Contacts of the helix formed by residues 75 - 82 (chain R) in PDB entry 2DFS
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 LYS 75 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R GLU* 2.6 33.2 + - - -
50R ASP* 5.3 4.6 - - - +
51R MET* 4.1 29.6 - - + +
54R GLU* 3.3 27.0 + - - +
71R MET 3.0 18.3 + - - +
72R MET* 3.5 2.5 - - - +
74R ARG* 1.3 86.5 - - + +
76R MET* 1.4 64.0 + - - +
77R LYS* 3.3 2.7 - - - -
78R ASP* 2.7 32.4 + - - +
79R THR* 3.1 33.2 + - + -
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Residues in contact with MET 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R MET 2.9 12.6 + - - +
73R ALA* 3.5 33.4 - - + +
74R ARG 3.5 1.5 + - - +
75R LYS* 1.4 74.7 - - - +
77R LYS* 1.3 59.4 + - + +
79R THR* 3.0 7.2 + - - -
80R ASP* 2.8 50.9 + - - +
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Residues in contact with LYS 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q ASP 5.3 5.9 + - - -
23Q GLY* 5.9 5.2 - - - -
74R ARG 6.1 0.2 - - - +
75R LYS 3.3 0.9 - - - -
76R MET* 1.3 84.9 - - + +
78R ASP* 1.3 101.4 + - - +
80R ASP* 4.1 8.6 - - - +
81R SER* 3.5 17.9 + - - -
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Residues in contact with ASP 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47R GLU* 3.7 22.6 - - + +
75R LYS* 2.7 41.0 + - - +
77R LYS* 1.3 111.5 + - - +
79R THR* 1.3 64.1 + - - +
81R SER* 3.2 21.9 + - - -
82R GLU* 3.5 10.8 + - - +
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Residues in contact with THR 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R MET* 4.2 10.8 - - + -
41R GLN* 3.3 35.1 + - - +
43R PRO* 5.1 5.6 - - + -
47R GLU* 3.7 20.4 - - - +
51R MET* 4.0 16.2 - - + -
72R MET 4.4 2.3 + - - -
75R LYS* 3.1 18.2 + - + +
76R MET* 3.0 22.0 + - - -
78R ASP* 1.3 76.4 - - + +
80R ASP* 1.4 60.3 + - - +
82R GLU* 3.4 21.0 + - - +
83R GLU* 4.1 9.5 + - - +
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Residues in contact with ASP 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R ALA 5.8 2.3 + - - -
41R GLN* 5.5 2.1 + - - -
76R MET* 2.8 44.0 + - - +
77R LYS* 4.0 8.2 + - - +
79R THR* 1.4 73.7 + - - +
81R SER* 1.4 56.5 + - - +
83R GLU* 3.0 32.0 + - - +
84R GLU* 3.4 8.7 + - - +
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Residues in contact with SER 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77R LYS* 3.5 11.4 + - - -
78R ASP* 3.2 15.1 + - - -
80R ASP* 1.4 77.1 - - - +
82R GLU* 1.3 61.4 + - - +
83R GLU 3.2 1.3 + - - -
84R GLU* 3.3 22.0 + - - +
85R ILE* 4.3 8.0 + - - +
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Residues in contact with GLU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869M ILE* 5.2 8.9 - - - +
872M LYS* 3.6 10.0 - - - +
873M HIS* 5.2 1.4 + - - -
42R ASN* 3.2 69.0 + - - +
43R PRO* 3.8 7.4 - - + -
44R THR* 3.5 28.4 + - - +
47R GLU* 5.9 4.6 - - + +
78R ASP 3.5 7.5 + - - +
79R THR* 3.4 14.8 + - - +
80R ASP 3.2 0.4 - - - -
81R SER* 1.3 77.2 - - - +
83R GLU* 1.3 56.0 + - - +
84R GLU 3.7 0.2 - - - -
85R ILE* 4.2 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