Contacts of the helix formed by residues 35 - 46 (chain B) in PDB entry 4UTX
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 ASP 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B SER* 3.1 20.0 + - - +
34B SER* 1.3 73.6 - - - +
36B LEU* 1.3 64.9 + - - +
37B THR* 3.1 20.4 + - - -
38B ALA* 3.3 26.6 + - + +
39B PHE* 3.3 12.3 + - - +
283B TYR* 4.3 2.5 - - - -
285B PHE* 4.2 4.1 - - - -
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Residues in contact with LEU 36 (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 SER 3.4 6.0 + - - +
35B ASP* 1.3 73.5 + - - +
37B THR* 1.3 60.0 + - + +
39B PHE* 3.1 14.4 + - + +
40B ARG* 2.9 47.9 + - + +
285B PHE* 3.8 22.4 - - + -
292B THR 6.1 0.4 - - - +
295B PRO* 5.1 14.6 - - + +
296B ALA* 4.3 14.8 - - + -
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Residues in contact with THR 37 (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 ASP* 3.1 14.2 + - - -
36B LEU* 1.3 78.6 - - + +
38B ALA* 1.3 62.3 + - - +
40B ARG* 3.4 11.3 + - + +
41B GLU* 3.1 29.6 + - + +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 4.7 1.6 - - - +
35B ASP* 3.3 29.7 + - + +
36B LEU 3.2 0.2 - - - -
37B THR* 1.3 79.8 + - - +
39B PHE* 1.3 61.8 + - - +
41B GLU* 3.2 24.8 + - - +
42B HIS* 3.4 14.2 + - - -
283B TYR* 4.0 17.3 - - + +
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Residues in contact with PHE 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 ASP 3.3 2.5 + - - +
36B LEU* 3.1 16.7 + - + +
38B ALA* 1.3 77.8 - - - +
40B ARG* 1.3 72.9 + - + +
42B HIS* 2.9 15.8 + - + +
43B PHE* 2.9 29.2 + + + -
240B LEU* 4.6 12.6 - - + -
242B LEU* 4.1 22.2 - - + -
268B ALA* 3.9 29.6 - - + -
270B PHE* 4.4 11.0 - + - -
283B TYR* 4.0 22.8 - + + -
285B PHE* 4.0 23.3 - + + -
296B ALA* 3.6 33.0 - - + -
297B LEU* 4.8 2.2 - - + -
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Residues in contact with ARG 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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106A ARG* 5.6 2.2 - - - +
36B LEU* 2.9 42.4 + - + +
37B THR* 3.8 12.1 - - + +
38B ALA 3.3 0.2 - - - -
39B PHE* 1.3 79.4 - - + +
41B GLU* 1.3 57.7 + - - +
43B PHE* 3.1 25.7 + - - +
44B ALA* 2.8 30.8 + - - +
295B PRO 3.7 8.7 + - - -
296B ALA 3.1 25.3 + - - -
298B GLU* 2.2 47.2 + - - +
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Residues in contact with GLU 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 THR* 3.1 18.9 + - + +
38B ALA* 3.3 15.7 - - - +
39B PHE 3.1 0.2 - - - -
40B ARG* 1.3 77.8 - - - +
42B HIS* 1.3 64.2 + - + +
44B ALA* 3.5 15.3 - - - +
45B LYS* 3.7 17.9 - - - +
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Residues in contact with HIS 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 ALA 3.4 16.9 + - - -
39B PHE* 2.9 8.8 + - + +
41B GLU* 1.3 75.9 - - + +
43B PHE* 1.3 60.2 - - - +
45B LYS* 2.8 30.4 + - - +
46B ALA* 3.0 11.8 + - - +
239B ASP 5.7 0.6 + - - -
240B LEU* 4.6 17.3 - - + -
266B PRO* 3.5 29.0 - - + +
283B TYR* 2.7 33.5 + + + -
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Residues in contact with PHE 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 PHE* 2.9 19.6 + + + +
40B ARG* 3.2 39.9 - - - +
42B HIS* 1.3 80.3 - - - +
44B ALA* 1.3 65.8 + - - +
45B LYS 3.2 0.9 + - - -
46B ALA* 3.2 6.9 + - - +
49B ILE* 4.0 24.2 - - + -
120B CYS* 4.0 15.9 - - - -
123B ARG* 4.5 3.1 - - - -
124B LEU* 4.5 10.5 - - + -
129B ARG* 2.8 20.1 + - - -
240B LEU* 4.0 12.9 - - + +
242B LEU* 6.2 0.2 - - + -
296B ALA 3.8 7.2 - - - -
297B LEU* 3.3 51.1 - - + -
298B GLU 3.8 2.2 - - - -
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Residues in contact with ALA 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 ARG 2.8 15.0 + - - +
41B GLU* 3.5 15.0 - - - +
43B PHE* 1.3 76.1 - - - +
45B LYS* 1.3 59.8 + - + +
129B ARG* 3.0 19.9 + - - +
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Residues in contact with LYS 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 GLU* 3.7 16.2 - - - +
42B HIS* 2.8 14.5 + - - +
44B ALA* 1.3 75.6 - - + +
46B ALA* 1.3 68.6 + - - +
47B LYS* 3.4 19.4 + - - +
129B ARG* 4.9 0.3 + - - -
239B ASP* 4.6 1.8 - - - +
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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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42B HIS 3.0 10.9 + - - +
43B PHE 3.2 13.4 + - - +
45B LYS* 1.3 76.2 - - - +
47B LYS* 1.3 58.8 + - - +
49B ILE* 3.5 31.4 - - + +
124B LEU* 5.0 0.3 - - - +
129B ARG* 2.7 33.6 + - - +
239B ASP* 3.5 15.9 - - - +
240B LEU* 3.9 13.0 - - + -
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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