Contacts of the helix formed by residues 28 - 42 (chain F) in PDB entry 4GDK
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 GLN 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E ARG 4.1 12.8 - - - +
16E ILE* 4.7 1.7 - - - +
17E PRO* 3.4 23.0 - - + +
41E ARG* 3.0 32.3 + - - +
87E PHE* 3.8 21.7 - - - -
92E SER* 5.9 1.4 - - - -
96E LEU* 3.8 18.9 - - + +
242E GLY* 5.5 2.8 + - - -
24F ARG* 2.8 34.4 + - + +
25F ASP* 5.1 0.4 - - - -
26F ARG 3.3 0.2 - - - -
27F LEU* 1.3 85.5 - - + +
29F ARG* 1.3 66.2 + - - +
31F ALA 3.7 2.0 + - - -
32F PHE* 3.6 11.6 - - - -
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Residues in contact with ARG 29 (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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13E PHE* 2.8 48.4 + - - +
15E ARG* 3.6 50.3 + - + +
38E LEU* 4.2 11.4 - - + +
25F ASP* 3.1 22.4 + - - +
28F GLN* 1.3 78.5 - - - +
30F GLN* 1.3 70.1 + - + +
31F ALA 3.1 0.4 - - - -
32F PHE* 3.0 14.4 + - - +
33F GLU* 3.0 47.2 + - - +
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Residues in contact with GLN 30 (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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95B ALA* 3.9 24.9 - - + +
96B LEU 3.5 8.3 - - - +
97B PRO* 5.0 0.9 - - - +
22F ARG 4.9 1.8 + - - -
25F ASP* 2.8 36.0 + - + +
26F ARG* 3.9 17.5 - - - +
29F ARG* 1.3 76.9 - - + +
31F ALA* 1.3 60.0 + - - +
32F PHE 3.3 0.6 + - - -
33F GLU* 4.4 11.7 + - - +
34F GLU* 5.3 2.9 + - - +
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Residues in contact with ALA 31 (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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96B LEU* 3.1 21.1 - - + +
97B PRO* 3.6 10.4 - - - +
32C PHE* 3.4 30.2 - - + -
26F ARG 3.7 9.9 + - - +
27F LEU* 3.6 20.2 - - - +
28F GLN 4.0 0.2 - - - +
29F ARG 3.0 1.0 + - - -
30F GLN* 1.3 78.3 - - - +
32F PHE* 1.3 78.9 + - + +
34F GLU 5.6 0.2 - - - -
35F ILE* 4.2 2.3 - - - +
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Residues in contact with PHE 32 (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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31C ALA* 3.6 28.0 - - + -
32C PHE* 4.0 24.2 - + - -
35C ILE* 4.4 15.3 - - + -
17E PRO* 3.6 29.2 - - + -
38E LEU* 4.6 1.3 - - + -
96E LEU* 3.8 31.9 - - + -
97E PRO* 3.9 14.6 - - + -
27F LEU 4.7 0.7 - - - -
28F GLN 3.6 14.6 - - - +
29F ARG 3.0 2.4 + - - +
31F ALA* 1.3 95.2 - - + +
33F GLU* 1.3 66.4 + - - +
34F GLU 3.3 2.2 - - - -
35F ILE* 3.3 15.2 - - + +
36F ILE* 3.0 33.6 + - + +
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Residues in contact with GLU 33 (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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38E LEU* 3.6 23.8 - - + +
29F ARG* 3.0 52.9 + - - +
30F GLN* 4.4 9.2 - - - +
31F ALA 3.9 0.2 - - - -
32F PHE* 1.3 77.1 - - - +
34F GLU* 1.3 61.9 + - + +
36F ILE* 4.0 1.6 - - - +
37F LEU* 3.1 41.1 + - + +
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Residues in contact with GLU 34 (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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36B TYR* 3.9 8.1 - - - +
97B PRO* 6.2 4.7 - - + -
99B ASN* 6.2 2.9 - - - +
30F GLN 5.3 3.3 + - - +
31F ALA 5.6 0.2 - - - -
32F PHE 3.3 0.4 - - - -
33F GLU* 1.3 80.4 - - + +
35F ILE* 1.3 60.6 + - - +
37F LEU* 3.2 20.9 + - - +
38F GLN* 2.8 46.1 + - - +
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Residues in contact with ILE 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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36B TYR* 3.3 52.0 + - + +
