Contacts of the helix formed by residues 27 - 36 (chain D) in PDB entry 6WNX
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 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D TYR 3.8 1.8 + - - -
26D LEU* 1.3 72.3 - - - +
28D ALA* 1.3 66.6 - - - +
29D ARG* 3.9 23.0 + - - +
30D SER* 2.6 31.3 + - - -
31D LEU* 3.0 19.8 + - - +
54D LEU* 4.9 1.8 - - - -
57D ARG* 4.3 4.7 - - - +
110E LYS* 4.1 11.7 - - + +
111E GLY* 5.9 1.0 - - - -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU 4.2 0.2 + - - -
27D ASP* 1.3 70.5 - - - +
29D ARG* 1.3 57.6 + - - +
31D LEU* 3.1 9.6 + - - +
32D CYS* 2.8 36.2 + - - -
51D TRP* 4.3 13.0 - - + -
54D LEU* 4.3 11.5 - - - +
96D TYR* 3.7 39.8 + - + +
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Residues in contact with ARG 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASP* 3.1 17.3 + - - +
28D ALA* 1.3 77.1 - - - +
30D SER* 1.3 61.5 + - - +
32D CYS* 3.4 12.9 - - + +
33D ALA* 3.3 18.4 + - - +
111E GLY* 6.3 2.9 - - - -
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Residues in contact with SER 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 4.2 15.7 - - - +
27D ASP* 2.6 28.9 + - - -
29D ARG* 1.3 74.1 - - - +
31D LEU* 1.3 54.6 + - - +
32D CYS 3.2 0.4 - - - -
33D ALA* 3.1 10.9 + - - +
34D ALA* 2.9 32.9 + - - +
109E ILE* 4.9 5.5 - - - +
110E LYS* 3.8 6.9 - - - -
111E GLY* 2.8 34.3 + - - +
112E LYS 5.2 2.2 - - - -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.8 11.9 - - + +
26D LEU* 4.1 14.8 - - + +
27D ASP 3.0 12.1 + - - +
28D ALA* 3.3 9.4 - - - +
30D SER* 1.3 75.0 - - - +
32D CYS* 1.3 61.0 + - - +
34D ALA* 3.3 8.5 + - - +
35D GLU* 3.1 22.3 + - - +
45D ILE* 3.9 30.5 - - + -
50D LEU* 4.3 20.2 - - + +
51D TRP* 3.5 49.1 - - + +
54D LEU* 4.1 13.9 - - + -
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Residues in contact with CYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ALA* 2.8 29.6 + - - -
29D ARG* 3.4 11.4 - - - +
31D LEU* 1.3 72.3 - - - +
33D ALA* 1.3 65.9 + - - +
35D GLU* 3.4 28.2 + - - +
36D LEU* 3.7 15.1 + - + +
51D TRP* 4.0 17.3 - - - -
139E ASN* 3.4 37.5 + - + +
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ARG 3.3 9.8 + - - +
30D SER* 3.1 12.3 + - - +
32D CYS* 1.3 73.8 - - - +
34D ALA* 1.3 60.9 + - - +
36D LEU* 3.0 23.6 + - - +
37D VAL* 3.4 14.2 + - - +
112E LYS 3.4 26.2 - - - +
113E THR* 4.8 0.4 - - - -
114E PRO* 3.5 23.4 - - + +
117E ILE* 5.4 2.5 - - + -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.7 2.2 - - + -
26D LEU* 4.2 16.8 - - + -
30D SER 2.9 12.8 + - - +
31D LEU* 3.3 11.0 + - - +
33D ALA* 1.3 76.2 - - - +
35D GLU* 1.3 61.0 + - - +
36D LEU 3.1 1.2 + - - -
37D VAL* 3.1 27.1 + - - +
41D TRP* 3.4 29.9 - - + +
45D ILE* 3.7 14.4 - - + -
109E ILE* 5.1 3.1 - - + -
117E ILE* 5.8 1.5 - - - +
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU 3.1 18.1 + - - +
32D CYS* 3.4 10.1 - - - +
33D ALA 3.2 0.2 - - - -
34D ALA* 1.3 75.4 - - - +
36D LEU* 1.3 62.6 + - + +
37D VAL 3.6 0.5 + - - -
38D CYS 3.7 2.6 - - - +
42D GLN* 3.4 33.2 - - + +
45D ILE* 3.5 26.9 - - + +
51D TRP* 3.2 17.5 + - - -
93D ARG* 2.5 30.4 + - - -
127E PHE* 3.5 9.0 - - - -
135E VAL* 4.8 3.6 - - + +
139E ASN* 2.7 31.5 + - - -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D CYS* 3.7 17.0 + - + +
33D ALA* 3.0 9.9 + - - +
35D GLU* 1.3 74.6 - - - +
37D VAL* 1.3 64.5 + - - +
38D CYS 3.4 1.6 - - - -
114E PRO* 3.6 23.3 - - + -
118E ARG* 3.6 13.6 + - - +
127E PHE* 3.2 22.1 - - + -
132E GLU* 3.8 33.6 - - + +
135E VAL* 3.4 36.8 - - + -
136E ARG* 3.6 25.4 - - - +
139E ASN* 4.7 3.8 - - - +
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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