Contacts of the helix formed by residues 37 - 51 (chain F) in PDB entry 2ZP8
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 THR 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F ASP 4.5 2.5 - - - +
7F ASP* 2.7 29.8 + - - +
8F LEU 3.0 16.6 + - - +
10F VAL* 4.0 23.8 - - + -
36F LEU* 1.3 76.3 - - - +
38F ALA* 1.3 65.1 + - - +
39F GLN* 3.4 4.4 + - - -
40F GLY 2.8 24.6 + - - -
41F TYR* 3.1 13.9 + - - -
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F THR* 1.3 73.9 - - - +
39F GLN* 1.3 63.2 + - - +
41F TYR* 3.3 14.8 + - - +
42F THR* 3.0 26.7 + - - -
1G MET* 4.3 12.3 - - + -
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Residues in contact with GLN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 4.7 16.7 - - + +
7F ASP* 3.5 21.1 - - + +
8F LEU* 3.7 19.9 - - + +
37F THR* 3.1 2.5 + - - +
38F ALA* 1.3 77.9 - - - +
40F GLY* 1.3 62.0 + - - +
42F THR* 3.5 3.3 + - - +
43F LEU* 3.3 21.5 + - - +
1G MET* 3.1 41.3 - - + +
2G VAL* 3.1 7.5 + - - +
3G ILE* 3.0 46.4 + - - +
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Residues in contact with GLY 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE* 3.4 15.5 - - - -
8F LEU* 3.8 24.9 - - - -
36F LEU* 4.5 3.6 - - - -
37F THR* 2.8 20.3 + - - -
39F GLN* 1.3 75.7 - - - +
41F TYR* 1.3 64.1 + - - -
43F LEU* 3.4 0.9 + - - +
44F LEU* 3.0 23.3 + - - +
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Residues in contact with TYR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ILE* 4.7 6.4 - - - +
36F LEU* 3.3 54.9 + - + +
37F THR 3.1 18.8 + - - -
38F ALA* 3.6 9.4 - - - +
40F GLY* 1.3 73.9 - - - +
42F THR* 1.3 59.8 + - - +
44F LEU* 3.0 9.1 + - + -
45F ASP* 2.6 51.1 + - - +
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Residues in contact with THR 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ALA 3.0 14.2 + - - -
39F GLN* 3.5 10.5 - - - +
41F TYR* 1.3 75.6 - - - +
43F LEU* 1.3 57.6 + - - +
45F ASP* 4.3 3.0 - - - +
46F PHE* 3.1 27.9 + - - +
1G MET* 3.3 20.7 - - - +
3G ILE* 3.7 11.2 - - + +
4G ALA* 3.6 8.1 - - - -
5G THR* 3.4 43.8 + - - +
8G LEU* 4.0 6.5 - - + +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.5 32.8 - - + -
46E PHE* 4.2 11.2 - - + -
47E ILE* 5.3 3.6 - - + -
3F ILE* 4.1 7.6 - - + -
8F LEU* 3.8 20.2 - - + -
39F GLN* 3.3 12.3 + - - +
40F GLY 3.6 7.2 - - - +
41F TYR 3.1 0.4 - - - -
42F THR* 1.3 77.8 - - - +
44F LEU* 1.3 56.4 + - - +
46F PHE* 3.1 7.6 + - + +
47F ILE* 2.8 58.6 + - + +
3G ILE* 6.1 2.7 - - + -
8G LEU* 5.0 4.7 - - + -
43G LEU* 4.0 28.0 - - + -
47G ILE* 6.2 1.3 - - + -
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Residues in contact with LEU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE* 4.3 7.2 - - + -
47E ILE* 3.8 25.1 - - + -
50E HIS* 3.9 39.9 - - + +
51E LEU* 4.4 12.1 - - + +
53E LYS* 4.8 7.9 - - - -
36F LEU* 3.9 24.2 - - + -
40F GLY 3.0 14.4 + - - +
41F TYR* 3.0 7.5 + - + +
43F LEU* 1.3 78.8 - - - +
