Contacts of the helix formed by residues 83 - 92 (chain B) in PDB entry 3NNJ
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 LYS 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2B ASN 5.8 2.2 + - - -
1B MSE 5.9 3.2 - - - +
24B ILE* 2.9 49.1 + - + +
25B PHE* 3.5 35.0 - - + +
26B ASP* 5.7 4.9 + - - +
79B PHE 3.8 5.2 - - - +
80B ILE* 2.9 9.6 + - + +
82B GLU* 1.3 96.3 + - - +
84B LEU* 1.3 65.4 + - - +
85B ALA 3.1 3.1 - - - -
86B LEU* 3.0 21.4 + - + +
87B LEU* 3.1 19.0 + - + +
133B ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 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 ILE* 3.6 30.5 - - + +
81B GLN* 3.4 13.7 + - - +
83B LYS* 1.3 78.9 - - - +
85B ALA* 1.3 53.0 + - - +
87B LEU* 3.6 13.4 - - + -
88B ASN* 2.7 45.6 + - - +
95B LEU* 4.3 12.1 - - + +
97B ILE* 4.2 5.6 - - + -
248B LEU* 4.0 19.7 - - + -
315B ARG 3.5 17.5 - - - +
316B MSE 3.4 31.2 - - - +
317B ALA* 3.7 15.5 - - + +
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Residues in contact with ALA 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 GLN 4.9 0.8 + - - -
82B GLU 4.8 6.0 + - - +
83B LYS 3.1 1.2 - - - -
84B LEU* 1.3 78.4 - - - +
86B LEU* 1.3 58.3 + - - +
88B ASN* 3.2 6.9 + - - +
89B TYR* 2.9 29.8 + - - +
317B ALA* 4.2 13.6 - - + +
318B ALA* 6.5 0.7 - - + -
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Residues in contact with LEU 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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1B MSE 4.2 24.2 - - + -
6B VAL* 3.9 36.8 - - + -
9B LEU* 5.6 0.7 - - + -
21B ILE* 4.7 3.6 - - + -
24B ILE* 4.3 27.4 - - + -
83B LYS* 3.0 16.7 + - + +
85B ALA* 1.3 79.8 - - - +
87B LEU* 1.3 59.3 + - + +
89B TYR* 3.0 10.9 + - + +
90B ILE* 2.8 47.3 + - + +
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Residues in contact with LEU 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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21B ILE* 3.7 30.3 - - + -
24B ILE* 4.4 10.1 - - + -
83B LYS* 3.1 16.5 + - + +
84B LEU* 3.9 16.8 - - + +
86B LEU* 1.3 82.0 - - + +
88B ASN* 1.3 62.0 + - - +
90B ILE* 4.2 9.9 - - + -
91B THR* 2.8 31.5 + - - +
95B LEU* 3.6 18.2 - - + -
133B ILE* 3.5 32.8 - - + -
221B PHE* 4.0 26.5 - - + -
248B LEU* 5.1 0.7 - - + -
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Residues in contact with ASN 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 LEU* 2.7 26.9 + - - +
85B ALA* 3.5 6.6 - - - +
87B LEU* 1.3 72.6 - - - +
89B TYR* 1.3 57.5 + - - +
91B THR* 4.0 1.3 - - - -
92B GLY* 2.9 27.9 + - - -
93B LYS 3.1 21.5 + - - +
94B ASN* 3.7 18.8 + - - +
95B LEU* 2.7 38.8 + - - +
317B ALA* 3.7 22.6 - - - +
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Residues in contact with TYR 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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6B VAL* 3.7 31.2 - - + -
7B GLU* 2.8 24.7 + - - -
10B LYS* 3.6 43.3 - - + +
85B ALA 2.9 13.8 + - - +
86B LEU* 3.3 10.8 - - + +
88B ASN* 1.3 76.9 - - - +
90B ILE* 1.3 69.7 + - + +
91B THR 3.3 0.3 + - - -
92B GLY* 3.6 6.5 + - - -
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Residues in contact with ILE 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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6B VAL 4.8 3.6 - - - +
9B LEU* 3.9 28.0 - - + +
10B LYS* 3.7 33.0 - - + +
13B TYR* 3.6 37.8 - - + -
14B GLU* 4.6 4.0 - - - +
19B CYS* 4.3 6.7 - - - -
21B ILE* 4.0 24.2 - - + -
86B LEU* 2.8 37.8 + - + +
87B LEU* 3.7 10.3 - - + +
88B ASN 3.3 0.2 - - - -
89B TYR* 1.3 82.6 - - + +
91B THR* 1.3 64.3 + - + +
221B PHE* 5.1 2.7 - - + -
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Residues in contact with THR 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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13B TYR* 3.9 30.7 + - + +
14B GLU* 6.1 0.9 - - - -
87B LEU 2.8 20.4 + - - +
88B ASN* 3.6 0.9 + - - -
90B ILE* 1.3 83.4 - - + +
92B GLY* 1.3 61.2 + - - +
93B LYS* 3.0 38.8 + - - +
95B LEU* 4.4 3.5 - - + +
129B PHE* 4.7 3.8 - - + -
221B PHE* 3.4 37.7 - - + -
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Residues in contact with GLY 92 (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* 6.0 1.1 - - - +
88B ASN 2.9 11.0 + - - -
89B TYR* 3.6 5.8 + - - -
90B ILE 3.5 1.8 - - - -
91B THR* 1.3 78.8 - - - +
93B LYS* 1.3 66.2 + - - +
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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