Contacts of the helix formed by residues 47 - 51 (chain Q) in PDB entry 2DYS
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 SER 47 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43Q LYS* 4.8 2.4 - - - +
46Q ALA* 1.3 77.0 - - - +
48Q TRP* 1.3 63.7 + - - +
49Q SER* 3.1 24.2 + - - -
50Q SER* 3.2 29.2 + - - -
51Q LEU* 4.0 4.2 + - - +
56R ARG* 4.1 5.6 - - - +
95R GLU 5.4 1.9 + - - -
96R LEU 4.9 1.6 + - - -
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Residues in contact with TRP 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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44Q GLU* 3.2 25.0 + - + +
46Q ALA 3.3 1.5 + - - -
47Q SER* 1.3 70.4 + - - +
49Q SER* 1.3 63.3 - - - +
50Q SER 3.1 0.9 - - - -
51Q LEU* 3.0 39.5 - - + +
56Q LYS* 3.5 11.4 - - - -
52R LEU 4.6 0.9 - - - -
55R CYS* 3.7 8.1 - - + -
56R ARG* 3.1 74.6 - - + +
60R ASP 3.6 13.7 - - - -
61R PHE* 3.5 37.9 - + + -
64R ALA* 4.2 7.2 - - + -
96R LEU* 3.1 28.5 + - + +
97R GLY 3.5 11.0 - - - +
98R ILE* 3.6 33.4 - - + -
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Residues in contact with SER 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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47Q SER* 3.1 13.0 + - - -
48Q TRP* 1.3 80.8 - - - +
50Q SER* 1.3 59.8 + - - +
51Q LEU 3.1 7.3 + - - +
56Q LYS* 5.1 2.6 + - - +
94R ASN 4.2 6.6 + - - -
95R GLU 4.5 3.3 + - - -
96R LEU 4.2 1.0 - - - -
97R GLY* 3.4 24.8 + - - -
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Residues in contact with SER 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q LYS* 3.3 26.5 + - - -
46Q ALA* 5.7 4.2 - - - +
47Q SER* 3.2 23.3 + - - -
48Q TRP 3.1 0.8 - - - -
49Q SER* 1.3 76.5 - - - +
51Q LEU* 1.3 59.5 + - - +
52Q SER 3.9 0.3 + - - -
55Q GLU* 4.0 0.2 - - - +
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Residues in contact with LEU 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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40Q LEU* 3.9 18.2 - - + -
43Q LYS* 3.9 32.1 - - + +
44Q GLU* 4.6 7.2 - - + +
47Q SER 4.0 2.8 + - - +
48Q TRP* 3.0 42.7 + - + +
49Q SER 3.6 8.5 - - - +
50Q SER* 1.3 78.4 - - - +
52Q SER* 1.3 63.2 + - - +
55Q GLU* 3.6 13.5 - - + +
56Q LYS* 4.0 24.1 + - + -
59Q LEU* 3.3 28.3 - - + -
61R PHE* 4.6 2.5 - - + -
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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