Contacts of the helix formed by residues 34 - 49 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU 3.8 2.8 + - - +
33A VAL* 1.3 72.5 - - - +
35A LEU* 1.3 62.8 + - - +
36A GLU* 3.3 21.0 + - - +
37A ARG* 3.2 24.7 + - + +
38A LEU* 3.2 22.9 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.0 21.9 + - + +
34A ASP* 1.3 72.5 + - - +
36A GLU* 1.3 62.6 + - + +
38A LEU* 3.3 5.6 + - + +
39A GLN* 2.9 45.7 + - - +
66A ALA* 3.6 32.2 - - + +
67A LYS* 4.2 25.6 - - + +
70A ALA* 3.9 18.6 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.2 10.5 - - - +
35A LEU* 1.3 80.5 - - + +
37A ARG* 1.3 61.8 + - - +
39A GLN* 3.4 27.8 + - - +
40A ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.2 30.4 + - + +
36A GLU* 1.3 75.8 - - - +
38A LEU* 1.3 61.4 + - + +
40A ALA* 3.2 25.5 + - - +
41A LEU* 2.9 62.7 + - + +
44A GLU* 5.5 5.9 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.4 28.7 - - + -
34A ASP 3.2 13.7 + - - +
35A LEU* 3.3 9.8 + - + +
37A ARG* 1.3 76.7 - - + +
39A GLN* 1.3 57.1 + - - +
41A LEU* 3.2 18.6 + - + +
42A ALA* 2.9 31.5 + - - +
66A ALA* 3.7 34.8 - - + +
69A TRP* 4.5 14.4 - - + -
70A ALA 4.8 1.1 - - - +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 2.9 29.4 + - - +
36A GLU* 3.5 31.2 + - - +
38A LEU* 1.3 76.3 - - - +
40A ALA* 1.3 57.3 + - - +
42A ALA 3.4 0.5 + - - -
43A ALA* 2.9 31.1 + - - +
62A PRO* 3.4 34.6 - - + +
63A GLU* 3.8 29.2 + - - +
66A ALA* 3.7 6.3 - - + +
67A LYS* 6.1 1.2 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLU 3.1 13.0 + - - +
37A ARG* 3.2 32.1 + - - +
39A GLN* 1.3 77.0 - - - +
41A LEU* 1.3 61.7 + - - +
43A ALA* 3.4 7.4 + - - +
44A GLU* 3.1 24.7 + - - +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.9 57.7 + - + +
38A LEU* 3.6 17.7 - - + +
40A ALA* 1.3 78.0 - - - +
42A ALA* 1.3 56.4 + - - +
44A GLU* 3.3 12.6 + - + +
45A TRP* 2.8 31.0 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 2.9 16.8 + - - +
39A GLN 3.7 4.0 - - - +
41A LEU* 1.3 73.9 - - - +
43A ALA* 1.3 66.0 + - - +
45A TRP* 3.1 9.5 + - - +
46A LEU* 3.0 29.2 + - + +
61A THR* 6.1 0.4 - - + -
62A PRO* 3.9 23.6 - - + +
65A VAL* 4.3 22.0 - - + -
66A ALA 5.5 0.2 - - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN 2.9 18.6 + - - +
40A ALA* 3.6 7.9 - - - +
41A LEU 3.3 0.2 - - - -
42A ALA* 1.3 78.2 - - - +
44A GLU* 1.3 61.7 + - - +
46A LEU* 3.4 13.8 + - - +
47A GLN* 3.5 10.4 + - - +
53A PRO* 3.8 15.7 - - + +
62A PRO* 3.9 19.2 - - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 5.5 5.0 + - - -
40A ALA 3.1 16.6 + - - +
41A LEU* 3.7 13.2 - - + +
43A ALA* 1.3 73.2 - - - +
45A TRP* 1.3 64.7 + - - +
47A GLN* 3.0 32.0 + - - +
48A VAL* 3.0 35.5 + - + +
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Residues in contact with TRP 45 (chain A).
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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41A LEU 2.8 15.5 + - - +
42A ALA* 3.1 14.5 + - - +
44A GLU* 1.3 77.1 - - - +
46A LEU* 1.3 66.8 + - + +
48A VAL* 3.2 9.0 + - + +
49A ILE* 3.1 54.0 + - + +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.0 18.8 + - + +
43A ALA* 3.5 8.5 - - - +
45A TRP* 1.3 81.3 - - + +
47A GLN* 1.3 60.1 + - - +
49A ILE* 3.2 23.3 - - + +
51A GLU* 3.0 33.8 + - + +
53A PRO* 4.0 16.6 - - + -
58A LEU* 4.2 42.4 - - + +
61A THR* 4.3 16.8 - - + -
62A PRO* 4.2 21.8 - - + -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.5 2.7 + - - +
44A GLU* 3.0 47.4 + - + +
46A LEU* 1.3 76.0 - - - +
48A VAL* 1.3 69.4 + - + +
50A GLY* 3.1 14.0 + - - -
51A GLU 3.8 9.7 - - - +
53A PRO* 3.9 17.9 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 3.0 34.4 + - + +
45A TRP* 3.2 8.7 + - + +
47A GLN* 1.3 82.9 - - + +
49A ILE* 1.3 62.8 + - + +
50A GLY* 3.3 1.6 + - - -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.1 41.9 + - + +
46A LEU* 3.2 33.2 - - + +
48A VAL* 1.3 78.8 - - + +
50A GLY* 1.3 56.6 + - - +
51A GLU* 4.2 13.9 - - + +
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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