEU* 3.2 30.5 + - + +
22C ASN 3.1 5.2 + - - +
24C THR* 1.3 78.8 - - + +
26C ALA* 1.3 62.7 + - - +
28C LEU* 2.9 27.7 + - + +
33C LYS* 3.1 15.4 + - - -
36C MET* 3.6 33.2 - - + -
37C TYR* 4.2 21.8 - - + +
40C LEU* 5.0 3.1 - - + -
176C GLN* 3.5 15.7 - - - +
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Residues in contact with ALA 26 (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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22C ASN 3.0 13.8 + - - +
23C HIS* 3.7 10.8 - - - +
24C THR 3.3 0.2 - - - -
25C LEU* 1.3 76.1 - - - +
27C GLN* 1.3 62.8 + - - +
33C LYS* 3.1 20.8 + - - +
169C GLN* 3.6 12.1 - - - +
173C SER* 3.4 24.9 + - - +
176C GLN* 4.5 6.8 + - - +
201C GLU 4.3 5.6 - - - +
203C ILE* 3.9 24.4 - - + +
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Residues in contact with GLN 27 (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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23C HIS* 2.8 52.0 + - - +
24C THR* 3.3 11.9 - - + +
26C ALA* 1.3 76.1 - - - +
28C LEU* 1.3 61.4 + - + +
29C PRO* 3.3 8.7 - - - +
90C SER* 3.3 27.8 + - - -
169C GLN* 5.5 0.9 - - - -
203C ILE* 3.8 15.9 - - + +
205C TYR* 4.5 6.1 + - - -
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Residues in contact with LEU 28 (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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24C THR* 3.5 10.5 - - + +
25C LEU* 2.9 45.2 + - + +
27C GLN* 1.3 75.5 - - + +
29C PRO* 1.3 73.5 - - + +
32C ALA* 4.2 5.8 - - + -
33C LYS* 2.9 29.6 + - + +
36C MET* 4.4 10.3 - - + -
84C LEU* 4.0 15.0 - - + -
87C SER* 3.4 35.0 - - - +
120C ILE* 4.1 9.2 - - + -
169C GLN* 2.8 22.1 - - - +
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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