Contacts of the helix formed by residues 95 - 103 (chain B) in PDB entry 3N2Z
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 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.6 10.3 - - + -
71B ARG* 3.1 21.8 + - - -
94B GLY* 1.3 68.8 - - - -
96B ILE* 1.4 61.4 + - - +
97B ILE* 2.9 44.6 + - - +
98B TRP* 3.0 30.3 + - + +
99B PHE* 3.3 7.8 - - - -
121B GLU* 3.6 5.6 - - - -
126B GLY* 4.1 12.6 - - - +
127B GLU* 5.7 0.2 - - - +
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Residues in contact with ILE 96 (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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71B ARG* 4.2 13.0 - - + +
73B LEU* 4.0 23.6 - - + -
89B TYR* 4.0 16.2 - - + -
91B GLY* 3.8 16.4 - - - -
94B GLY 3.5 2.4 + - - +
95B ASP* 1.4 70.3 + - - +
97B ILE* 1.4 58.0 + - - +
99B PHE* 3.2 15.0 + - + +
100B CYS* 3.0 27.2 + - - +
119B PHE* 3.7 29.2 - - + +
120B ALA 3.4 21.8 - - - +
121B GLU* 2.9 42.4 + - + +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B NAG 3.9 23.3 - - + +
48B TYR* 3.5 26.9 - - + +
50B VAL* 5.5 6.1 - - + -
71B ARG* 3.3 28.9 - - - +
73B LEU* 4.4 14.8 - - + -
95B ASP* 2.9 15.8 + - - +
96B ILE* 1.4 71.8 - - - +
98B TRP* 1.3 54.5 + - - +
100B CYS* 3.0 6.8 + - + +
101B ASN* 2.8 46.1 + - - +
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Residues in contact with TRP 98 (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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1B NAG 3.7 32.8 - - + +
94B GLY* 5.8 0.9 - - - -
95B ASP* 3.0 20.0 + - + +
97B ILE* 1.3 77.9 - - - +
99B PHE* 1.3 85.6 + + - +
101B ASN* 4.4 0.4 - - - -
102B ASN* 2.9 71.8 + - + +
296B ASN 5.8 0.4 - - - -
297B PHE* 3.9 42.0 - + + -
298B LEU* 5.4 7.6 - - + -
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Residues in contact with PHE 99 (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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89B TYR* 3.4 32.8 - + + -
92B ASN* 3.3 50.7 - - - -
93B GLU* 4.2 3.8 - - - -
94B GLY* 3.5 33.4 - - - -
95B ASP 3.3 19.7 + - - -
96B ILE* 3.2 22.2 + - + +
98B TRP* 1.3 93.5 - + - +
100B CYS* 1.3 58.8 + - - +
102B ASN* 5.2 1.8 - - - -
103B THR* 2.5 38.0 + - - -
119B PHE* 3.9 3.9 - - + -
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Residues in contact with CYS 100 (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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48B TYR* 3.8 19.3 - - - -
73B LEU* 3.6 28.5 - - + -
96B ILE 3.0 12.8 + - - +
97B ILE* 3.3 9.2 - - - +
99B PHE* 1.3 77.5 - - - +
101B ASN* 1.4 62.9 + - - +
102B ASN 3.3 0.7 + - - -
103B THR 3.7 4.5 + - - -
107B TRP* 3.2 53.3 + - - -
119B PHE* 3.6 22.6 - - + -
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Residues in contact with ASN 101 (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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1B NAG 1.4 69.2 + - - +
48B TYR* 4.6 9.9 + - - -
97B ILE* 2.8 26.7 + - - +
98B TRP* 3.6 6.1 - - - +
100B CYS* 1.4 71.7 - - - +
102B ASN* 1.4 69.9 + - - +
104B GLY* 5.3 1.3 + - - -
461B THR* 5.4 3.3 + - - -
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Residues in contact with ASN 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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1B NAG 5.1 0.2 + - - -
98B TRP* 2.9 65.5 + - + +
99B PHE* 4.7 1.3 - - - +
100B CYS 3.2 0.2 - - - -
101B ASN* 1.4 88.3 - - - +
103B THR* 1.3 55.3 + - - +
104B GLY 3.1 7.5 + - - -
297B PHE* 3.5 26.5 - - + -
459B LEU 3.7 0.2 - - - +
460B ARG* 2.6 42.0 + - - +
461B THR* 5.0 2.1 + - - -
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Residues in contact with THR 103 (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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89B TYR* 3.9 18.8 + - + -
99B PHE* 2.5 27.6 + - - -
100B CYS 3.7 2.0 + - - -
102B ASN* 1.3 71.4 - - - +
104B GLY* 1.3 64.1 + - - +
105B PHE 3.3 0.7 - - - -
106B MET* 3.2 35.3 + - + +
107B TRP* 3.4 16.2 + - - -
119B PHE* 4.4 9.6 - - - -
176B ILE* 4.9 0.4 - - + -
459B LEU* 3.5 40.8 - - + +
460B ARG* 4.0 4.8 + - - +
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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