Contacts of the helix formed by residues 36 - 46 (chain C) in PDB entry 4WLU
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 ILE 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLY* 1.3 73.6 - - - +
37C GLY* 1.3 66.8 + - - +
38C GLN 3.2 0.3 + - - -
39C PRO* 3.3 3.3 - - - +
40C LEU* 2.9 39.9 + - + +
99C PRO* 4.0 15.9 - - + -
140C ILE* 4.0 8.1 - - + -
247C ALA 3.8 14.1 - - - +
248C THR* 3.9 13.5 - - - +
251C MET* 3.6 17.0 - - + -
252C ALA* 4.1 10.7 - - - +
402C NAD 2.9 73.3 + - + +
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Residues in contact with GLY 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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29C VAL* 4.4 1.7 - - - +
31C GLY 3.4 23.5 + - - -
32C ALA* 3.0 12.6 - - - -
34C GLY 3.4 4.9 + - - -
36C ILE* 1.3 79.0 - - - +
38C GLN* 1.3 54.0 + - - +
40C LEU* 3.7 3.1 - - - +
41C SER* 2.7 36.9 + - - -
99C PRO* 4.2 10.4 - - - +
402C NAD 4.3 1.4 + - - -
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Residues in contact with GLN 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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32C ALA 3.1 17.8 + - - +
33C SER* 2.9 22.1 + - - +
34C GLY 3.1 14.7 + - - +
37C GLY* 1.3 72.1 - - - +
39C PRO* 1.3 67.8 - - + +
41C SER* 3.2 6.6 + - - -
42C LEU* 2.9 26.0 + - - +
60C HIS* 5.7 2.2 - - - +
64C VAL* 3.7 24.2 - - + +
67C ASP* 5.4 0.2 - - - +
241D LYS* 4.9 3.9 + - - +
248D THR* 4.2 8.8 + - - -
249D LEU* 3.7 34.9 - - + +
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Residues in contact with PRO 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 GLY 3.0 29.2 - - - +
36C ILE* 3.3 7.4 - - - +
38C GLN* 1.3 88.2 - - + +
40C LEU* 1.3 62.7 + - - +
42C LEU* 3.2 11.2 + - + +
43C LEU* 3.0 27.7 + - - +
248C THR 4.5 1.3 - - - +
249C LEU* 4.1 17.9 - - + -
252C ALA* 3.7 17.9 - - + -
39D PRO* 5.0 7.0 - - + -
42D LEU* 3.8 18.2 - - + -
249D LEU* 4.3 5.6 - - + -
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Residues in contact with LEU 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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29C VAL* 4.4 8.5 - - + -
36C ILE* 2.9 23.3 + - + +
37C GLY 3.7 2.7 - - - +
39C PRO* 1.3 75.3 - - - +
41C SER* 1.3 58.6 + - - +
43C LEU* 3.2 3.4 + - - +
44C LEU* 3.0 45.6 + - + +
97C VAL* 3.7 32.1 - - + -
99C PRO* 4.4 14.1 - - + -
140C ILE* 4.1 13.0 - - + -
252C ALA* 3.4 19.3 - - + +
255C GLY* 3.9 5.6 - - - -
256C ALA* 3.5 33.4 - - + +
259C VAL* 5.5 1.1 - - + -
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Residues in contact with SER 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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29C VAL* 3.8 12.0 - - - +
32C ALA* 3.9 3.6 - - - +
37C GLY 2.7 22.8 + - - -
38C GLN* 3.5 6.1 - - - -
40C LEU* 1.3 75.1 - - - +
42C LEU* 1.3 59.1 + - - +
44C LEU* 4.4 8.7 - - - -
45C LYS* 2.9 31.9 + - - +
53C LEU* 3.6 4.8 - - - +
55C LEU* 3.3 27.1 - - - +
64C VAL* 5.3 0.4 - - - -
68C LEU* 3.7 20.4 - - - -
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Residues in contact with LEU 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 GLN 2.9 12.9 + - - +
39C PRO* 3.2 12.8 + - + +
41C SER* 1.3 76.1 - - - +
43C LEU* 1.3 59.9 + - + +
45C LYS* 3.3 1.9 + - - +
46C ASN* 3.0 50.4 + - - +
68C LEU* 3.8 13.4 - - + +
71C ILE* 3.7 22.0 - - + -
39D PRO* 3.9 28.0 - - + +
42D LEU* 5.7 2.2 - - + -
43D LEU* 4.2 23.3 - - + -
249D LEU* 3.6 31.2 - - + +
252D ALA* 4.5 0.2 - - + -
253D TYR* 4.4 4.5 - - + -
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Residues in contact with LEU 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 PRO 3.0 16.9 + - - +
40C LEU 3.2 6.3 + - - +
42C LEU* 1.3 77.3 - - + +
44C LEU* 1.3 62.0 + - - +
46C ASN* 3.5 9.6 + - + +
47C SER 3.4 14.0 + - - -
252C ALA 3.6 28.3 - - - +
253C TYR* 3.8 15.7 - - + +
256C ALA* 3.7 17.3 - - + -
260C PHE* 3.6 15.1 - - + -
42D LEU* 4.4 14.4 - - + -
43D LEU* 4.0 21.8 - - + -
46D ASN* 3.9 22.0 - - - +
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Residues in contact with LEU 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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27C VAL* 4.0 10.8 - - + -
29C VAL* 3.4 33.2 - - + -
40C LEU* 3.0 36.4 + - + +
41C SER 3.7 3.8 - - - +
43C LEU* 1.3 74.2 - - - +
45C LYS* 1.3 64.1 + - - +
47C SER* 3.1 18.7 + - - -
50C VAL* 3.6 25.7 - - + +
53C LEU* 3.8 18.2 - - + -
97C VAL* 4.8 3.6 - - + -
256C ALA* 4.9 1.8 - - - -
259C VAL* 3.9 31.9 - - + -
260C PHE* 4.0 16.4 - - + -
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Residues in contact with LYS 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 SER 2.9 17.9 + - - +
42C LEU 3.7 4.5 - - - +
44C LEU* 1.3 76.7 - - - +
46C ASN* 1.3 57.7 + - - +
47C SER 3.3 3.8 + - - +
53C LEU* 3.9 13.4 - - + +
68C LEU* 3.2 34.5 - - + +
69C SER* 4.7 5.0 + - - +
71C ILE* 3.4 29.9 + - + -
73C THR* 2.7 59.2 + - - +
75C ALA* 2.5 36.2 + - + +
77C VAL* 3.7 18.3 - - + +
179D THR* 6.0 0.4 - - - +
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Residues in contact with ASN 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 LEU* 3.0 40.5 + - - +
43C LEU* 3.7 10.8 - - + +
44C LEU 3.2 0.6 - - - -
45C LYS* 1.3 76.9 - - - +
47C SER* 1.3 59.5 + - - +
48C PRO* 3.9 4.2 - - - +
71C ILE* 3.9 8.7 - - - +
73C THR* 4.1 16.2 - - - +
43D LEU* 3.9 22.6 - - - +
253D TYR* 3.5 30.5 - - + -
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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