Contacts of the helix formed by residues 76 - 86 (chain B) in PDB entry 2NUG
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 SER 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B ALA 3.7 7.2 - - - -
73B TYR* 2.6 28.8 + - - -
75B ILE* 1.3 83.6 - - - +
77B GLU* 1.3 65.8 + - - +
78B GLU* 3.6 10.8 + - - +
79B PHE* 3.1 14.0 + - - +
80B PHE* 3.0 22.9 + - - -
11C C 3.6 11.7 - - - -
12C G 3.4 17.5 - - - -
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Residues in contact with GLU 77 (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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75B ILE 4.0 0.6 + - - -
76B SER* 1.3 73.2 - - - +
78B GLU* 1.3 63.0 + - - +
80B PHE* 3.2 10.7 + - - +
81B ASN* 2.8 42.6 + - - +
102B GLU* 3.7 27.7 - - + +
103B THR* 3.4 30.1 + - - +
106B GLY* 4.6 6.7 - - - -
107B ASP* 5.6 0.7 - - - +
200B LYS* 5.8 1.9 + - - -
12C G 3.2 13.5 + - - +
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Residues in contact with GLU 78 (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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73B TYR* 4.0 17.4 + - + +
76B SER* 3.1 10.4 + - - +
77B GLU* 1.3 80.4 - - - +
79B PHE* 1.3 61.8 + - - +
81B ASN* 3.2 17.8 + - - +
82B LEU* 3.3 17.6 + - + +
102B GLU* 6.5 0.4 - - - -
149B LYS* 3.3 42.2 + - - +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.3 53.3 - + + +
74B LEU* 3.3 44.0 - - + +
76B SER* 3.1 6.7 + - - +
78B GLU* 1.3 79.2 - - - +
80B PHE* 1.3 63.8 + + - +
82B LEU* 3.0 27.3 + - + +
83B LEU* 3.0 50.2 + - + +
138B ASP* 4.7 3.1 - - + -
139B ILE* 3.9 23.1 - - + -
142B ALA* 4.4 12.6 - - + -
147B ARG* 5.4 0.9 - - - -
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Residues in contact with PHE 80 (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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47B VAL* 3.5 25.1 - - + -
48B ASN* 4.4 3.4 - - - -
51B ILE* 3.8 10.8 - - + -
74B LEU 3.3 22.9 - - - -
75B ILE* 3.6 25.1 - - + -
76B SER 3.0 16.1 + - - -
77B GLU* 3.6 11.7 - - - +
79B PHE* 1.3 77.0 - - - +
81B ASN* 1.3 58.5 + - - +
83B LEU* 3.3 10.2 + - + +
84B ALA* 2.8 30.5 + - - +
106B GLY* 4.2 13.5 - - - -
109B PHE* 3.6 29.0 - + + -
110B GLU* 3.3 42.4 - - + -
507B MG 4.3 0.2 - - - -
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Residues in contact with ASN 81 (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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77B GLU* 2.8 32.1 + - - +
78B GLU* 3.4 10.9 - - - +
79B PHE 3.1 0.2 - - - -
80B PHE* 1.3 76.0 - - - +
82B LEU* 1.3 64.6 + - + +
84B ALA* 3.4 7.8 + - - +
85B GLN* 3.2 28.1 + - - +
102B GLU* 3.0 42.9 + - - +
105B ILE* 3.4 30.4 - - - +
106B GLY 3.9 5.3 - - - +
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Residues in contact with LEU 82 (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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73B TYR* 3.6 23.6 - - - +
78B GLU* 3.3 15.7 + - + +
79B PHE* 3.0 23.1 + - + +
81B ASN* 1.3 80.0 - - + +
83B LEU* 1.3 63.3 + - + +
85B GLN* 3.3 43.6 + - - +
86B LYS* 4.0 2.6 + - - +
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Residues in contact with LEU 83 (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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51B ILE* 5.6 0.7 - - + -
74B LEU 5.5 0.2 - - - +
79B PHE* 3.0 52.2 + - + +
80B PHE* 3.8 11.2 - - + +
82B LEU* 1.3 77.2 - - + +
84B ALA* 1.3 62.5 + - - +
86B LYS* 3.2 21.8 + - - +
87B LEU* 4.1 1.0 + - - +
109B PHE* 3.8 31.0 - - + -
131B PHE* 4.3 11.0 - - + -
135B PHE* 3.4 45.2 - - + -
138B ASP* 4.3 14.4 - - + +
139B ILE* 4.9 3.1 - - + -
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Residues in contact with ALA 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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80B PHE 2.8 19.2 + - - +
81B ASN 3.7 5.8 - - - +
82B LEU 3.2 0.2 - - - -
83B LEU* 1.3 75.4 - - - +
85B GLN* 1.3 58.2 + - - +
87B LEU* 2.8 23.8 + - - +
88B GLU 3.1 8.1 + - - -
89B LEU* 3.4 27.4 + - + -
105B ILE* 3.7 24.0 - - + -
109B PHE* 4.1 12.1 - - + -
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Residues in contact with GLN 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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81B ASN* 3.2 18.4 + - - +
82B LEU* 3.4 34.3 + - - +
83B LEU 3.2 0.4 - - - -
84B ALA* 1.3 76.1 - - - +
86B LYS* 1.3 59.1 + - - +
88B GLU* 2.8 28.5 + - - +
90B HIS* 5.6 5.6 - - + +
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Residues in contact with LYS 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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10B LYS* 4.5 10.7 + - - +
82B LEU 4.0 1.9 + - - +
83B LEU* 3.2 14.7 + - - +
84B ALA 3.1 0.2 - - - -
85B GLN* 1.3 77.8 - - - +
87B LEU* 1.3 63.3 + - + +
88B GLU* 5.0 1.5 - - - +
133B LYS 5.3 0.8 + - - -
134B LEU* 2.8 38.2 + - + +
135B PHE* 4.0 11.2 - - + -
138B ASP* 3.1 25.6 + - - +
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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