Contacts of the helix formed by residues 80 - 87 (chain D) in PDB entry 5J7F
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 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D TYR* 2.6 33.3 + - - -
64D LYS* 3.4 20.1 + - - +
66D LEU* 4.3 14.8 - - + +
77D CYS* 3.0 19.1 + - - +
78D SER 3.1 2.0 - - - +
79D ASN* 1.3 80.3 - - - +
81D LEU* 1.3 57.2 + - - +
82D LEU* 2.8 26.1 + - - +
83D GLY* 2.6 26.4 + - - +
84D ASP* 3.2 12.8 + - - +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.9 35.2 - - + +
36D LYS* 4.7 12.8 - - - +
37D LEU* 3.5 16.4 - - + -
60D TYR* 4.4 7.2 - - - +
80D ASP* 1.3 77.5 - - - +
82D LEU* 1.3 63.7 + - - +
84D ASP* 3.2 24.2 + - + +
85D LEU* 3.1 49.0 + - + +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.1 12.2 - - + +
57D LEU* 4.2 18.8 - - + -
60D TYR* 4.0 10.8 - - + -
61D ILE* 4.0 31.4 - - + -
66D LEU* 4.0 12.3 - - + -
75D VAL* 4.5 1.3 - - + -
77D CYS* 4.0 16.2 - - + -
80D ASP* 2.8 22.0 + - - +
81D LEU* 1.3 74.2 - - - +
83D GLY* 1.3 57.0 + - - +
85D LEU* 3.5 3.8 + - + +
86D PHE* 2.9 58.7 + - + +
91D PHE* 4.4 12.3 - - + -
201D 6GG 5.6 0.2 - - + -
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Residues in contact with GLY 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D CYS* 3.2 27.1 + - - +
78D SER* 4.9 2.0 - - - -
79D ASN 5.4 0.7 - - - -
80D ASP 2.6 12.6 + - - -
82D LEU* 1.3 70.1 - - - +
84D ASP* 1.3 57.1 + - - -
86D PHE 4.4 0.2 - - - -
87D GLY* 2.8 32.4 + - - -
88D VAL 3.7 17.6 + - - +
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Residues in contact with ASP 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 6.0 1.6 - - + -
79D ASN* 5.5 4.5 + - - -
80D ASP 3.2 12.1 + - - +
81D LEU* 3.2 28.8 + - + +
83D GLY* 1.3 78.1 - - - +
85D LEU* 1.3 63.5 + - + +
87D GLY* 3.8 5.2 + - - -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 4.1 13.2 - - - +
33D LEU* 3.7 35.7 - - + -
34D LEU* 3.8 28.5 - - + -
37D LEU* 3.8 16.2 - - + -
81D LEU* 3.1 33.5 + - + +
82D LEU* 3.6 8.7 - - + +
84D ASP* 1.3 83.7 - - + +
86D PHE* 1.3 68.2 + - + +
87D GLY* 3.5 0.5 + - - -
102D MET 4.9 0.2 - - - +
105D ARG* 5.9 0.2 - - - +
106D ASN* 3.2 36.5 + - - +
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 5.6 5.4 - - + -
57D LEU* 4.0 13.9 - - + -
77D CYS* 4.9 1.3 - - - -
82D LEU* 2.9 41.2 + - + +
83D GLY* 4.8 1.3 - - - -
85D LEU* 1.3 86.9 - - + +
87D GLY* 1.3 62.7 + - - +
88D VAL* 3.6 10.5 + - + +
91D PHE* 3.6 34.5 - + - -
99D ILE* 4.5 3.4 - - + -
102D MET* 3.5 60.4 - - + +
103D ILE* 3.9 31.9 - - + -
105D ARG* 4.8 6.8 + - - -
106D ASN* 4.5 4.3 - - - -
201D 6GG 4.0 8.5 - - + -
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLY 2.8 15.7 + - - -
84D ASP* 3.8 5.1 + - - -
85D LEU 3.3 3.4 + - - -
86D PHE* 1.3 78.0 - - - +
88D VAL* 1.3 64.9 + - - +
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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