Contacts of the helix formed by residues 44 - 54 (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 THR 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868A ILE* 3.8 29.8 - - + -
869A ILE* 5.9 1.6 - - + -
872A LYS* 3.5 16.6 - - + +
37F ARG* 3.6 1.7 + - - -
42F ASN 3.4 0.6 + - - -
43F PRO* 1.4 77.7 - - - +
45F GLU* 1.4 66.1 + - - +
46F ALA* 3.8 6.6 - - - +
47F GLU* 3.3 24.3 + - - +
48F LEU 3.1 17.2 + - - -
82F GLU* 3.1 23.1 + - - +
114F GLU* 3.5 17.3 - - - +
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Residues in contact with GLU 45 (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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872A LYS* 4.8 1.7 - - - +
875A ARG* 3.4 29.3 + - - +
37F ARG* 2.7 44.9 + - - +
44F THR* 1.4 70.5 - - - +
46F ALA* 1.3 60.7 + - - +
48F LEU* 3.4 16.0 - - + +
49F GLN* 3.1 29.2 + - + +
114F GLU* 2.9 29.2 + - + +
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Residues in contact with ALA 46 (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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44F THR* 3.8 7.6 - - - +
45F GLU* 1.3 74.4 - - - +
47F GLU* 1.4 50.0 + - - +
49F GLN* 2.9 26.6 + - - +
50F ASP* 2.9 29.8 + - - +
114F GLU* 2.9 13.6 + - - +
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Residues in contact with GLU 47 (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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43F PRO* 3.8 10.1 - - + +
44F THR* 3.3 27.0 + - - +
46F ALA* 1.4 75.3 - - - +
48F LEU* 1.3 56.7 + - - +
50F ASP* 3.4 10.1 + - - +
51F MET* 3.0 55.1 + - - +
75F LYS* 2.6 38.2 + - - -
78F ASP* 3.6 16.7 - - + +
79F THR* 3.7 11.4 - - - +
82F GLU* 5.2 5.8 - - + +
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Residues in contact with LEU 48 (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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30F LYS* 5.7 4.5 - - - +
32F LEU* 3.6 26.2 - - + +
33F GLY* 3.3 43.1 - - - +
36F MET* 5.7 1.8 - - - -
37F ARG* 3.8 4.0 - - - +
43F PRO* 4.7 4.8 - - + +
44F THR 3.1 12.4 + - - +
45F GLU* 3.4 28.0 - - + +
47F GLU* 1.3 76.8 + - - +
49F GLN* 1.3 74.1 + - - +
51F MET* 3.4 18.1 - - - +
52F ILE* 3.3 23.6 - - + +
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Residues in contact with GLN 49 (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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30F LYS* 2.9 33.4 + - - +
45F GLU* 3.1 13.8 + - + +
46F ALA* 2.9 16.4 + - - +
48F LEU* 1.3 96.3 + - - +
50F ASP* 1.3 58.4 + - - +
52F ILE* 3.3 8.5 + - - +
53F ASN* 2.9 32.3 + - - +
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Residues in contact with ASP 50 (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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46F ALA* 2.9 28.3 + - - +
47F GLU* 3.7 13.1 + - - +
49F GLN* 1.3 75.2 - - - +
51F MET* 1.4 56.0 + - - +
53F ASN* 3.2 7.4 + - - +
54F GLU* 3.0 34.7 + - - +
75F LYS* 5.5 4.3 - - - +
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Residues in contact with MET 51 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F LEU* 4.0 22.2 - - + -
36F MET* 3.6 39.0 - - + +
43F PRO* 4.8 1.6 - - + -
47F GLU* 3.0 43.2 + - - +
48F LEU* 3.4 18.2 - - - +
50F ASP* 1.4 76.3 - - - +
52F ILE* 1.4 62.5 + - - +
54F GLU* 3.5 19.8 - - - +
55F VAL* 3.7 10.6 - - - +
71F MET* 3.9 21.4 - - + +
75F LYS* 4.1 25.0 - - + +
79F THR* 4.0 10.1 - - + -
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Residues in contact with ILE 52 (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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29F THR* 3.9 27.8 - - + +
30F LYS* 3.7 26.7 - - + +
32F LEU* 3.5 23.3 - - + -
48F LEU* 3.3 20.4 - - + +
49F GLN* 3.3 12.9 + - - +
51F MET* 1.4 76.7 - - - +
53F ASN* 1.3 57.5 + - - +
55F VAL* 3.0 32.8 - - - +
57F ALA* 4.5 18.6 - - + +
71F MET* 5.8 0.7 - - - -
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Residues in contact with ASN 53 (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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49F GLN* 2.9 19.8 + - - +
50F ASP* 3.2 7.6 + - - +
52F ILE* 1.3 77.4 - - - +
54F GLU* 1.3 60.7 + - - +
55F VAL 3.2 7.6 + - - +
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Residues in contact with GLU 54 (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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50F ASP 3.0 18.4 + - - +
51F MET* 3.5 12.8 - - - +
52F ILE 3.3 0.2 - - - -
53F ASN* 1.3 75.6 - - - +
55F VAL* 1.3 54.3 + - - +
74F ARG* 2.6 61.9 + - - +
75F LYS* 3.3 30.2 + - - +
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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