Contacts of the helix formed by residues 83 - 91 (chain B) in PDB entry 1NUE
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLU* 3.4 26.6 + - + +
6B ARG* 3.8 15.9 - - - -
7B THR* 3.7 17.5 - - + +
28B PHE* 5.6 1.3 - - + -
33B PHE* 3.8 40.2 - - + -
78B TRP* 3.9 13.5 - - + +
80B GLY 3.3 21.8 - - - +
81B LEU 3.1 3.7 + - - -
82B ASN* 1.3 75.9 - - - +
84B VAL* 1.3 61.3 + - - +
86B THR* 4.5 0.2 - - - -
87B GLY* 2.7 27.3 + - - +
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Residues in contact with VAL 84 (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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5B GLU* 3.0 25.0 + - + +
6B ARG 3.4 24.5 - - - +
7B THR* 3.7 15.7 + - - +
83B VAL* 1.3 78.2 - - - +
85B LYS* 1.3 64.8 + - + +
87B GLY* 3.9 0.3 - - - -
88B ARG* 3.1 22.1 + - + +
120B SER 3.7 10.3 - - - +
121B ASP 4.0 3.4 - - - +
122B SER* 3.6 35.9 - - - +
123B VAL* 4.1 9.9 - - + +
126B ALA* 4.1 10.3 - - + -
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Residues in contact with LYS 85 (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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5B GLU* 4.4 0.4 + - - -
82B ASN* 3.4 23.6 + - - +
84B VAL* 1.3 81.2 - - + +
86B THR* 1.3 63.6 + - - +
88B ARG* 3.2 12.6 + - + +
89B VAL* 3.1 34.7 + - + +
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Residues in contact with THR 86 (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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96A PRO 6.1 0.4 - - - +
97A ALA* 5.2 12.8 + - - +
31B LYS* 3.7 31.9 - - - +
33B PHE* 3.9 18.6 - - + -
81B LEU 4.6 1.2 + - - -
82B ASN* 2.9 25.9 + - - +
85B LYS* 1.3 74.0 - - - +
87B GLY* 1.3 67.8 + - - +
89B VAL* 3.0 12.6 + - + +
90B MET* 2.9 25.7 + - + +
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Residues in contact with GLY 87 (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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7B THR* 5.5 0.7 - - - -
9B ILE* 5.1 8.1 - - - -
28B PHE* 4.3 20.6 - - - -
33B PHE* 4.9 2.0 - - - -
83B VAL* 2.7 25.1 + - - -
84B VAL 3.9 0.4 - - - -
86B THR* 1.3 73.4 - - - +
88B ARG* 1.3 61.6 + - - +
90B MET* 3.2 8.0 + - - +
91B LEU* 3.0 29.6 + - - +
119B GLY* 6.3 0.4 - - - -
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Residues in contact with ARG 88 (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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84B VAL* 3.1 15.4 + - + +
85B LYS* 3.3 16.4 - - + +
86B THR 3.1 0.6 - - - -
87B GLY* 1.3 77.0 - - - +
89B VAL* 1.3 62.3 + - + +
91B LEU* 3.2 16.1 + - + +
92B GLY 3.1 26.7 + - - +
94B THR* 4.9 2.4 + - - -
105B ARG* 5.7 1.5 - - - +
118B HIS* 5.1 0.2 - - - -
119B GLY 2.8 33.0 + - - +
120B SER 3.4 13.8 + - - +
121B ASP* 3.7 26.7 + - - +
160B GDP 2.6 45.7 + - - -
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Residues in contact with VAL 89 (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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97A ALA 5.8 3.6 - - - +
99A SER 4.9 5.4 - - - +
100A LYS* 4.4 22.7 - - + +
101A PRO* 3.8 23.9 - - + +
85B LYS* 3.1 33.7 + - + +
86B THR* 3.0 14.0 + - + +
88B ARG* 1.3 77.3 - - + +
90B MET* 1.3 64.1 + - + +
92B GLY* 3.4 8.0 + - - -
103B THR* 3.5 14.4 - - - +
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Residues in contact with MET 90 (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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101A PRO* 4.0 17.9 - - + -
106A GLY 5.3 3.8 - - - +
107A ASP 5.9 0.2 - - - +
27B ARG* 3.6 39.7 - - + +
28B PHE* 3.9 25.4 - - + +
31B LYS* 4.1 16.2 - - + -
33B PHE* 3.9 25.1 - - - -
86B THR* 2.9 23.3 + - + +
87B GLY* 3.2 8.3 + - - +
89B VAL* 1.3 77.9 - - + +
91B LEU* 1.3 58.3 + - - +
103B THR* 3.3 6.1 - - - -
104B ILE* 2.9 35.0 + - + +
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Residues in contact with LEU 91 (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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9B ILE* 4.9 2.9 - - + -
28B PHE* 4.3 9.2 - - + -
87B GLY 3.0 22.5 + - - +
88B ARG* 3.2 19.9 + - - +
90B MET* 1.3 77.5 - - - +
92B GLY* 1.3 62.8 + - - +
103B THR* 3.8 0.4 - - - -
104B ILE* 3.6 12.4 + - + -
105B ARG* 2.9 59.2 + - - +
117B ILE* 3.5 34.1 - - + -
118B HIS 4.0 3.1 - - - -
119B GLY* 3.6 34.1 - - - +
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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