Contacts of the helix formed by residues 94 - 103 (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 ASP 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C GLY* 1.3 73.5 - - - +
95C ASP* 1.3 54.7 + - - +
96C ILE 3.0 5.4 - - - -
97C ILE* 3.0 31.1 + - + +
98C ALA* 3.4 5.2 + - - +
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Residues in contact with ASP 95 (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* 4.7 16.2 - - + +
91C LEU* 4.0 25.7 - - + +
92C ARG 4.1 15.3 - - - +
93C GLY 3.4 1.9 - - - +
94C ASP* 1.3 78.7 - - - +
96C ILE* 1.3 54.8 + - - +
97C ILE 3.3 0.2 - - - -
98C ALA* 3.5 10.5 - - - +
99C LEU* 3.3 22.5 + - - +
144C TYR* 4.5 3.3 + - - -
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Residues in contact with ILE 96 (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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91C LEU* 4.6 17.0 - - + +
93C GLY* 3.0 23.5 + - - +
94C ASP 3.0 0.6 - - - -
95C ASP* 1.3 79.1 - - - +
97C ILE* 1.3 62.8 + - - +
99C LEU* 3.9 7.0 - - - +
100C ALA* 3.2 25.1 + - - +
116C LEU* 6.3 3.1 - - + -
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Residues in contact with ILE 97 (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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93C GLY 3.7 2.2 + - - +
94C ASP* 3.0 21.2 + - + +
96C ILE* 1.3 76.5 - - - +
98C ALA* 1.3 68.5 + - - +
100C ALA* 3.6 4.9 + - - +
101C LYS* 3.3 19.2 + - - +
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Residues in contact with ALA 98 (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* 5.1 11.2 - - + +
94C ASP 3.4 5.4 + - - +
95C ASP* 3.5 15.0 - - - +
97C ILE* 1.3 81.9 - - - +
99C LEU* 1.3 65.2 + - - +
101C LYS* 3.0 3.7 + - - +
102C GLU* 2.9 37.6 + - + +
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Residues in contact with LEU 99 (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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91C LEU* 4.0 15.5 - - + -
95C ASP 3.3 9.7 + - - +
96C ILE* 3.9 5.8 - - + +
97C ILE 3.4 0.2 - - - -
98C ALA* 1.3 78.3 - - - +
100C ALA* 1.3 63.7 + - - +
102C GLU* 3.1 14.4 + - - +
103C LEU* 2.9 60.1 + - + +
116C LEU* 4.0 17.3 - - + -
118C LEU* 4.9 3.1 - - + -
140C THR* 3.8 23.6 - - + +
143C PRO* 4.4 6.7 - - + -
144C TYR* 3.4 37.7 - - + +
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Residues in contact with ALA 100 (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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96C ILE 3.2 16.5 + - - +
97C ILE* 3.8 5.2 - - - +
99C LEU* 1.3 81.8 - - - +
101C LYS* 1.3 58.7 + - - +
103C LEU* 3.6 2.9 + - - +
104C ASN* 2.5 36.2 + - - +
116C LEU* 5.9 6.3 - - + -
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Residues in contact with LYS 101 (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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97C ILE 3.3 7.7 + - - +
98C ALA* 3.0 9.6 + - - +
100C ALA* 1.3 76.0 - - - +
102C GLU* 1.3 68.4 + - - +
104C ASN* 2.8 24.8 + - - +
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Residues in contact with GLU 102 (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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18C ARG* 4.2 27.6 + - - -
20C GLU* 5.7 1.6 - - - +
98C ALA* 2.9 21.6 + - + +
99C LEU* 3.1 36.9 + - + +
101C LYS* 1.3 76.7 - - + +
103C LEU* 1.3 59.7 + - + +
104C ASN 3.1 10.7 + - - +
143C PRO* 4.6 16.3 - - + +
144C TYR* 4.5 7.2 + - - -
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Residues in contact with LEU 103 (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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99C LEU* 2.9 54.2 + - + +
100C ALA* 3.9 5.6 - - - +
101C LYS 3.2 0.2 - - - -
102C GLU* 1.3 71.7 - - - +
104C ASN* 1.3 66.3 + - - +
116C LEU* 4.6 8.7 - - + -
139C ARG* 4.0 20.4 - - + +
140C THR* 4.0 18.2 - - + +
142C GLU* 6.1 0.2 - - - +
143C PRO* 3.8 21.8 - - + -
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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