Contacts of the helix formed by residues 33 - 54 (chain F) in PDB entry 6ACQ
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 LYS 33 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ILE* 1.3 89.7 + - + +
34F ASP* 1.3 66.2 + - - +
35F GLU* 4.1 27.6 + - + +
36F PHE* 3.0 39.0 + - + +
37F VAL* 3.3 11.6 + - - +
73F VAL* 3.7 5.8 - - - -
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Residues in contact with ASP 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LYS* 1.3 70.5 - - - +
35F GLU* 1.3 56.2 + - - +
37F VAL* 3.3 8.1 + - - +
38F ASP* 2.9 44.5 + - - +
72F THR* 5.4 1.6 - - - -
73F VAL* 3.6 23.5 + - - +
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LYS* 4.1 27.9 + - + +
34F ASP* 1.3 79.4 - - - +
36F PHE* 1.3 79.3 + - + +
38F ASP* 3.6 7.9 + - - +
39F ARG* 3.1 25.1 + - - +
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Residues in contact with PHE 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA* 3.4 9.9 - - + +
31F ASP* 3.6 31.4 - - - +
32F ILE* 4.5 9.2 - - + -
33F LYS* 3.0 38.3 + - + +
35F GLU* 1.3 99.2 - - + +
37F VAL* 1.3 68.0 + - - +
39F ARG* 3.2 17.6 + - - +
40F GLY 2.9 18.0 + - - -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA* 3.8 9.3 - - + +
29F LEU* 4.4 5.6 - - + +
30F ARG 4.6 0.4 - - - -
31F ASP* 3.7 21.3 - - + +
33F LYS 3.3 7.4 + - - +
34F ASP* 3.3 10.3 + - - +
36F PHE* 1.3 77.3 - - - +
38F ASP* 1.3 57.1 + - - +
40F GLY* 3.0 4.2 + - - -
41F LEU* 2.8 47.9 + - + +
71F GLY* 3.7 28.0 - - - -
72F THR 3.4 28.0 - - - +
73F VAL* 4.5 4.0 - - + -
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Residues in contact with ASP 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ASP* 2.9 30.2 + - - +
35F GLU* 3.7 7.8 - - - +
37F VAL* 1.3 80.5 - - - +
39F ARG* 1.3 65.3 + - - +
41F LEU* 3.9 12.7 - - - +
42F ASP* 2.9 27.2 + - - +
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA 5.0 5.5 + - - +
10F GLY* 4.4 19.2 - - - -
11F THR* 4.7 11.4 + - - +
35F GLU* 3.1 15.1 + - + +
36F PHE* 3.2 20.2 + - + +
38F ASP* 1.3 76.9 - - - +
40F GLY* 1.3 56.3 + - - +
42F ASP* 3.3 6.1 + - - +
43F PHE* 2.9 29.8 + - + +
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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
----------------------------------------------------------
9F ALA* 3.3 24.2 - - - -
10F GLY 5.8 0.2 - - - -
14F SER* 3.8 13.3 + - - -
29F LEU* 4.7 0.9 - - - -
36F PHE 2.9 10.5 + - - -
37F VAL 3.4 3.8 - - - -
39F ARG* 1.3 74.2 - - - +
41F LEU* 1.3 65.9 + - - +
43F PHE* 3.0 16.8 + - - +
44F ILE* 3.0 17.9 + - - +
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F LEU* 3.5 26.7 - - + -
37F VAL* 2.8 35.2 + - + +
38F ASP* 3.9 14.1 - - - +
40F GLY* 1.3 71.6 - - - -
42F ASP* 1.3 57.9 + - - +
44F ILE* 3.5 8.7 + - + +
45F ASN* 3.0 27.5 + - - +
66F LEU* 4.3 11.5 - - + +
69F ILE* 3.8 24.5 - - + +
71F GLY* 4.4 11.9 - - - +
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASP 2.9 19.1 + - - +
39F ARG* 3.6 7.0 - - - +
41F LEU* 1.3 75.5 - - - +
43F PHE* 1.3 60.0 + - - +
45F ASN* 3.5 11.5 + - - +
46F LYS* 3.0 30.4 + - - +
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Residues in contact with PHE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F GLY 4.7 0.4 - - - -
11F THR* 3.5 42.8 - - + -
14F SER* 2.9 21.5 - - - +
15F GLY* 4.4 6.7 - - - -
39F ARG* 2.9 15.3 + - + +
40F GLY* 3.2 9.2 - - - +
42F ASP* 1.3 78.7 - - - +
44F ILE* 1.3 63.2 + - + +
46F LYS* 3.3 10.7 + - + +
47F ASN* 3.0 59.1 + - - +
142F PRO* 6.4 2.5 - - + -
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Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F SER* 3.2 40.8 - - - +