97B PRO* 5.6 2.5 - - + -
32C PHE* 4.7 9.2 - - + -
35C ILE* 3.8 46.0 - - + +
36C ILE* 4.2 12.1 - - + +
39C TYR* 4.8 6.6 - - + -
31F ALA 4.2 6.3 + - - +
32F PHE* 3.3 27.6 - - + +
34F GLU* 1.3 79.0 - - - +
36F ILE* 1.3 60.2 + - - +
38F GLN* 3.4 1.9 + - - +
39F TYR* 2.8 28.9 + - + +
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Residues in contact with ILE 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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35C ILE* 4.1 13.9 - - + -
17E PRO* 4.2 14.1 - - + -
18E THR 4.7 0.9 - - - +
36E TYR* 3.8 36.6 - - + +
37E LEU* 4.1 20.9 - - + +
38E LEU* 4.4 11.0 - - + +
97E PRO* 5.9 0.4 - - + -
32F PHE* 3.0 35.3 + - + +
33F GLU* 4.0 2.9 - - - +
35F ILE* 1.3 73.8 - - - +
37F LEU* 1.3 67.2 + - - +
39F TYR* 3.3 6.8 + - - +
40F ASN* 3.0 39.2 + - - +
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Residues in contact with LEU 37 (chain F).
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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33F GLU* 3.1 30.2 + - + +
34F GLU* 3.5 22.0 - - - +
36F ILE* 1.3 79.3 - - - +
38F GLN* 1.3 64.9 + - - +
40F ASN* 3.5 7.3 + - - +
41F LYS* 3.3 40.9 + - + +
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Residues in contact with GLN 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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31B GLU* 5.5 0.2 + - - -
33B GLU* 5.2 2.1 - - - +
34B PRO* 3.6 36.8 - - + +
36B TYR* 4.3 9.0 - - + +
39C TYR* 3.9 17.2 + - + -
34F GLU* 2.8 31.1 + - - +
35F ILE 3.8 4.7 - - - +
37F LEU* 1.3 77.7 - - + +
39F TYR* 1.3 65.5 + - - +
41F LYS* 3.4 45.4 + - - +
42F LEU* 3.5 24.4 - - - +
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Residues in contact with TYR 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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35C ILE* 4.9 5.2 - - + -
38C GLN* 3.9 29.1 - - + +
39C TYR* 4.0 29.6 - + + -
42C LEU* 4.4 15.0 - - + +
33E GLU* 4.2 6.4 + - - +
34E PRO* 3.2 31.3 + - - +
36E TYR* 3.6 36.3 - + + -
35F ILE* 2.8 20.3 + - + +
36F ILE* 3.3 6.7 + - - +
38F GLN* 1.3 78.9 - - - +
40F ASN* 1.3 70.0 + - - +
42F LEU* 3.3 15.0 + - + +
43F LEU* 3.4 36.7 + - + +
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Residues in contact with ASN 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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35E TYR* 3.8 20.3 + - - -
36E TYR* 3.3 24.0 + - - +
37E LEU* 5.6 3.0 - - - +
36F ILE* 3.0 29.6 + - - +
37F LEU* 3.5 6.8 + - - +
38F GLN 3.3 0.4 - - - -
39F TYR* 1.3 81.0 - - - +
41F LYS* 1.3 64.6 + - - +
42F LEU 3.3 0.2 - - - -
43F LEU* 3.7 33.8 + - + +
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Residues in contact with LYS 41 (chain F).
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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31B GLU* 3.5 25.8 + - - -
37F LEU* 3.3 28.2 + - + +
38F GLN* 3.4 42.3 + - - +
39F TYR 3.2 0.6 - - - -
40F ASN* 1.3 77.9 - - - +
42F LEU* 1.3 70.4 + - + +
43F LEU 3.3 4.0 + - - +
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Residues in contact with LEU 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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33B GLU* 3.9 26.7 - - + +
39C TYR* 3.5 34.1 - - + +
42C LEU* 3.3 46.8 - - + +
43C LEU* 3.6 20.2 - - + -
38F GLN* 3.5 12.3 - - - +
39F TYR* 3.3 9.2 + - + +
41F LYS* 1.3 89.0 - - + +
43F LEU* 1.3 61.3 + - - +
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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