Contacts of the helix formed by residues 77 - 88 (chain D) in PDB entry 1VQ9
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 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30329 G 5.7 1.4 + - - -
30449 A 3.8 20.1 + - - +
18D ILE* 4.9 8.4 + - - +
19D GLU 5.1 0.2 + - - -
76D ARG* 1.3 74.4 - - - +
78D GLU* 1.3 72.4 + - + +
80D ALA* 3.0 7.4 + - - +
81D GLU* 3.0 31.6 + - - +
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Residues in contact with GLU 78 (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 ASP* 1.3 79.6 - - + +
79D MET* 1.3 69.1 + - + +
80D ALA 3.0 0.3 + - - -
81D GLU* 3.1 11.0 + - - +
82D GLU* 2.7 51.6 + - + +
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Residues in contact with MET 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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45D THR 3.9 12.2 - - - +
46D GLY* 3.5 35.2 - - - +
47D GLN* 3.5 27.8 - - + +
75D LEU* 3.1 33.8 - - + +
76D ARG 3.7 12.3 + - - +
77D ASP 3.4 0.6 - - - -
78D GLU* 1.3 78.4 - - + +
80D ALA* 1.3 61.9 - - - +
82D GLU* 4.2 12.7 - - - +
83D PHE* 3.3 11.1 + - - +
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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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18D ILE* 4.1 12.3 - - + -
21D VAL* 3.5 24.2 - - + +
75D LEU* 3.6 28.8 - - - +
76D ARG* 3.8 0.8 + - - -
77D ASP 3.0 17.8 + - - +
78D GLU 3.0 0.6 - - - -
79D MET* 1.3 76.6 - - - +
81D GLU* 1.3 67.8 + - - +
83D PHE* 3.0 14.4 + - - +
84D LEU* 3.1 16.6 + - - +
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Residues in contact with GLU 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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18D ILE* 4.6 18.8 - - + -
77D ASP* 3.0 19.9 + - - +
78D GLU* 3.8 10.1 + - - +
80D ALA* 1.3 75.6 - - + +
82D GLU* 1.3 58.0 + - + +
83D PHE 2.7 15.4 + - - -
84D LEU* 2.8 19.4 + - - +
85D GLN* 2.9 22.1 + - + +
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Residues in contact with GLU 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 GLU* 2.7 47.4 + - + +
79D MET* 4.3 12.1 + - - +
81D GLU* 1.3 72.2 - - + +
83D PHE* 1.3 60.3 + - - +
85D GLN* 4.1 25.7 + - - +
86D THR* 3.7 12.0 + - - +
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Residues in contact with PHE 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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21D VAL* 3.6 16.4 - - + -
23D VAL* 3.4 25.1 - - + -
44D ILE* 3.3 54.1 - - + -
45D THR* 3.9 18.4 - - + +
75D LEU* 3.7 8.1 - - + -
79D MET 3.3 14.0 + - - +
80D ALA* 3.0 9.6 + - - +
81D GLU 2.7 1.6 + - - -
82D GLU* 1.3 77.4 - - - +
84D LEU* 1.3 64.0 + - + +
86D THR* 3.1 11.7 + - - -
87D ALA* 2.8 49.8 + - + +
128D LEU* 5.5 0.2 - - + -
130D VAL* 3.5 21.8 - - + -
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Residues in contact with LEU 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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18D ILE* 3.2 35.4 - - + -
21D VAL* 4.0 12.3 - - + -
80D ALA 3.1 10.8 + - - +
81D GLU* 2.8 12.6 + - - +
83D PHE* 1.3 87.2 - - + +
85D GLN* 1.3 66.7 + - - +
87D ALA* 3.9 2.9 - - + -
88D LEU* 2.8 56.2 + - + +
104D PHE* 5.4 1.1 - - + -
106D PHE* 4.3 10.8 - - + -
130D VAL* 4.4 0.7 - - + -
132D VAL* 3.8 32.3 - - + -
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Residues in contact with GLN 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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81D GLU* 2.9 20.9 + - + +
82D GLU* 4.1 25.7 - - - +
84D LEU* 1.3 76.3 - - - +
86D THR* 1.3 63.0 + - + +
88D LEU* 5.6 0.7 - - - -
89D PRO* 3.1 22.6 - - - +
170D TYR* 4.6 23.6 - - + -
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Residues in contact with THR 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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44D ILE 5.7 0.9 + - - -
82D GLU 3.7 9.6 + - - +
83D PHE* 3.1 13.2 + - - -
84D LEU 3.0 0.2 - - - -
85D GLN* 1.3 82.2 - - + +
87D ALA* 1.3 59.6 + - - +
89D PRO* 3.7 4.7 - - - +
90D LEU* 3.0 29.7 - - - +
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Residues in contact with ALA 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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44D ILE* 6.2 0.7 - - + -
83D PHE* 2.8 50.3 + - + +
84D LEU* 3.9 3.4 - - - -
86D THR* 1.3 76.7 - - - +
88D LEU* 1.3 68.2 + - - +
89D PRO 3.2 1.8 - - - -
90D LEU* 2.9 30.1 + - + +
106D PHE* 3.6 22.2 - - + -
130D VAL* 5.0 1.1 - - + -
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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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84D LEU* 2.8 47.9 + - + +
85D GLN* 5.6 0.4 - - - -
87D ALA* 1.3 72.3 - - - +
89D PRO* 1.3 68.1 - - + +
91D ALA* 2.9 23.6 + - - +
93D LEU* 4.0 21.0 - - + +
104D PHE* 3.8 33.2 - - + -
106D PHE* 3.9 14.3 - - + -
166D ILE* 4.9 8.5 - - + -
169D THR 5.0 5.4 - - - +
170D TYR* 5.5 3.6 - - + +
171D ASP* 4.0 22.7 - - - +
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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