Contacts of the helix formed by residues 75 - 82 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47F GLU* 2.6 31.1 + - - -
50F ASP* 5.3 5.0 - - - +
51F MET* 4.1 31.0 - - + +
54F GLU* 3.3 26.9 + - - +
71F MET* 3.0 18.7 + - - +
72F MET* 3.5 2.7 - - - +
73F ALA 3.3 0.2 - - - -
74F ARG* 1.3 86.6 - - + +
76F MET* 1.4 65.8 + - - +
77F LYS* 3.3 2.5 - - - -
78F ASP* 2.7 32.6 + - - +
79F THR* 3.1 30.1 + - + -
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Residues in contact with MET 76 (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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72F MET 2.9 13.2 + - - +
73F ALA* 3.5 33.2 - - + +
74F ARG 3.5 1.9 + - - +
75F LYS* 1.4 72.8 - - - +
77F LYS* 1.3 59.7 + - + +
79F THR* 3.0 9.6 + - - -
80F ASP* 2.8 50.0 + - - +
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Residues in contact with LYS 77 (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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23E GLY 6.0 1.5 + - - -
74F ARG 5.4 0.2 + - - -
75F LYS 3.3 1.5 - - - -
76F MET* 1.3 83.6 - - + +
78F ASP* 1.3 102.8 + - - +
80F ASP* 3.9 8.5 + - - +
81F SER* 3.6 18.3 + - - -
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Residues in contact with ASP 78 (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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47F GLU* 3.6 21.8 - - + +
75F LYS* 2.7 40.0 + - - +
77F LYS* 1.3 111.8 + - - +
79F THR* 1.3 63.9 + - - +
81F SER* 3.2 21.2 + - - -
82F GLU* 3.5 11.0 + - - +
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Residues in contact with THR 79 (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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36F MET* 4.2 10.9 - - + +
41F GLN* 3.3 36.8 + - - +
43F PRO* 5.2 4.0 - - + -
47F GLU* 3.7 20.9 - - - +
51F MET* 4.0 15.9 - - + -
72F MET* 4.4 2.8 + - - +
75F LYS* 3.1 17.8 + - + +
76F MET* 3.0 22.4 + - - -
78F ASP* 1.3 75.7 - - - +
80F ASP* 1.4 61.6 + - - +
82F GLU* 3.4 21.2 + - - +
83F GLU* 4.0 9.7 + - - +
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Residues in contact with ASP 80 (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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10F ALA 5.8 2.3 + - - -
41F GLN* 5.6 1.6 + - - -
76F MET* 2.8 45.1 + - - +
77F LYS* 3.8 8.6 + - - +
79F THR* 1.4 73.0 + - - +
81F SER* 1.4 57.2 + - - +
83F GLU* 3.0 31.4 + - - +
84F GLU* 3.4 8.5 + - - +
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Residues in contact with SER 81 (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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77F LYS* 3.6 12.9 + - - -
78F ASP* 3.2 14.7 + - - -
80F ASP* 1.4 78.2 - - - +
82F GLU* 1.3 58.7 + - - +
83F GLU 3.2 4.7 + - - -
84F GLU* 3.2 21.8 + - - +
85F ILE* 4.3 8.1 + - - +
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Residues in contact with GLU 82 (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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869A ILE* 5.5 7.9 - - - +
872A LYS* 4.0 7.6 - - - +
873A HIS* 5.3 0.7 + - - -
42F ASN* 2.9 61.8 + - - +
43F PRO* 4.0 6.5 - - + -
44F THR* 3.1 36.7 + - - +
47F GLU* 5.2 6.2 - - + +
78F ASP 3.5 9.8 + - - +
79F THR* 3.4 13.9 + - - +
80F ASP 3.2 0.2 - - - -
81F SER* 1.3 76.7 - - - +
83F GLU* 1.4 56.0 + - - +
84F GLU 3.7 0.2 - - - -
85F ILE* 4.3 21.8 - - - +
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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