Contacts of the helix formed by residues 44 - 53 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843M ILE* 5.1 13.7 - - + -
847M ALA* 4.7 11.6 - - + +
850M ARG* 5.3 0.7 - - - +
37Q ARG* 4.2 3.1 - - - +
42Q ASN 3.8 0.2 + - - -
43Q PRO* 1.3 77.0 - - - +
45Q GLU* 1.3 59.1 + - - +
46Q ALA* 3.2 10.9 + - - +
47Q GLU* 3.2 28.4 + - - +
48Q LEU* 3.2 23.2 + - - +
82Q GLU* 3.0 15.7 + - - +
114Q GLU* 4.5 22.4 - - - +
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Residues in contact with GLU 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850M ARG* 2.8 29.4 + - - +
33Q GLY* 6.0 2.9 - - - -
37Q ARG* 2.7 37.4 + - - +
43Q PRO 4.5 0.2 - - - +
44Q THR* 1.3 71.7 - - - +
46Q ALA* 1.3 61.3 + - - +
48Q LEU* 3.4 24.8 - - + +
49Q GLN* 3.4 21.0 + - - +
114Q GLU* 4.5 5.5 + - - +
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Residues in contact with ALA 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q THR* 4.1 9.6 - - - +
45Q GLU* 1.3 75.8 - - - +
47Q GLU* 1.4 58.8 + - - +
49Q GLN* 2.9 8.9 + - - +
50Q ASP* 2.9 37.3 + - - +
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Residues in contact with GLU 47 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q PRO* 4.4 9.4 - - + +
44Q THR* 3.2 26.8 + - - +
46Q ALA* 1.4 76.2 - - - +
48Q LEU* 1.3 61.2 + - - +
50Q ASP* 3.3 10.3 + - - +
51Q MET* 3.1 29.8 + - - +
75Q LYS* 2.7 42.4 + - - -
78Q ASP* 3.8 16.2 - - - +
82Q GLU* 4.8 9.6 - - + +
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Residues in contact with LEU 48 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q THR 5.2 1.3 - - - +
30Q LYS* 4.8 11.0 - - - +
32Q LEU* 3.9 18.1 - - + +
33Q GLY* 3.1 38.8 - - - +
36Q MET* 4.5 13.9 - - - -
43Q PRO* 5.0 2.0 - - + +
44Q THR 3.2 12.4 + - - +
45Q GLU* 3.4 24.2 - - + +
47Q GLU* 1.3 78.3 - - - +
49Q GLN* 1.3 77.7 + - + +
51Q MET* 3.3 8.1 + - - +
52Q ILE* 2.7 42.6 + - + +
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Residues in contact with GLN 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q LYS* 5.9 0.9 + - - -
45Q GLU 3.4 14.7 + - - +
46Q ALA* 2.9 14.5 + - - +
48Q LEU* 1.3 85.4 - - + +
50Q ASP* 1.3 61.7 + - - +
52Q ILE* 3.4 22.4 - - - +
53Q ASN* 2.9 30.3 + - - +
58Q ASP* 5.7 1.2 + - - -
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Residues in contact with ASP 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Q ALA* 2.9 23.2 + - - +
47Q GLU* 3.3 12.5 + - - +
49Q GLN* 1.3 74.6 - - - +
51Q MET* 1.4 56.9 + - - +
53Q ASN* 3.0 23.6 + - - +
75Q LYS* 5.6 4.8 - - - +
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Residues in contact with MET 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q LEU* 4.7 4.5 - - + +
36Q MET* 3.4 34.5 - - + -
43Q PRO* 6.3 1.6 - - - -
47Q GLU* 3.1 22.0 + - - +
48Q LEU 3.8 3.6 - - - +
50Q ASP* 1.4 78.7 - - - +
52Q ILE* 1.4 62.3 + - - +
53Q ASN 3.4 9.6 - - - +
57Q ALA* 5.6 0.2 - - - +
68Q PHE* 6.0 0.9 - - + -
71Q MET* 3.7 61.9 - - + +
72Q MET* 4.6 2.0 - - - +
74Q ARG* 5.9 4.3 - - - +
75Q LYS* 3.8 43.3 - - + -
79Q THR* 4.5 9.0 - - - +
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Residues in contact with ILE 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Q THR* 4.1 39.0 - - + +
32Q LEU* 3.6 25.4 - - + -
48Q LEU* 2.7 30.3 + - + +
49Q GLN* 3.4 34.5 - - - +
51Q MET* 1.4 68.8 - - - +
53Q ASN* 1.4 68.3 + - - +
57Q ALA* 3.5 23.2 - - + +
58Q ASP* 3.3 21.6 + - - +
63Q ILE* 5.0 4.9 - - + -
67Q GLU* 5.4 0.9 - - - +
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Residues in contact with ASN 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q GLN* 2.9 25.1 + - - +
50Q ASP* 3.0 29.5 + - - +
51Q MET* 3.5 13.0 - - - +
52Q ILE* 1.4 85.7 - - + +
54Q GLU* 1.3 64.2 + - - +
58Q ASP* 3.4 23.3 - - - +
74Q ARG* 5.5 2.1 + - - -
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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