45F ASP* 1.3 62.9 + - - +
47F ILE* 3.4 0.5 + - - +
48F GLN* 2.8 40.6 + - + +
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Residues in contact with ASP 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TYR* 2.6 39.5 + - - +
42F THR* 4.3 2.5 - - - +
44F LEU* 1.3 73.3 - - - +
46F PHE* 1.3 66.3 + - - +
48F GLN* 3.4 7.0 + - - +
49F LYS* 2.9 26.8 + - - +
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Residues in contact with PHE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F THR 3.1 19.6 + - - +
43F LEU* 3.1 6.4 + - + +
45F ASP* 1.3 81.0 - - - +
47F ILE* 1.3 97.8 + - + +
49F LYS* 3.2 6.2 + - - +
50F HIS* 3.2 45.5 + + - +
5G THR* 5.4 6.0 - - + +
8G LEU* 3.5 43.5 - - + -
9G GLU* 4.0 11.7 - - + -
36G LEU* 3.5 17.5 - - + -
40G GLY* 3.4 36.6 - - - -
43G LEU* 4.7 2.0 - - + -
44G LEU* 4.5 11.7 - - + -
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Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ILE* 4.1 30.3 - - + -
51E LEU* 4.4 2.7 - - + -
43F LEU* 2.8 41.2 + - + +
44F LEU 3.8 2.5 - - - +
46F PHE* 1.3 95.2 - - + +
48F GLN* 1.3 65.1 + - - +
49F LYS 2.9 0.5 + - - -
50F HIS 3.0 1.2 + - - -
51F LEU* 2.9 55.3 + - + +
43G LEU* 4.7 2.0 - - + -
44G LEU* 4.5 16.8 - - + +
47G ILE* 4.1 21.8 - - + -
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Residues in contact with GLN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E HIS 4.7 2.4 + - - -
51E LEU* 3.4 29.0 - - + +
52E ASN* 3.1 38.5 + - - +
53E LYS 5.3 0.6 - - - +
44F LEU* 2.8 29.6 + - + +
45F ASP* 3.7 8.5 - - - +
47F ILE* 1.3 72.6 - - - +
49F LYS* 1.3 62.3 + - - +
51F LEU* 4.2 9.7 + - - +
53F LYS* 4.6 4.9 + - - -
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Residues in contact with LYS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ASP 2.9 18.5 + - - +
46F PHE* 3.3 5.4 - - - +
47F ILE 3.0 0.2 - - - -
48F GLN* 1.3 77.3 - - - +
50F HIS* 1.3 64.5 + - + +
53F LYS* 3.1 21.1 + - - -
9G GLU* 3.2 29.1 + - - +
17G ARG* 5.8 3.2 - - - +
32G LYS* 3.1 31.0 + - - +
34G VAL* 3.8 25.2 - - - +
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Residues in contact with HIS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 3.2 37.2 + + - +
47F ILE 3.0 2.4 + - - -
49F LYS* 1.3 80.9 - - + +
51F LEU* 1.3 65.8 + - - +
52F ASN 3.5 1.6 + - - -
53F LYS* 3.3 15.3 + - - +
9G GLU* 2.5 26.1 + - - -
32G LYS* 3.2 30.4 + - + +
34G VAL* 3.4 26.5 - - + -
36G LEU* 3.3 25.9 - - + +
44G LEU* 3.5 32.6 - - + +
48G GLN* 5.1 0.3 + - - -
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 4.4 18.2 - - + -
47F ILE* 2.9 38.6 + - + +
48F GLN* 4.6 6.4 - - - +
49F LYS 3.5 1.2 - - - -
50F HIS* 1.3 77.1 - - - +
52F ASN* 1.3 101.0 + - + +
53F LYS* 3.3 15.8 - - - -
44G LEU* 3.9 9.1 - - + +
47G ILE* 4.1 19.3 - - + -
48G GLN* 3.4 19.1 - - + +
51G LEU* 4.3 15.0 - - + -
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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