Contacts of the helix formed by residues 38 - 51 (chain X) in PDB entry 2OU0
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 SER 38 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25X TYR* 3.7 3.4 - - - -
34X THR* 4.6 0.2 - - - +
36X SER* 3.1 15.6 + - - +
37X PRO* 1.3 78.0 - - - +
39X LEU* 1.3 64.1 + - - +
40X ASN* 3.5 9.7 + - - +
41X ALA* 3.1 24.7 + - - +
42X ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ILE* 3.8 29.8 - - + -
25X TYR* 3.6 40.4 - - + +
37X PRO 3.6 2.4 + - - -
38X SER* 1.3 69.0 + - - +
40X ASN* 1.3 56.5 + - - +
42X ALA* 3.1 3.5 + - + +
43X LYS* 2.8 59.7 + - - +
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Residues in contact with ASN 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X SER* 3.3 8.0 + - - +
39X LEU* 1.3 79.8 - - - +
41X ALA* 1.3 56.4 + - - +
43X LYS* 3.3 19.2 + - - +
44X SER* 3.0 27.4 + - - -
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Residues in contact with ALA 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X THR* 4.4 3.8 - - + +
36X SER* 3.9 15.7 - - - +
38X SER* 3.1 29.7 + - - +
40X ASN* 1.3 76.1 - - - +
42X ALA* 1.3 58.5 + - - +
44X SER* 3.3 8.3 + - - -
45X GLU* 3.0 31.9 + - + +
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Residues in contact with ALA 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ILE* 4.4 7.9 - - + -
25X TYR* 3.5 40.2 - - + -
33X LEU* 3.9 11.8 - - + +
34X THR* 3.7 16.2 - - + +
38X SER 3.1 5.5 + - - -
39X LEU* 3.1 9.6 + - - +
41X ALA* 1.3 74.7 - - - +
43X LYS* 1.3 59.7 + - - +
45X GLU* 3.3 5.4 + - - +
46X LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ILE* 3.7 19.5 - - + -
39X LEU* 2.8 46.0 + - + +
40X ASN* 3.7 20.9 + - - +
41X ALA 3.3 0.2 - - - -
42X ALA* 1.3 73.8 - - - +
44X SER* 1.3 57.0 + - - +
46X LEU* 3.4 3.6 + - - +
47X ASP* 3.0 39.3 + - - +
55X ASN* 3.7 26.6 + - - +
56X GLY* 4.4 17.7 - - - +
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Residues in contact with SER 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X ASN 3.0 13.0 + - - -
41X ALA* 3.4 12.6 - - - -
43X LYS* 1.3 74.5 - - - +
45X GLU* 1.3 67.7 + - - +
47X ASP* 3.4 8.2 + - - +
48X LYS* 3.0 26.5 + - - +
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Residues in contact with GLU 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X LEU* 3.5 33.3 - - + +
34X THR* 4.3 9.9 - - - -
41X ALA* 3.0 17.4 + - + +
42X ALA 3.3 7.4 + - - +
44X SER* 1.3 77.8 + - - +
46X LEU* 1.3 57.8 + - - +
48X LYS* 2.9 40.2 + - - +
49X ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X ILE* 4.0 7.4 - - + -
27X ILE* 3.6 47.6 - - + -
33X LEU* 3.7 13.8 - - + +
42X ALA 2.9 13.8 + - - +
43X LYS* 3.5 9.4 - - - +
45X GLU* 1.3 74.9 - - - +
47X ASP* 1.3 58.7 + - - +
49X ALA* 3.2 3.2 + - + +
50X ILE* 2.9 51.9 + - + +
54X THR* 3.1 25.4 - - + +
56X GLY* 3.7 19.7 - - - +
58X ILE* 3.8 9.2 - - + -
66X LEU* 4.8 3.1 - - + -
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Residues in contact with ASP 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X LYS* 3.0 23.4 + - - +
44X SER* 3.8 8.0 - - - +
46X LEU* 1.3 74.4 - - - +
48X LYS* 1.3 54.2 + - - +
51X GLY* 2.7 32.2 + - - -
52X ARG 3.2 23.1 + - - +
53X ASN* 3.6 23.4 + - - +
54X THR* 2.7 40.2 + - - -
55X ASN 4.0 2.1 + - - -
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Residues in contact with LYS 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X SER* 3.0 17.6 + - - +
45X GLU* 2.9 44.5 + - - +
47X ASP* 1.3 78.5 - - - +
49X ALA* 1.3 61.2 + - - +
50X ILE 3.6 0.2 + - - -
51X GLY* 3.8 7.0 + - - -
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Residues in contact with ALA 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X HIS* 4.4 16.6 - - + +
45X GLU 2.9 18.7 + - - +
46X LEU* 3.6 7.0 - - - +
48X LYS* 1.3 78.0 - - - +
50X ILE* 1.3 61.2 + - - +
65X LYS* 6.2 0.5 - - - -
66X LEU* 4.0 30.7 - - + +
69X GLN* 5.2 3.3 + - - -
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Residues in contact with ILE 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X LEU* 2.9 32.4 + - + +
47X ASP 4.2 0.4 - - - +
49X ALA* 1.3 76.0 - - - +
51X GLY* 1.3 59.9 + - - +
52X ARG* 3.7 21.0 - - + +
54X THR* 4.0 9.2 - - + -
58X ILE* 3.9 16.8 - - + -
62X GLU* 3.6 41.1 - - + +
66X LEU* 3.7 36.8 - - + -
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Residues in contact with GLY 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X ASP 2.7 16.9 + - - -
48X LYS* 3.8 6.0 + - - -
49X ALA 3.6 1.8 - - - -
50X ILE* 1.3 73.9 - - - +
52X ARG* 1.3 58.8 + - - +
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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