Contacts of the helix formed by residues 44 - 54 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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772A ILE* 3.3 33.4 - - + -
776A LYS* 3.3 18.5 - - + +
779A ARG* 3.9 1.3 - - - +
37B ARG* 3.1 7.7 + - - -
43B PRO* 1.4 76.6 - - - +
45B GLU* 1.3 62.1 + - - +
46B ALA* 3.5 7.0 - - + +
47B GLU* 2.7 60.6 + - - +
48B LEU* 3.3 16.6 + - - +
114B GLU* 3.4 10.8 - - - +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ARG* 3.0 23.2 - - - +
30B LYS* 5.4 2.9 + - - -
37B ARG* 2.6 40.8 + - - -
44B THR* 1.3 72.3 - - - +
46B ALA* 1.3 57.0 + - - +
48B LEU* 3.3 25.6 - - - +
49B GLN* 3.0 39.7 + - + +
114B GLU* 2.9 15.5 + - + +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B THR* 3.5 9.2 - - + +
45B GLU* 1.3 74.8 - - - +
47B GLU* 1.4 57.7 + - + +
49B GLN* 3.0 8.6 + - - +
50B ASP* 2.8 39.0 + - - +
114B GLU* 2.7 13.4 + - + +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A LYS* 2.7 32.6 + - - -
43B PRO* 3.4 13.7 - - + +
44B THR* 2.7 47.6 + - - +
45B GLU 3.5 0.2 - - - -
46B ALA* 1.4 70.7 - - - +
48B LEU* 1.3 57.0 + - - +
50B ASP* 3.4 11.9 + - - +
51B MET* 2.9 39.4 + - + +
75B LYS* 5.1 3.7 - - - +
78B ASP* 5.5 9.5 - - + +
79B THR* 6.5 0.7 - - + -
82B GLU* 3.9 6.8 - - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR 5.8 0.7 - - - +
30B LYS* 5.3 7.0 - - - +
32B LEU* 3.5 30.3 - - + -
33B GLY* 3.3 43.1 - - - +
36B MET* 3.7 14.6 - - + -
37B ARG* 4.7 1.1 - - - +
43B PRO* 4.9 2.4 - - + +
44B THR 3.3 12.9 + - - +
45B GLU* 3.3 35.0 - - - +
47B GLU* 1.3 79.5 - - - +
49B GLN* 1.3 72.4 + - - +
51B MET* 3.6 8.1 + - - +
52B ILE* 3.2 26.2 + - + +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.7 33.3 + - - +
45B GLU* 3.0 22.5 + - + +
46B ALA* 3.0 8.9 + - - +
48B LEU* 1.3 98.3 + - - +
50B ASP* 1.3 56.3 + - - +
52B ILE* 3.3 13.5 + - - +
53B ASN* 2.8 37.5 + - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 2.8 29.1 + - - +
47B GLU* 3.4 13.1 + - - +
49B GLN* 1.3 71.5 - - - +
51B MET* 1.4 57.2 + - - +
53B ASN* 3.1 6.9 + - - +
54B GLU* 2.9 38.9 + - - +
75B LYS* 5.2 7.2 - - - +
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Residues in contact with MET 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 5.2 2.2 - - + -
36B MET* 3.4 39.3 - - + +
43B PRO* 5.7 1.3 - - - -
47B GLU* 2.9 28.5 + - + +
48B LEU* 3.6 7.0 - - - +
50B ASP* 1.4 73.0 - - - +
52B ILE* 1.4 62.1 + - + +
54B GLU* 3.5 20.0 + - - +
55B VAL* 3.7 10.7 - - - +
71B MET* 3.4 49.8 - - + +
72B MET* 4.2 3.8 - - - +
75B LYS* 3.7 29.4 - - + -
79B THR* 4.0 22.0 - - + -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B THR* 3.8 36.1 - - + +
30B LYS* 4.8 6.3 - - + +
32B LEU* 3.5 25.6 - - + -
48B LEU* 3.2 15.7 + - + +
49B GLN* 3.7 23.3 - - - +
51B MET* 1.4 75.7 - - - +
53B ASN* 1.3 59.5 + - - +
55B VAL* 2.9 35.3 - - - +
57B ALA* 4.5 21.5 - - + +
63B ILE* 6.6 0.7 - - + -
67B GLU* 6.0 0.2 - - - -
71B MET* 6.0 0.9 - - - -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLN* 2.8 22.6 + - - +
50B ASP* 3.7 6.5 - - - +
52B ILE* 1.3 73.7 - - - +
54B GLU* 1.3 58.7 + - - +
55B VAL 3.2 8.7 + - - +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASP* 2.9 20.3 + - - +
51B MET* 3.5 12.1 - - - +
53B ASN* 1.3 75.0 - - - +
55B VAL* 1.3 55.3 + - - +
74B ARG* 2.7 64.7 + - - +
75B LYS* 3.1 37.0 + - - +
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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