Contacts of the helix formed by residues 34 - 49 (chain E) in PDB entry 1WUR
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 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E VAL* 1.3 72.4 - - - +
35E LEU* 1.3 61.9 + - - +
36E GLU* 3.2 15.8 + - - +
37E ARG* 3.1 45.5 + - + +
38E LEU* 3.1 23.0 + - - +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.1 19.6 + - + +
34E ASP* 1.3 70.2 + - - +
36E GLU* 1.3 60.8 + - + +
38E LEU* 3.3 3.2 + - + -
39E GLN* 3.0 45.0 + - - +
66E ALA* 3.5 33.8 - - + +
67E LYS* 4.1 24.0 - - + +
70E ALA* 3.7 20.4 - - + -
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ASP* 3.2 10.4 - - - +
35E LEU* 1.3 80.3 - - + +
37E ARG* 1.3 61.3 + - - +
39E GLN* 3.4 24.7 + - - +
40E ALA* 3.2 21.0 + - - +
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Residues in contact with ARG 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ASP* 3.1 37.4 + - + +
36E GLU* 1.3 73.8 - - - +
38E LEU* 1.3 68.0 + - + +
40E ALA* 3.2 8.9 + - + +
41E LEU* 3.0 42.3 + - + +
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.6 28.5 - - + -
34E ASP 3.1 14.9 + - - +
35E LEU* 3.6 8.5 - - + +
37E ARG* 1.3 76.0 - - + +
39E GLN* 1.3 58.2 + - - +
41E LEU* 3.2 20.1 + - + +
42E ALA* 2.8 30.9 + - - +
66E ALA* 3.5 35.4 - - + +
69E TRP* 4.4 15.7 - - + -
70E ALA 4.8 0.7 - - - +
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Residues in contact with GLN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.0 32.8 + - - +
36E GLU* 3.5 27.4 + - - +
38E LEU* 1.3 75.5 - - - +
40E ALA* 1.3 56.8 + - - +
42E ALA 3.2 0.7 + - - -
43E ALA* 2.9 27.3 + - - +
62E PRO* 3.4 38.7 - - + +
63E GLU* 3.6 32.6 + - - +
66E ALA* 3.5 5.8 - - + +
67E LYS* 5.6 3.2 - - - +
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLU 3.2 9.4 + - - +
37E ARG* 3.2 12.2 + - + +
39E GLN* 1.3 77.6 - - - +
41E LEU* 1.3 63.8 + - + +
43E ALA* 3.4 7.5 + - - +
44E GLU* 3.2 23.6 + - - +
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Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 3.0 37.2 + - + +
38E LEU* 3.5 21.3 - - + +
40E ALA* 1.3 77.2 - - + +
42E ALA* 1.3 58.7 + - - +
44E GLU* 3.4 11.4 + - - +
45E TRP* 2.9 30.6 + - - +
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU 2.8 17.1 + - - +
39E GLN 3.2 4.7 + - - +
41E LEU* 1.3 74.3 - - - +
43E ALA* 1.3 64.4 + - - +
45E TRP* 3.2 9.3 + - - +
46E LEU* 3.1 29.8 + - + +
61E THR* 6.2 0.4 - - + -
62E PRO* 3.9 23.3 - - + +
65E VAL* 4.3 22.0 - - + -
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E GLN 2.9 16.5 + - - +
40E ALA* 3.6 8.5 - - - +
42E ALA* 1.3 74.8 - - - +
44E GLU* 1.3 61.5 + - - +
46E LEU* 3.4 9.5 + - - +
47E GLN* 3.4 25.6 + - - +
53E PRO* 3.6 10.2 - - + +
62E PRO* 3.9 19.7 - - + +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA 3.2 13.5 + - - +
41E LEU* 3.8 9.9 - - - +
43E ALA* 1.3 76.6 - - - +
45E TRP* 1.3 66.6 + - - +
47E GLN* 3.1 20.7 + - - +
48E VAL* 3.0 36.7 + - + +
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Residues in contact with TRP 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU 2.9 15.9 + - - +
42E ALA* 3.4 13.2 - - - +
44E GLU* 1.3 77.3 - - - +
46E LEU* 1.3 66.4 + - + +
48E VAL* 3.3 5.6 + - + +
49E ILE* 3.2 51.7 + - + +
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 3.1 19.9 + - + +
43E ALA* 3.4 6.5 - - - +
44E GLU 3.2 0.2 - - - -
45E TRP* 1.3 79.9 - - + +
47E GLN* 1.3 59.9 + - - +
49E ILE* 3.2 23.4 - - + +
51E GLU* 2.8 36.0 + - + +
53E PRO* 3.9 24.7 - - + -
58E LEU* 4.4 27.1 - - + -
61E THR* 4.4 15.0 - - + -
62E PRO* 4.0 28.9 - - + -
65E VAL* 6.4 0.2 - - + -
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Residues in contact with GLN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA* 3.4 10.9 + - - +
44E GLU* 3.1 31.6 + - - +
46E LEU* 1.3 74.1 - - - +
48E VAL* 1.3 62.5 + - + +
50E GLY* 3.0 20.1 + - - -
51E GLU 3.7 8.5 + - - +
53E PRO* 3.5 21.3 - - + +
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLU* 3.0 33.7 + - + +
45E TRP* 3.3 6.9 + - + +
47E GLN* 1.3 78.2 - - + +
49E ILE* 1.3 62.7 + - + +
50E GLY* 3.1 1.7 + - - -
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Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E TRP* 3.2 39.7 + - + +
46E LEU* 3.2 31.2 - - + +
48E VAL* 1.3 79.5 - - + +
50E GLY* 1.3 56.9 + - - +
51E GLU* 4.3 13.6 - - + +
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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