Contacts of the helix formed by residues 75 - 82 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47S GLU* 4.6 18.1 + - - +
50S ASP* 5.1 8.5 + - - +
51S MET* 3.8 35.3 - - + +
71S MET 3.3 13.7 + - - +
72S MET 3.6 1.6 - - - -
73S ALA 3.3 0.2 - - - -
74S ARG* 1.3 103.7 - - - +
76S MET* 1.4 61.0 + - - +
77S LYS* 3.3 3.4 + - - -
78S ASP* 2.6 46.0 + - - +
79S THR* 2.7 34.5 + - - +
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Residues in contact with MET 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72S MET* 3.0 24.4 + - + +
73S ALA* 3.2 17.5 + - - +
74S ARG 3.6 0.6 - - - -
75S LYS* 1.4 75.0 - - - +
77S LYS* 1.3 65.5 + - + +
79S THR* 3.2 4.8 + - - -
80S ASP* 2.9 57.7 + - - +
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Residues in contact with LYS 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951A MET* 5.5 4.6 - - - +
952A ASN* 4.5 2.6 - - - +
955A GLU* 2.8 41.6 + - - -
55G VAL* 3.6 20.3 - - - +
74S ARG 5.7 5.6 - - - +
75S LYS 3.3 0.6 - - - -
76S MET* 1.3 84.7 - - + +
78S ASP* 1.4 66.1 + - - +
80S ASP* 4.2 4.4 - - - +
81S SER* 3.3 21.0 + - - -
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Residues in contact with ASP 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S PRO* 5.4 0.4 - - - -
47S GLU* 6.3 0.9 - - + -
74S ARG 5.3 0.3 - - - +
75S LYS* 2.6 55.2 + - - +
77S LYS* 1.4 81.2 - - - +
79S THR* 1.3 60.8 + - - +
81S SER* 3.3 20.3 - - - -
82S GLU* 3.5 13.0 - - - +
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Residues in contact with THR 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S MET* 5.9 9.1 - - + +
41S GLN* 3.5 43.6 - - + +
43S PRO* 4.1 15.5 - - + +
47S GLU* 6.0 0.9 - - - +
51S MET* 4.9 8.5 - - - +
72S MET* 4.9 12.7 + - + -
75S LYS* 2.7 33.5 + - - +
76S MET* 3.6 6.5 - - - -
78S ASP* 1.3 77.2 - - - +
80S ASP* 1.3 59.7 + - - +
82S GLU* 3.5 17.7 + - - +
83S GLU 4.4 0.5 + - - -
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Residues in contact with ASP 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S GLN* 3.6 21.4 + - - -
76S MET* 2.9 43.0 + - - +
77S LYS* 4.2 4.4 - - - +
79S THR* 1.3 72.6 - - - +
81S SER* 1.4 63.3 + - - +
82S GLU 3.1 2.5 - - - -
83S GLU* 3.1 26.2 + - + +
84S GLU* 4.0 3.5 + - - +
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Residues in contact with SER 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77S LYS 3.3 15.4 + - - -
78S ASP* 3.3 15.9 - - - -
79S THR 3.4 0.2 - - - -
80S ASP* 1.4 75.8 - - - +
82S GLU* 1.3 67.9 + - - +
84S GLU* 3.3 23.3 - - - +
85S ILE* 4.9 1.9 + - - +
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Residues in contact with GLU 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895M CYS* 5.2 2.7 - - - +
896M CYS* 4.2 7.5 - - - -
42S ASN* 2.9 29.7 + - + +
43S PRO* 3.3 53.1 - - + +
44S THR* 3.8 16.6 + - - +
47S GLU* 5.5 2.1 - - - +
78S ASP 3.5 17.0 - - - +
79S THR 3.6 4.0 - - - +
80S ASP 3.1 0.8 - - - -
81S SER* 1.3 85.6 + - - +
83S GLU* 1.4 56.2 + - - +
84S GLU 3.4 1.9 + - - -
85S ILE* 4.4 5.2 + - - +
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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