17F ALA* 4.3 6.1 - - + -
18F GLN* 3.7 29.8 - - + +
29F LEU* 4.4 7.6 - - + -
40F GLY 3.3 16.2 - - - +
41F LEU* 3.7 10.8 - - + +
43F PHE* 1.3 75.8 - - + +
45F ASN* 1.3 66.8 + - - +
47F ASN* 3.1 3.9 + - - +
48F LEU* 3.0 33.5 + - + +
65F ILE* 5.7 0.2 - - + -
66F LEU* 3.8 19.1 - - + -
69F ILE* 4.1 23.1 - - + -
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Residues in contact with ASN 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU 3.0 18.3 + - - +
42F ASP* 3.5 16.5 + - - +
44F ILE* 1.3 76.9 - - - +
46F LYS* 1.3 53.7 + - - +
48F LEU* 3.4 4.0 + - - +
49F SER* 2.7 38.5 + - - -
62F LYS* 3.1 23.4 + - - +
66F LEU* 3.8 26.6 - - + +
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ASP* 3.0 20.0 + - - +
43F PHE* 3.5 10.8 - - + +
44F ILE 3.1 0.2 - - - -
45F ASN* 1.3 76.5 - - - +
47F ASN* 1.3 71.3 + - - +
49F SER* 3.2 8.6 + - - -
50F LYS* 3.2 51.4 + - - +
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Residues in contact with ASN 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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18F GLN* 3.1 30.2 + - - +
43F PHE* 3.0 50.7 + - - +
44F ILE 3.1 5.6 + - - +
46F LYS* 1.3 80.6 - - - +
48F LEU* 1.3 61.8 + - - +
50F LYS* 3.2 17.0 + - - +
51F LEU* 3.2 24.0 + - + +
144F PRO* 4.6 9.3 - - - +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLN* 3.4 25.8 - - + +
22F ALA* 5.7 2.0 - - + -
44F ILE* 3.0 27.6 + - + +
45F ASN 3.7 3.4 - - - +
47F ASN* 1.3 75.9 - - - +
49F SER* 1.3 60.5 + - - +
51F LEU* 3.1 18.3 + - + +
52F VAL* 2.8 30.7 + - - +
57F ILE* 4.0 10.7 - - + +
62F LYS* 3.7 39.9 - - + +
65F ILE* 4.4 22.0 - - + -
66F LEU* 3.8 21.3 - - + -
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Residues in contact with SER 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 ASN* 2.7 19.8 + - - -
46F LYS* 3.2 9.1 + - - -
48F LEU* 1.3 73.3 - - - +
50F LYS* 1.3 61.1 + - - +
52F VAL* 3.3 8.6 + - - +
53F LYS* 2.8 27.7 + - - +
59F GLU* 5.8 0.2 - - - -
62F LYS* 2.5 31.9 + - - +
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Residues in contact with LYS 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 LYS* 3.2 43.4 + - - +
47F ASN* 3.3 15.2 + - - +
48F LEU 3.2 0.2 - - - -
49F SER* 1.3 74.4 - - - +
51F LEU* 1.3 61.5 + - + +
53F LYS* 2.8 10.4 + - - -
54F LYS* 2.8 46.9 + - + +
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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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18F GLN* 4.4 9.2 - - - +
47F ASN* 3.2 13.4 + - + +
48F LEU* 3.1 27.1 + - + +
50F LYS* 1.3 80.8 - - + +
52F VAL* 1.3 61.0 + - - +
54F LYS* 3.4 6.8 + - + -
55F GLY 3.2 2.9 + - - -
56F LYS* 2.9 50.9 + - + +
57F ILE* 3.5 22.8 + - + -
144F PRO* 6.4 0.7 - - + -
145F VAL* 6.3 3.8 - - + -
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU 2.8 17.8 + - - +
49F SER* 3.6 9.0 - - - +
51F LEU* 1.3 76.6 - - - +
53F LYS* 1.3 64.7 + - - +
55F GLY* 3.1 13.7 + - - -
57F ILE* 3.5 25.1 - - + +
58F GLU 3.9 1.8 - - - +
59F GLU* 3.5 51.1 - - + +
62F LYS* 3.9 11.4 - - + -
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F SER 2.8 15.2 + - - +
50F LYS* 2.8 11.4 + - + +
52F VAL* 1.3 79.6 - - - +
54F LYS* 1.3 64.7 + - + +
55F GLY 3.2 0.9 + - - -
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Residues in contact with LYS 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LYS* 2.8 38.2 + - + +
51F LEU* 3.4 9.4 + - + +
52F VAL 3.2 0.2 - - - -
53F LYS* 1.3 77.6 - - + +
55F GLY* 1.3 62.6 + - - +
56F LYS* 3.3 19.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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