Contacts of the helix formed by residues 34 - 49 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C GLU 3.5 4.7 + - - +
33C VAL* 1.3 72.8 - - - +
35C LEU* 1.3 61.6 + - - +
36C GLU* 3.4 21.3 + - - +
37C ARG* 3.2 35.2 + - + +
38C LEU* 3.2 22.5 + - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.0 23.5 + - + +
34C ASP* 1.3 71.4 + - - +
36C GLU* 1.3 61.3 + - + +
38C LEU* 3.2 7.0 + - + +
39C GLN* 2.9 42.4 + - - +
66C ALA* 3.7 31.3 - - + +
67C LYS* 4.3 26.5 - - + +
70C ALA* 3.9 19.1 - - + -
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 3.3 11.6 - - - +
35C LEU* 1.3 79.8 - - + +
37C ARG* 1.3 63.3 + - - +
39C GLN* 3.3 28.1 + - - +
40C ALA* 3.1 21.8 + - - +
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 3.2 35.9 + - + +
36C GLU* 1.3 78.2 - - - +
38C LEU* 1.3 58.7 + - + +
40C ALA* 3.3 7.4 + - + +
41C LEU* 3.0 48.9 + - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.6 28.5 - - + -
34C ASP 3.2 10.0 + - - +
35C LEU* 3.2 9.5 + - + +
37C ARG* 1.3 77.2 - - + +
39C GLN* 1.3 54.8 + - - +
41C LEU* 3.2 18.5 + - + +
42C ALA* 2.8 36.8 + - - +
66C ALA* 3.8 35.0 - - + +
69C TRP* 4.7 13.2 - - + -
70C ALA 5.1 0.7 - - - +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 2.9 25.0 + - - +
36C GLU* 3.3 33.0 + - - +
38C LEU* 1.3 75.5 - - - +
40C ALA* 1.3 58.4 + - - +
42C ALA 3.3 0.2 + - - -
43C ALA* 2.8 28.2 + - - +
62C PRO* 3.3 39.5 - - + +
63C GLU* 3.8 30.1 + - - +
66C ALA* 3.7 6.5 - - + +
67C LYS* 5.8 1.2 + - - -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLU 3.1 10.0 + - - +
37C ARG* 3.6 10.8 - - + +
38C LEU 3.2 0.2 - - - -
39C GLN* 1.3 78.1 - - - +
41C LEU* 1.3 65.1 + - + +
43C ALA* 3.3 7.7 + - - +
44C GLU* 3.1 23.6 + - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ARG* 3.0 38.3 + - + +
38C LEU* 3.2 21.5 + - + +
40C ALA* 1.3 79.1 - - + +
42C ALA* 1.3 56.5 + - - +
44C GLU* 3.3 11.6 + - + +
45C TRP* 2.9 29.9 + - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 2.8 20.1 + - - +
39C GLN 3.6 4.5 - - - +
41C LEU* 1.3 70.7 - - - +
43C ALA* 1.3 64.3 + - - +
45C TRP* 3.2 9.6 + - - +
46C LEU* 3.1 28.9 + - + +
61C THR* 6.0 0.7 - - + -
62C PRO* 3.7 24.7 - - + +
65C VAL* 4.4 20.6 - - + -
66C ALA 5.6 0.2 - - - +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN 2.8 17.7 + - - +
40C ALA* 3.5 8.3 - - - +
41C LEU 3.3 0.2 - - - -
42C ALA* 1.3 76.8 - - - +
44C GLU* 1.3 60.1 + - - +
46C LEU* 3.4 18.5 + - - +
47C GLN* 3.5 10.4 + - - +
53C PRO* 3.8 15.4 - - + +
62C PRO* 4.0 13.0 - - + +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 3.1 16.1 + - - +
41C LEU* 3.8 11.4 - - + +
43C ALA* 1.3 74.2 - - - +
45C TRP* 1.3 64.0 + - - +
47C GLN* 3.1 20.0 - - + +
48C VAL* 3.0 44.9 + - + +
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Residues in contact with TRP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU 2.9 15.2 + - - +
42C ALA* 3.3 14.4 - - - +
43C ALA 3.2 0.4 - - - -
44C GLU* 1.3 78.0 - - - +
46C LEU* 1.3 66.1 + - + +
48C VAL* 3.5 6.0 + - + +
49C ILE* 3.2 58.0 + - + +
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 3.1 19.2 + - + +
43C ALA* 3.6 10.8 - - - +
44C GLU 3.3 0.2 - - - -
45C TRP* 1.3 80.1 - - + +
47C GLN* 1.3 59.1 + - - +
49C ILE* 3.2 21.6 - - + +
51C GLU* 2.9 34.7 + - + +
53C PRO* 3.9 16.2 - - + +
58C LEU* 4.1 37.7 - - + +
61C THR* 4.2 24.7 - - + -
62C PRO* 4.2 15.7 - - + -
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Residues in contact with GLN 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA 3.5 3.2 + - - +
44C GLU* 3.1 28.9 + - - +
46C LEU* 1.3 77.1 - - - +
48C VAL* 1.3 76.6 + - + +
50C GLY* 3.1 14.7 + - - -
51C GLU 3.6 10.6 + - - +
53C PRO* 3.8 18.6 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLU* 3.0 33.1 + - + +
45C TRP* 3.5 7.2 + - + +
47C GLN* 1.3 85.7 - - + +
49C ILE* 1.3 63.9 + - + +
50C GLY* 3.1 1.4 + - - -
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C TRP* 3.2 44.3 + - + +
46C LEU* 3.2 32.1 - - + +
48C VAL* 1.3 77.8 - - + +
50C GLY* 1.3 57.1 + - - +
51C GLU* 4.2 12.3 - - + +
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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