Contacts of the helix formed by residues 82 - 90 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C LYS* 3.8 3.0 - - - +
81C GLY* 1.3 79.1 + - - +
83C PRO* 1.3 74.8 - - + +
84C GLY 2.8 4.2 + - - -
85C ALA* 3.2 24.1 + - - +
86C ILE* 3.1 15.1 + - - +
33I LEU* 5.1 1.1 - - - -
34I THR* 4.4 5.4 - - - +
37I HIS* 3.9 24.5 - - + +
94I ASP* 3.5 18.0 + - + -
95I TYR* 3.7 39.3 + - + +
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Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR* 1.3 88.4 - - - +
84C GLY* 1.3 58.6 + - - +
86C ILE* 2.8 23.2 - - + +
87C ILE* 3.4 12.0 + - - +
30I ASP* 2.8 37.9 - - - +
33I LEU* 4.7 11.2 - - + -
34I THR* 4.2 6.1 - - - +
83I PRO* 5.3 4.4 - - + +
86I ILE* 3.4 35.0 - - + -
87I ILE* 5.3 7.4 - - + +
90I ARG* 3.5 13.9 - - - +
94I ASP* 3.9 4.5 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C THR 2.8 2.8 + - - -
83C PRO* 1.3 73.8 - - - +
85C ALA* 1.3 67.1 + - - +
86C ILE 2.8 3.5 + - - -
87C ILE* 2.8 28.8 + - - +
88C LYS* 3.3 5.8 + - - +
87I ILE* 5.6 1.8 - - - -
90I ARG* 4.5 2.9 - - - +
94I ASP* 2.9 28.1 + - - -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 4.2 0.4 - - - -
80C LYS* 3.5 53.8 - - + +
82C THR* 3.2 18.1 + - - +
84C GLY* 1.3 71.9 - - - +
86C ILE* 1.3 61.1 + - - +
88C LYS* 3.3 10.3 + - - +
89C ASP* 3.1 32.7 + - - +
94I ASP* 4.9 0.4 + - - -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 3.7 27.0 + - - +
29C ASN* 4.0 13.5 - - + +
30C ASP* 3.5 26.7 - - + +
33C LEU* 5.1 4.3 - - + -
80C LYS 5.3 0.4 + - - -
81C GLY* 5.5 2.6 - - - -
82C THR 3.1 13.4 + - - +
83C PRO* 2.8 33.9 - - + +
84C GLY 2.8 4.0 + - - -
85C ALA* 1.3 69.7 - - - +
87C ILE* 1.3 59.4 + - - +
88C LYS 2.8 10.2 + - - -
89C ASP* 3.2 1.7 + - - +
90C ARG* 3.2 27.0 + - + +
33I LEU* 5.2 5.4 - - + -
83I PRO* 3.3 36.6 - - + -
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PRO 3.4 12.3 - - - +
84C GLY* 2.8 32.5 + - - +
86C ILE* 1.3 77.9 - - - +
88C LYS* 1.3 61.0 + - + +
90C ARG* 3.1 53.2 - - - +
83I PRO* 5.4 9.0 - - + +
84I GLY* 5.6 1.3 - - - -
87I ILE* 5.2 22.7 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LYS* 4.9 13.8 - - - +
84C GLY 3.3 8.3 + - - +
85C ALA* 3.5 13.5 - - - +
86C ILE 2.8 2.0 + - - -
87C ILE* 1.3 78.3 - - + +
89C ASP* 1.3 71.0 + - - +
90C ARG 3.1 10.8 + - - +
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Residues in contact with ASP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.2 30.1 + - - +
23C LYS* 4.7 23.9 - - + +
26C SER* 3.1 33.1 + - - +
80C LYS* 5.5 0.9 - - - +
85C ALA* 3.1 15.2 + - - +
88C LYS* 1.3 83.5 - - - +
90C ARG* 1.3 61.3 + - - +
91C THR* 3.9 9.2 + - - +
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C SER* 5.0 4.2 - - - +
27C THR* 6.2 0.2 - - - -
30C ASP* 3.2 18.4 + - + -
86C ILE* 3.2 18.4 + - + +
87C ILE* 3.1 46.6 - - - +
88C LYS 3.1 11.5 - - - +
89C ASP* 1.3 80.4 - - - +
91C THR* 1.3 62.9 + - - +
92C TRP* 3.4 45.8 + - + +
93C ASP* 4.2 1.6 - - - +
94C ASP* 3.1 56.5 + - - +
83I PRO* 3.5 11.5 - - - +
84I GLY* 4.7 0.6 - - - +
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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