Contacts of the helix formed by residues 34 - 45 (chain B) in PDB entry 4DKE
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 GLU 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLU* 1.3 92.2 - - + +
35B CYS* 1.3 69.7 + - - +
36B THR 3.0 6.4 + - - -
37B VAL* 3.1 21.6 + - + +
38B THR* 3.3 16.3 + - + +
88B ARG* 5.3 7.8 + - - -
91B ARG* 4.0 20.1 + - - -
129B VAL* 5.8 2.1 - - - +
132B GLY* 5.3 5.7 - - - +
133B LEU* 5.7 4.5 - - - +
176B TYR* 4.1 24.8 + - + +
179B CYS* 5.5 5.9 - - - -
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Residues in contact with CYS 35 (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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33B GLU 3.5 7.3 - - - +
34B GLU* 1.3 83.8 - - - +
36B THR* 1.3 57.3 + - - +
38B THR* 3.1 11.3 + - - -
39B GLY* 3.1 22.0 + - - -
176B TYR* 4.5 8.1 - - - -
179B CYS* 4.4 9.9 - - - -
180B CYS* 2.0 53.2 - - + -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 2.6 36.4 - - - +
35B CYS* 1.3 77.3 - - - +
37B VAL* 1.3 70.2 + - + +
39B GLY* 3.4 2.6 + - - -
40B PHE* 3.4 35.1 + - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU 4.4 4.0 - - - +
34B GLU* 3.5 13.2 - - + +
36B THR* 1.3 84.1 - - + +
38B THR* 1.3 57.6 + - - +
39B GLY 3.0 4.5 - - - -
40B PHE* 2.9 31.4 + - + +
41B LEU* 3.2 10.1 + - + +
125B LEU* 3.8 15.6 - - + +
128B ASN* 3.9 26.0 - - + +
129B VAL* 3.8 26.7 - - + +
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Residues in contact with THR 38 (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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34B GLU* 3.3 7.6 + - + +
35B CYS* 3.1 23.2 + - - -
37B VAL* 1.3 75.2 - - - +
39B GLY* 1.3 57.0 + - - +
41B LEU* 3.3 14.8 - - + +
42B ARG* 2.9 26.3 + - - +
94B TRP* 5.1 1.8 - - + -
129B VAL* 4.3 18.4 - - + -
172B MET* 3.9 18.8 - - - +
176B TYR* 3.6 44.7 - - + +
180B CYS* 5.3 0.7 - - - -
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Residues in contact with GLY 39 (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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35B CYS 3.1 16.2 + - - -
36B THR* 3.8 4.0 - - - -
37B VAL 3.0 1.2 - - - -
38B THR* 1.3 76.6 - - - +
40B PHE* 1.3 59.8 + - - +
42B ARG* 3.1 10.4 + - - +
43B ASP* 2.9 28.8 + - - +
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Residues in contact with PHE 40 (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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36B THR* 3.4 32.2 + - + -
37B VAL* 2.9 16.7 + - + +
39B GLY* 1.3 75.2 - - - +
41B LEU* 1.3 57.5 + - - +
43B ASP* 3.2 10.6 + - + +
44B LYS* 2.9 31.8 + - + +
125B LEU* 4.2 21.1 - - + -
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Residues in contact with LEU 41 (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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37B VAL 3.2 7.3 + - - +
38B THR* 3.3 15.3 - - - +
39B GLY 3.2 0.2 - - - -
40B PHE* 1.3 79.2 - - - +
42B ARG* 1.3 52.9 + - - +
44B LYS* 2.7 8.9 + - + +
45B LEU* 2.6 54.0 + - + +
94B TRP* 3.9 17.5 - - + -
122B VAL* 4.1 19.5 - - + +
125B LEU* 3.8 30.7 - - + +
126B LEU* 4.5 15.9 - - + +
129B VAL* 4.6 12.3 - - + -
172B MET* 3.9 24.2 - - + -
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Residues in contact with ARG 42 (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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38B THR 2.9 16.8 + - - +
39B GLY* 3.4 12.8 - - - +
41B LEU* 1.3 74.6 - - - +
43B ASP* 1.3 60.9 + - - +
45B LEU 3.9 1.0 - - - -
46B GLN* 3.4 20.8 + - - +
169B PHE* 4.1 15.7 - - + -
172B MET* 3.9 16.1 - - + +
173B GLU* 3.0 41.1 + - - +
177B CYS* 4.9 16.2 - - - +
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Residues in contact with ASP 43 (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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39B GLY 2.9 12.7 + - - +
40B PHE* 3.5 13.4 - - + +
42B ARG* 1.3 76.2 - - - +
44B LYS* 1.3 61.8 + - + +
46B GLN* 3.1 38.2 + - - +
49B SER* 4.8 0.5 + - - -
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Residues in contact with LYS 44 (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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40B PHE* 2.9 15.6 + - + +
41B LEU* 2.7 15.5 + - + +
43B ASP* 1.3 76.9 - - - +
45B LEU* 1.3 54.0 + - + +
46B GLN 3.2 3.6 + - - -
49B SER* 3.4 13.3 + - - -
118B TYR* 2.7 45.2 + - - -
121B GLU* 2.8 39.7 + - - -
122B VAL* 4.7 13.2 - - + -
125B LEU* 3.6 22.0 - - + -
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Residues in contact with LEU 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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41B LEU* 2.6 39.5 + - + +
42B ARG 3.9 2.9 - - - -
44B LYS* 1.3 72.3 - - + +
46B GLN* 1.3 57.0 + - - +
50B ARG* 2.7 40.7 + - + +
118B TYR* 3.5 17.7 - - - +
122B VAL* 4.3 18.6 - - + -
165B LEU* 3.9 29.8 - - + -
168B CYS* 4.0 27.1 - - + -
169B PHE* 3.3 27.4 - - + +
172B MET* 5.0 4.0 - - + -
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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