Contacts of the helix formed by residues 34 - 45 (chain F) in PDB entry 4IVZ
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28F ALA* 3.9 0.4 - - - -
33F LEU* 1.3 72.6 - - - +
35F ARG* 1.3 77.8 + - - +
36F THR* 3.0 29.3 + - - +
37F PHE* 3.2 18.9 - - + +
38F ILE* 3.4 6.9 + - - +
14G T 2.5 51.1 + - + +
15G C 3.2 38.3 + - - +
16G G 5.0 0.7 - - - +
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Residues in contact with ARG 35 (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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24F GLN* 3.3 27.0 + - + +
25F GLU* 3.8 48.7 - - + +
28F ALA* 3.7 14.1 - - + +
33F LEU 3.7 1.8 + - - -
34F ASP* 1.3 77.5 + - - +
36F THR* 1.3 71.5 + - + +
38F ILE* 3.1 14.0 + - - +
39F SER* 3.2 10.8 + - - -
17G A 4.6 3.2 - - - +
18G C 4.9 1.0 - - - +
2H T 3.6 35.0 - - - +
3H G 3.0 44.2 + - - -
4H T 3.8 8.3 + - - +
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Residues in contact with THR 36 (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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34F ASP* 3.0 21.5 + - - +
35F ARG* 1.3 83.2 - - + +
37F PHE* 1.3 74.5 + - - +
39F SER* 2.8 19.2 + - - -
40F GLY 3.1 8.5 + - - -
46F ARG* 5.7 2.0 - - - -
14G T 3.8 8.7 - - - +
15G C 3.4 16.1 + - + +
16G G 3.1 29.8 - - + +
17G A 4.4 2.7 - - - +
4H T 3.8 31.2 - - + +
5H C 4.4 1.3 - - - -
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Residues in contact with PHE 37 (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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33F LEU* 4.7 8.5 - - + -
34F ASP* 3.2 14.8 + - + +
36F THR* 1.3 79.1 + - - +
38F ILE* 1.3 69.9 + - + +
40F GLY* 2.8 15.5 + - - +
41F ILE* 3.0 46.2 + - + -
46F ARG* 4.4 21.9 - - - +
47F ASN 4.7 2.9 - - - -
48F LEU* 4.4 10.1 - - + -
52F SER* 4.7 4.5 - - - -
12G A 4.1 9.9 - - + -
13G G 2.8 82.6 - + + -
14G T 3.7 12.5 - - + +
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Residues in contact with ILE 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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13F ILE* 5.8 2.2 - - + -
24F GLN* 4.1 27.1 - - + -
27F LEU* 4.5 19.5 - - + -
28F ALA* 3.7 31.4 - - + +
31F SER* 5.2 0.7 - - - +
33F LEU* 3.9 30.5 - - + -
34F ASP 3.7 3.4 - - - +
35F ARG* 3.1 7.1 + - - +
37F PHE* 1.3 76.7 - - - +
39F SER* 1.3 67.1 + - - +
41F ILE* 2.8 30.1 + - + +
42F GLU* 3.0 23.7 + - + +
56F ILE* 4.4 14.4 - - + -
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Residues in contact with SER 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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24F GLN* 3.5 17.6 + - - +
35F ARG* 3.2 5.1 + - - -
36F THR* 2.8 16.0 + - - -
38F ILE* 1.3 75.8 - - - +
40F GLY* 1.3 53.1 + - - -
42F GLU* 3.1 1.6 + - - +
43F ARG* 2.7 38.8 + - - +
3H G 2.3 51.7 + - - +
4H T 4.4 12.7 - - - +
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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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36F THR 3.1 4.0 + - - -
37F PHE 2.8 12.3 + - - -
39F SER* 1.3 74.1 + - - +
41F ILE* 1.3 56.3 + - - -
43F ARG* 4.5 1.6 - - - -
44F ASN* 2.8 35.9 + - - -
45F SER 3.1 7.3 + - - -
46F ARG* 3.2 24.5 + - - -
4H T 5.7 1.0 - - - +
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Residues in contact with ILE 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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10F SER* 3.0 26.7 + - - -
13F ILE* 3.7 30.3 - - + -
33F LEU* 5.3 2.7 - - + -
37F PHE* 3.0 51.4 + - + +
38F ILE* 2.8 27.2 + - + +
40F GLY* 1.3 74.4 - - - +
42F GLU* 1.3 60.2 + - + +
45F SER* 3.6 8.7 + - - -
46F ARG* 3.8 20.5 - - + +
48F LEU* 4.5 20.4 - - + -
52F SER* 6.5 0.4 - - - -
56F ILE* 4.6 9.4 - - + -
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Residues in contact with GLU 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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10F SER* 4.0 13.3 - - - +
13F ILE* 5.0 8.0 - - + +
14F LYS* 3.2 60.0 + - + +
17F ARG* 2.7 39.4 + - - +
24F GLN* 3.5 22.7 + - - +
38F ILE* 3.0 18.3 + - + +
39F SER 3.7 5.4 - - - +
41F ILE* 1.3 76.6 - - + +
43F ARG* 1.3 68.9 + - + +
45F SER* 4.7 1.0 + - - -
3H G 4.9 2.9 + - - +
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Residues in contact with ARG 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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18A LEU* 3.9 42.4 - - - +
39F SER* 2.7 24.8 + - - +
40F GLY* 4.5 0.4 - - - -
42F GLU* 1.3 78.7 + - - +
44F ASN* 1.3 81.0 - - - +
45F SER* 3.4 2.0 + - - -
3H G 3.2 43.2 + - - +
4H T 3.5 24.2 + - - +
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Residues in contact with ASN 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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2F GLU* 4.4 5.5 - - - +
40F GLY* 2.8 16.4 + - - +
43F ARG* 1.3 102.2 + - - +
45F SER* 1.3 68.8 + - - +
46F ARG* 3.4 5.1 + - + +
4H T 3.1 24.4 + - - -
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Residues in contact with SER 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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51E LYS* 5.5 0.5 + - - -
2F GLU* 3.9 18.9 + - - -
3F SER 6.0 0.4 - - - -
6F LEU* 3.1 24.5 - - - +
7F SER* 3.5 19.8 - - - -
10F SER* 3.4 17.9 + - - -
40F GLY 3.1 2.2 + - - -
41F ILE 3.6 11.3 + - - -
42F GLU 4.6 0.9 + - - -
43F ARG 3.4 5.0 + - - -
44F ASN* 1.3 80.5 - - - +
46F ARG* 1.3 70.1 + - - +
47F ASN 3.3 0.2 + - - -
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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