Contacts of the helix formed by residues 68 - 72 (chain F) in PDB entry 3VZC
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 GLU 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E SER* 4.1 15.9 - - - +
68E GLU* 4.6 20.7 - - + +
71E ARG* 5.3 0.6 - - - +
66F SER 3.7 2.2 + - - -
67F GLU* 1.3 78.6 - - - +
69F LEU* 1.3 62.5 + - - +
70F GLY* 3.4 23.2 + - - +
71F ARG* 3.3 44.8 + - + +
72F TRP* 4.0 0.7 - - - -
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 4.5 3.1 - - + +
67F GLU* 3.2 32.9 + - + +
68F GLU* 1.3 69.0 + - - +
70F GLY* 1.3 64.8 + - - +
71F ARG 3.0 2.7 - - - -
72F TRP* 2.9 18.4 + - - +
75F LEU* 4.5 26.5 - - + -
91F LEU* 3.7 21.8 - - + -
94F ARG* 3.5 30.1 - - - +
96F ASP* 5.3 0.9 - - - +
100F ALA* 3.8 16.8 - - + +
103F LYS* 3.2 32.9 + - + -
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Residues in contact with GLY 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 5.0 3.6 + - - -
68F GLU* 3.4 15.8 + - - -
69F LEU* 1.3 76.6 - - - +
71F ARG* 1.3 61.3 + - - +
72F TRP 3.2 4.1 + - - +
103F LYS* 4.7 4.4 + - - -
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E MET* 4.9 4.6 - - - +
63E LEU* 2.6 47.8 + - - +
66E SER* 2.9 32.6 + - - +
67E GLU* 2.7 37.4 + - - +
68E GLU 5.0 0.6 - - - +
71E ARG* 4.6 1.4 - - - +
16F ARG* 3.1 37.0 + - - +
52F MET* 5.2 0.4 - - - +
67F GLU* 2.7 31.5 + - - -
68F GLU* 3.3 34.5 + - + +
69F LEU 3.0 0.2 + - - -
70F GLY* 1.3 77.3 - - - +
72F TRP* 1.3 88.3 + - + +
73F ASP* 5.6 0.2 - - - -
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Residues in contact with TRP 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 4.0 9.2 - - + -
16F ARG* 4.1 13.2 - - + -
17F VAL 3.7 16.4 - - - -
18F LEU* 3.5 45.0 - - + +
50F THR* 3.2 39.0 - - + -
52F MET* 5.6 0.2 - - + -
67F GLU* 3.1 26.3 + - + -
68F GLU 4.0 9.0 - - - -
69F LEU* 2.9 8.9 + - - +
70F GLY 3.2 2.8 - - - +
71F ARG* 1.3 125.5 - - + +
73F ASP* 1.3 61.4 + - - +
74F ALA 3.6 15.9 - - - +
75F LEU* 3.8 17.7 - - + -
103F LYS* 2.7 33.1 + - + +
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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