Contacts of the helix formed by residues 34 - 49 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D GLU 3.8 2.2 + - - -
33D VAL* 1.3 69.2 - - - +
35D LEU* 1.3 64.0 + - - +
36D GLU* 3.1 22.7 + - - +
37D ARG* 3.2 33.1 + - + +
38D LEU* 3.2 25.3 + - - +
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Residues in contact with LEU 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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32D GLU* 6.1 0.4 - - - +
33D VAL* 3.0 20.2 + - + +
34D ASP* 1.3 71.8 + - - +
36D GLU* 1.3 60.3 + - + +
38D LEU* 4.4 4.5 - - + -
39D GLN* 2.9 47.8 + - - +
66D ALA* 3.6 32.2 - - + +
67D LYS* 4.2 15.9 - - + +
70D ALA* 3.9 18.6 - - + -
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Residues in contact with GLU 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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34D ASP* 3.1 11.1 + - - +
35D LEU* 1.3 78.6 - - + +
37D ARG* 1.3 61.9 + - - +
39D GLN* 3.5 21.9 + - - +
40D ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 37 (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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34D ASP* 3.2 31.2 + - + +
36D GLU* 1.3 76.2 - - - +
38D LEU* 1.3 67.5 + - + +
40D ALA* 3.3 7.1 + - + +
41D LEU* 2.9 47.1 + - + +
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Residues in contact with LEU 38 (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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33D VAL* 4.5 21.5 - - + -
34D ASP 3.2 17.5 + - - +
35D LEU* 3.7 3.8 - - + +
36D GLU 3.3 0.2 - - - -
37D ARG* 1.3 76.8 - - + +
39D GLN* 1.3 58.0 + - - +
41D LEU* 3.2 17.3 + - + +
42D ALA* 2.8 31.3 + - - +
66D ALA* 3.6 39.0 - - + +
69D TRP* 4.6 14.6 - - + -
70D ALA 4.9 1.1 - - - +
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Residues in contact with GLN 39 (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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35D LEU* 2.9 39.3 + - - +
36D GLU* 3.7 25.1 + - - +
37D ARG 3.3 0.2 - - - -
38D LEU* 1.3 77.0 - - - +
40D ALA* 1.3 55.8 + - - +
42D ALA* 3.3 0.6 + - - -
43D ALA* 2.9 32.0 + - - +
62D PRO* 3.5 34.1 - - + +
63D GLU* 3.8 32.6 + - - +
66D ALA* 3.6 6.0 - - + +
67D LYS* 5.7 1.6 - - - +
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Residues in contact with ALA 40 (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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36D GLU 3.1 17.0 + - - +
37D ARG* 3.7 8.1 - - + +
39D GLN* 1.3 77.3 - - - +
41D LEU* 1.3 63.7 + - + +
43D ALA* 3.5 6.7 + - - +
44D GLU* 3.2 23.7 + - - +
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Residues in contact with LEU 41 (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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37D ARG* 2.9 40.5 + - + +
38D LEU* 3.6 18.6 - - + +
40D ALA* 1.3 77.0 - - + +
42D ALA* 1.3 58.0 + - - +
44D GLU* 3.4 9.7 + - - +
45D TRP* 2.9 30.4 + - + +
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Residues in contact with ALA 42 (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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38D LEU 2.8 17.5 + - - +
39D GLN 3.7 3.8 - - - +
41D LEU* 1.3 75.1 - - - +
43D ALA* 1.3 65.0 + - - +
45D TRP* 3.1 9.6 + - - +
46D LEU* 3.0 28.6 + - + +
61D THR* 6.2 0.2 - - + -
62D PRO* 3.9 21.3 - - + +
65D VAL* 4.3 23.6 - - + -
66D ALA 5.5 0.2 - - - +
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Residues in contact with ALA 43 (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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39D GLN 2.9 17.8 + - - +
40D ALA* 3.8 8.5 - - - +
41D LEU 3.3 0.2 - - - -
42D ALA* 1.3 75.6 - - - +
44D GLU* 1.3 62.5 + - - +
46D LEU* 3.4 8.3 + - - +
47D GLN* 3.4 25.3 + - - +
53D PRO* 3.7 9.6 - - + +
62D PRO* 3.9 20.4 - - + +
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Residues in contact with GLU 44 (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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40D ALA 3.2 15.2 + - - +
41D LEU* 3.8 9.4 - - - +
42D ALA 3.2 0.2 - - - -
43D ALA* 1.3 76.6 - - - +
45D TRP* 1.3 66.3 + - - +
47D GLN* 3.0 20.3 + - + +
48D VAL* 2.9 38.0 + - + +
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Residues in contact with TRP 45 (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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41D LEU 2.9 16.5 + - - +
42D ALA* 3.1 14.6 + - - +
44D GLU* 1.3 77.3 - - - +
46D LEU* 1.3 65.2 + - + +
48D VAL* 3.3 6.0 + - + +
49D ILE* 3.1 54.0 + - + +
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Residues in contact with LEU 46 (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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42D ALA* 3.0 19.3 + - + +
43D ALA 3.5 6.7 - - - +
45D TRP* 1.3 79.4 - - + +
47D GLN* 1.3 59.1 + - - +
49D ILE* 3.3 23.1 - - + +
51D GLU* 2.9 34.5 + - + +
53D PRO* 4.0 17.9 - - + -
58D LEU* 4.2 42.2 - - + -
61D THR* 4.4 11.7 - - + -
62D PRO* 4.2 26.2 - - + -
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Residues in contact with GLN 47 (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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43D ALA* 3.4 7.2 - - - +
44D GLU* 3.0 28.2 + - + +
46D LEU* 1.3 76.3 - - - +
48D VAL* 1.3 64.8 + - + +
50D GLY* 3.0 15.9 + - - -
51D GLU 3.7 9.6 + - - +
53D PRO* 3.3 28.7 - - + +
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Residues in contact with VAL 48 (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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44D GLU* 2.9 34.2 + - + +
45D TRP* 3.9 6.7 - - + +
47D GLN* 1.3 77.7 - - + +
49D ILE* 1.3 60.7 + - + +
50D GLY* 3.1 4.2 + - - -
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Residues in contact with ILE 49 (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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45D TRP* 3.1 48.1 + - + +
46D LEU* 3.3 26.5 - - + +
48D VAL* 1.3 79.0 - - + +
50D GLY* 1.3 57.1 + - - +
51D GLU* 4.3 11.5 - - + +
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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