Contacts of the helix formed by residues 101 - 106 (chain B) in PDB entry 5NXR
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 VAL 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 3.2 0.6 - - - -
100B VAL* 1.3 78.0 - - + +
102B TYR* 1.3 59.1 + - - +
103B ASP 3.5 0.2 + - - -
104B THR 4.0 1.0 + - - -
119B MET* 3.9 22.0 - - + -
126B MET* 3.2 20.6 - - + +
127B THR* 4.5 5.2 - - - +
193B GLY* 5.0 3.6 - - - +
194B TYR* 4.0 6.1 - - - +
195B SER* 3.6 37.7 - - - +
225B ALA* 3.8 22.7 - - + +
226B TRP* 4.5 0.9 - - - -
227B ASN* 2.7 50.3 + - - +
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 3.5 44.3 + + + -
99B GLY 2.9 14.4 + - - +
101B VAL* 1.3 77.9 - - - +
103B ASP* 1.3 66.3 + - - +
105B ASN* 2.8 23.6 + - + +
106B ALA* 2.9 41.5 + - + +
109B ASP* 2.8 36.8 + - + +
120B ALA* 3.7 28.7 - - + -
126B MET 3.6 2.0 + - - -
127B THR 3.2 18.5 + - - +
128B SER* 3.9 10.5 - - - -
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 4.8 6.6 - - - +
99B GLY 3.7 8.1 - - - +
100B VAL* 3.1 17.5 + - - +
102B TYR* 1.3 79.6 - - - +
104B THR* 1.3 61.2 + - - +
106B ALA* 3.4 17.2 - - - +
107B TRP* 4.0 12.0 + - - -
137B ARG* 2.8 42.1 + - - -
179B SER* 2.7 27.7 + - - +
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL 4.5 0.4 + - - -
101B VAL 4.0 2.0 + - - -
102B TYR 3.2 0.4 - - - -
103B ASP* 1.3 76.4 - - - +
105B ASN* 1.3 64.7 + - - +
106B ALA 3.2 0.2 - - - -
107B TRP* 3.1 40.9 + - + +
108B THR 4.4 1.0 + - - -
179B SER* 5.1 0.3 - - - -
180B THR 4.8 1.2 + - - -
191B GLY* 3.7 9.1 - - - +
192B GLY* 3.3 28.7 + - - +
193B GLY* 3.7 1.0 + - - -
227B ASN* 3.7 15.8 + - - -
228B VAL 4.0 4.9 - - - +
229B GLY* 3.6 34.5 - - - +
242B MET* 4.7 8.7 - - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 2.8 27.0 + - + +
104B THR* 1.3 73.6 - - - +
106B ALA* 1.3 63.1 + - - +
107B TRP 3.1 2.5 - - - -
108B THR* 3.1 13.2 + - - -
109B ASP* 3.1 6.6 + - - +
116B ALA* 4.2 11.3 - - - +
119B MET* 3.9 9.7 - - - +
120B ALA* 3.7 30.3 + - - +
127B THR 5.2 0.6 - - - +
227B ASN* 3.9 8.0 - - - +
242B MET* 3.6 24.1 - - - +
266B GLU* 2.9 29.3 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 2.9 38.0 + - + +
103B ASP* 3.4 16.8 - - - +
104B THR 3.2 0.2 - - - -
105B ASN* 1.3 75.3 - - - +
107B TRP* 1.3 68.6 + - + +
109B ASP* 3.2 18.2 + - - +
110B VAL* 4.0 5.0 - - - +
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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