Contacts of the helix formed by residues 78 - 89 (chain D) in PDB entry 5UQ9
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 GLY 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D LYS 3.6 1.0 + - - -
77D ALA* 1.3 77.0 - - - +
79D GLN* 1.3 64.7 + - - -
80D ALA 3.2 3.2 + - - -
81D VAL* 3.4 9.6 + - - +
82D ASP* 3.8 1.9 - - - +
104D SER* 5.1 1.6 + - - -
108D ASP* 5.4 4.7 - - - -
112D ARG* 3.3 25.6 + - - +
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Residues in contact with GLN 79 (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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78D GLY* 1.3 70.0 - - - -
80D ALA* 1.3 54.0 + - - +
81D VAL 3.2 0.2 - - - -
82D ASP* 3.1 16.8 + - + +
83D ASP* 2.7 58.6 + - - +
382E ARG* 4.4 26.7 - - - +
392E ASP* 5.5 0.5 - - - +
393E ASP* 3.1 27.2 + - - +
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Residues in contact with ALA 80 (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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75D VAL* 4.0 15.7 - - + -
76D LYS* 3.3 22.2 - - + +
78D GLY* 3.2 1.0 - - - -
79D GLN* 1.3 78.8 - - - +
81D VAL* 1.3 61.1 + - - +
83D ASP* 3.4 5.1 + - - +
84D PHE* 3.2 31.0 + - + -
381E ASP 4.9 2.0 - - - +
382E ARG* 3.7 38.8 - - + +
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Residues in contact with VAL 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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73D LEU* 4.1 15.2 - - + +
75D VAL* 4.0 20.0 - - + +
76D LYS 4.1 9.6 - - - +
77D ALA* 4.4 2.5 - - - -
78D GLY 3.4 13.8 + - - +
79D GLN 3.2 0.4 - - - -
80D ALA* 1.3 77.7 - - - +
82D ASP* 1.3 61.7 + - - +
84D PHE* 3.4 3.6 + - - +
85D ILE* 3.0 31.1 + - + +
100D ASP* 3.6 39.3 - - + +
102D GLY* 6.0 0.4 - - - -
104D SER* 4.3 8.1 - - - +
112D ARG* 3.6 26.2 - - - +
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Residues in contact with ASP 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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78D GLY 3.8 5.4 - - - +
79D GLN* 3.1 18.9 + - + +
81D VAL* 1.3 73.9 - - - +
83D ASP* 1.3 63.3 + - - +
85D ILE* 4.4 4.3 - - - +
86D GLU* 2.8 49.5 + - - +
108D ASP* 5.2 0.9 - - - +
111D ARG* 2.7 42.4 + - - -
112D ARG* 3.0 24.3 + - - +
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Residues in contact with ASP 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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34D ARG* 5.5 5.1 + - - +
79D GLN* 2.7 48.2 + - - +
80D ALA* 3.6 7.2 - - - +
82D ASP* 1.3 75.0 - - - +
84D PHE* 1.3 62.1 + - + +
86D GLU* 3.5 4.8 + - - +
87D LYS* 3.1 40.1 + - - +
382E ARG* 3.3 23.0 - - - +
383E ASN* 4.8 5.9 - - - +
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Residues in contact with PHE 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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9D ILE* 3.4 30.3 - - + -
32D PHE* 4.4 3.8 - + - -
34D ARG* 3.3 44.9 - - + -
58D LEU* 4.3 25.8 - - + -
73D LEU* 3.9 25.6 - - + -
75D VAL* 3.5 33.2 - - + -
80D ALA* 3.2 22.4 + - + +
81D VAL 3.9 3.4 - - - +
83D ASP* 1.3 76.7 - - + +
85D ILE* 1.3 60.4 + - - +
87D LYS* 3.2 8.0 + - + +
88D LEU* 2.7 37.3 + - + +
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Residues in contact with ILE 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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73D LEU* 4.1 12.6 - - + -
81D VAL* 3.0 19.6 + - + +
82D ASP* 3.8 3.1 - - - +
84D PHE* 1.3 76.4 - - - +
86D GLU* 1.3 75.0 + - - +
88D LEU* 3.0 5.7 + - - +
89D VAL* 3.0 33.7 + - + +
98D ILE* 4.5 9.2 - - + -
112D ARG* 3.6 33.9 - - + -
115D ASP* 5.0 3.1 - - - +
116D LEU* 3.7 36.1 - - + -
123D PHE* 3.7 21.3 - - + -
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Residues in contact with GLU 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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82D ASP* 2.8 41.6 + - - +
83D ASP* 3.9 5.2 - - - +
85D ILE* 1.3 87.0 - - - +
87D LYS* 1.3 61.5 + - + +
89D VAL* 4.7 3.9 - - - +
90D PRO* 3.4 17.5 - - - +
111D ARG* 5.6 2.9 + - - -
115D ASP* 5.6 1.6 - - - +
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Residues in contact with LYS 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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34D ARG* 3.9 28.4 - - - +
58D LEU* 3.6 25.9 - - + +
83D ASP* 3.1 27.5 + - - +
84D PHE* 3.6 12.6 - - + +
86D GLU* 1.3 80.0 - - + +
88D LEU* 1.3 60.2 + - - +
90D PRO* 3.6 8.4 - - - +
91D LEU* 3.9 17.8 - - - +
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Residues in contact with LEU 88 (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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9D ILE* 4.3 9.2 - - + -
58D LEU* 3.9 28.7 - - + -
61D MET* 4.1 5.2 - - + -
62D VAL* 4.3 11.2 - - + -
71D ILE* 3.7 40.8 - - + -
73D LEU* 4.4 8.5 - - + -
84D PHE* 2.7 28.6 + - - +
85D ILE 3.0 2.7 + - - +
87D LYS* 1.3 75.2 - - - +
89D VAL* 1.3 65.8 + - - +
91D LEU* 3.1 14.8 + - + +
92D LEU* 3.2 18.2 + - + +
98D ILE* 3.9 28.7 - - + -
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Residues in contact with VAL 89 (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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460B LYS* 4.9 0.5 + - - -
463B GLN* 3.6 32.2 + - + +
85D ILE* 3.0 24.0 + - + +
86D GLU* 4.7 3.8 - - - +
88D LEU* 1.3 78.1 - - - +
90D PRO* 1.3 69.1 - - + +
91D LEU 3.1 1.0 + - - -
92D LEU* 3.3 15.6 + - - +
98D ILE* 5.3 2.0 - - + -
116D LEU* 3.6 29.8 - - + -
119D LYS* 3.7 20.0 - - + -
121D ILE* 3.8 22.8 - - + +
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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