Contacts of the helix formed by residues 82 - 90 (chain B) in PDB entry 1VEQ
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 THR 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B LYS* 3.8 2.8 - - - +
81B GLY* 1.3 79.3 + - - +
83B PRO* 1.3 74.3 - - + +
84B GLY 2.8 3.5 + - - -
85B ALA* 3.2 24.5 + - - +
86B ILE* 3.0 16.0 + - - +
33E LEU* 5.1 1.1 - - - -
34E THR* 4.6 4.9 - - - +
37E HIS* 3.9 26.3 - - + +
94E ASP* 3.6 17.0 + - + -
95E TYR* 3.8 38.7 + - + +
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Residues in contact with PRO 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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82B THR* 1.3 86.8 - - - +
84B GLY* 1.3 59.9 + - - +
86B ILE* 2.8 24.2 - - + +
87B ILE* 3.4 12.1 + - - +
30E ASP* 2.9 33.4 - - - +
33E LEU* 4.5 14.3 - - + -
34E THR* 4.3 6.7 - - - +
83E PRO* 5.4 4.3 - - + +
86E ILE* 3.4 33.9 - - + -
87E ILE* 5.4 6.9 - - + +
90E ARG* 3.6 13.2 - - - +
94E ASP* 4.0 4.5 - - + -
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Residues in contact with GLY 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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82B THR 2.8 3.0 + - - -
83B PRO* 1.3 74.9 - - - +
85B ALA* 1.3 66.9 + - - -
86B ILE 2.7 4.0 + - - -
87B ILE* 2.8 29.5 + - - +
88B LYS* 3.3 6.2 + - - +
87E ILE* 5.6 1.6 - - - -
90E ARG* 4.6 2.2 - - - +
94E ASP* 3.0 28.6 + - - -
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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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26B SER* 4.2 0.2 - - - -
80B LYS* 3.6 52.7 - - + +
82B THR* 3.2 19.2 + - - +
84B GLY* 1.3 71.8 - - - +
86B ILE* 1.3 61.5 + - - +
88B LYS* 3.3 10.5 + - - +
89B ASP* 3.1 33.6 + - - +
94E ASP* 5.1 0.4 + - - -
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Residues in contact with ILE 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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26B SER* 3.7 27.4 + - - +
29B ASN* 4.0 13.0 - - + +
30B ASP* 3.5 27.8 - - + +
33B LEU* 5.2 4.0 - - + -
81B GLY* 5.5 1.8 - - - -
82B THR 3.0 13.2 + - - +
83B PRO* 2.8 30.5 - - + +
84B GLY 2.7 4.0 + - - -
85B ALA* 1.3 70.1 - - - +
87B ILE* 1.3 59.3 + - - +
88B LYS 2.8 11.3 + - - -
89B ASP* 3.2 1.7 + - - +
90B ARG* 3.2 26.9 + - + +
33E LEU* 5.2 5.8 - - + -
83E PRO* 3.4 35.0 - - + -
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Residues in contact with ILE 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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83B PRO 3.4 11.4 - - - +
84B GLY* 2.8 34.1 + - - +
86B ILE* 1.3 77.2 - - + +
88B LYS* 1.3 61.2 + - + +
90B ARG* 3.2 52.6 - - - +
83E PRO* 5.3 9.0 - - + +
84E GLY* 5.7 2.0 - - - -
87E ILE* 5.3 23.3 - - + -
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Residues in contact with LYS 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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80B LYS* 4.9 14.2 - - - +
84B GLY 3.3 8.7 + - - +
85B ALA* 3.5 13.2 - - - +
86B ILE 2.8 1.8 + - - -
87B ILE* 1.3 79.5 - - + +
89B ASP* 1.3 69.2 - - - +
90B ARG 3.1 10.4 + - - +
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Residues in contact with ASP 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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22B GLN* 3.2 29.3 + - - +
23B LYS* 4.7 23.3 - - + +
26B SER* 3.1 33.8 + - - +
80B LYS* 5.5 0.7 - - - +
85B ALA* 3.1 14.3 + - - +
88B LYS* 1.3 85.8 - - - +
90B ARG* 1.3 61.4 + - - +
91B THR* 3.9 9.0 + - - +
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Residues in contact with ARG 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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26B SER* 5.0 4.7 - - - +
27B THR* 6.2 0.4 - - - +
30B ASP* 3.2 19.1 + - + -
86B ILE* 3.2 19.8 + - + +
87B ILE* 3.2 44.8 - - - +
88B LYS 3.1 12.2 - - - +
89B ASP* 1.3 78.9 - - - +
91B THR* 1.3 61.9 + - - +
92B TRP* 3.4 46.7 + - + +
93B ASP* 4.2 1.8 - - - +
94B ASP* 3.1 58.0 + - - +
83E PRO* 3.6 11.9 - - - +
84E GLY* 4.8 0.4 - - - +
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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