Contacts of the helix formed by residues 25 - 39 (chain F) in PDB entry 4LQL
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 ALA 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F PRO 3.8 13.0 - - - +
22F GLU* 3.2 9.3 + - - +
24F LEU* 1.3 81.4 - - - +
26F GLU* 1.3 64.9 + - - +
27F VAL* 3.0 2.9 - - - +
28F GLU* 3.3 17.6 + - + +
29F LYS* 3.0 25.3 + - - +
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Residues in contact with GLU 26 (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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22F GLU* 3.2 31.9 + - + +
23F ALA* 4.6 2.0 - - - -
24F LEU 3.8 0.4 - - - +
25F ALA* 1.3 77.7 - - - +
27F VAL* 1.3 55.7 + - - +
29F LYS* 3.1 18.4 - - + +
30F ASP* 3.0 24.7 - - - -
81F HIS* 5.1 0.4 - - - -
123F LEU* 3.5 40.1 - - + +
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F VAL* 4.8 3.2 - - + +
14F GLY 3.8 14.8 - - - +
15F SER* 4.4 9.9 - - - +
19F TYR* 5.9 0.2 - - + -
23F ALA 5.3 1.3 - - - +
24F LEU* 3.2 32.1 - - - +
26F GLU* 1.3 75.3 - - - +
28F GLU* 1.3 57.3 + - + +
29F LYS 3.0 4.9 - - - -
30F ASP* 2.9 23.3 + - - +
31F ALA* 3.3 12.1 + - - +
53F VAL* 4.0 24.0 - - + -
81F HIS* 3.2 36.2 - - + +
82F THR* 3.8 6.1 - - + +
123F LEU* 4.2 9.9 - - + -
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU 5.2 1.1 - - - +
25F ALA* 3.3 23.8 + - + +
27F VAL* 1.3 78.8 - - + +
29F LYS* 1.3 65.9 + - + +
30F ASP 3.2 0.2 - - - -
31F ALA* 3.9 9.6 - - - +
32F ARG* 3.4 31.4 + - + +
53F VAL* 4.7 15.5 - - + -
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Residues in contact with LYS 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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25F ALA 3.0 22.3 + - - +
26F GLU* 3.1 19.7 - - + +
28F GLU* 1.3 82.7 - - + +
30F ASP* 1.3 61.4 - - - +
31F ALA 3.5 0.7 + - - -
32F ARG* 3.9 5.8 + - - +
33F LYS* 3.6 16.1 - - - +
107F PHE* 4.7 6.2 - - + -
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Residues in contact with ASP 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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26F GLU 3.0 21.1 - - - -
27F VAL 2.9 8.4 + - - +
29F LYS* 1.3 78.5 - - - +
31F ALA* 1.3 56.8 + - - +
33F LYS* 4.3 2.5 - - - -
34F LEU* 3.4 26.5 + - - +
79F TRP* 4.4 7.6 - - + -
81F HIS* 3.4 26.2 - - + -
107F PHE* 3.3 54.3 - - + -
123F LEU* 6.4 0.2 - - - -
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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
----------------------------------------------------------
11F PHE* 5.2 6.5 - - + -
13F VAL* 4.2 23.1 - - + +
27F VAL 3.3 10.8 + - - +
28F GLU* 3.8 7.8 + - - +
29F LYS 3.3 0.4 - - - -
30F ASP* 1.3 78.6 - - - +
32F ARG* 1.3 59.0 + - - +
33F LYS 2.9 10.6 + - - -
34F LEU* 5.1 0.7 - - - -
35F VAL* 3.1 21.6 + - - +
50F PHE* 3.1 31.6 - - + +
51F LYS 5.8 0.4 - - - +
53F VAL* 5.7 2.9 - - + -
79F TRP* 5.7 0.7 - - - -
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Residues in contact with ARG 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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28F GLU* 3.4 23.1 + - + +
29F LYS* 3.9 4.7 + - - +
31F ALA* 1.3 73.5 - - - +
33F LYS* 1.3 59.9 + - - +
36F ASP* 3.2 20.0 - - - +
50F PHE* 4.3 15.0 - - + +
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Residues in contact with LYS 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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29F LYS 3.6 15.9 - - - +
30F ASP 4.2 4.3 - - - +
31F ALA 2.9 3.6 + - - -
32F ARG* 1.3 79.9 - - - +
34F LEU* 1.3 59.1 + - - +
36F ASP* 3.2 11.4 - - - +
37F GLY* 2.5 35.2 + - - -
107F PHE* 4.2 19.3 - - + -
151F TRP* 5.1 1.6 - - + -
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Residues in contact with LEU 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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11F PHE* 5.4 8.5 - - + -
30F ASP 3.4 18.8 + - - +
31F ALA* 5.1 0.7 - - - -
33F LYS* 1.3 78.6 - - - +
35F VAL* 1.3 65.1 + - + +
37F GLY* 3.4 1.4 + - - -
38F LEU* 3.1 30.3 + - + +
79F TRP* 5.3 9.6 - - + -
107F PHE* 5.2 6.0 - - + -
151F TRP* 4.2 31.6 - - + +
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Residues in contact with VAL 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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11F PHE* 3.4 38.8 - - + -
31F ALA* 3.1 21.8 - - - +
33F LYS 3.3 0.2 - - - -
34F LEU* 1.3 76.1 - - + +
36F ASP* 1.3 55.4 + - - +
38F LEU* 3.6 9.8 + - - +
39F ASN* 2.1 40.9 + - - +
48F VAL* 3.0 43.3 - - + +
49F GLU 4.1 0.4 - - - -
50F PHE* 3.6 21.1 - - + +
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Residues in contact with ASP 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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31F ALA 4.6 0.4 - - - -
32F ARG* 3.2 35.9 - - - +
33F LYS* 2.8 12.4 + - - +
35F VAL* 1.3 79.8 - - - +
37F GLY* 1.3 57.3 + - - +
38F LEU 3.5 0.2 - - - -
39F ASN* 4.0 8.0 - - - +
40F LYS* 3.3 28.2 + - - +
50F PHE* 5.9 1.3 - - - -
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Residues in contact with GLY 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 LYS 2.5 17.8 + - - -
35F VAL 3.3 0.2 - - - -
36F ASP* 1.3 73.3 - - - +
38F LEU* 1.3 54.9 + - - +
39F ASN 3.3 0.2 - - - -
40F LYS* 4.1 5.6 - - - -
41F GLY* 2.3 37.8 + - - -
42F GLY 3.6 0.2 + - - -
151F TRP* 3.6 24.9 - - - -
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Residues in contact with LEU 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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11F PHE* 5.2 11.4 - - + -
34F LEU* 3.1 21.9 + - + +
35F VAL* 3.8 12.1 - - - +
37F GLY* 1.3 75.0 - - - +
39F ASN* 1.3 59.3 + - - +
41F GLY 2.8 23.7 - - - +
42F GLY* 3.0 25.7 + - - +
43F LYS 3.8 1.6 + - - -
44F LEU* 4.9 10.9 - - + +
48F VAL* 4.5 20.0 - - + -
151F TRP* 3.4 34.7 - - + -
157F GLN* 3.7 15.9 - - + -
160F ILE* 5.1 19.5 - - + -
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Residues in contact with ASN 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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35F VAL* 2.1 36.8 + - - +
36F ASP* 4.0 8.3 - - - +
38F LEU* 1.3 75.6 - - - +
40F LYS* 1.3 61.6 + - - +
41F GLY 4.5 0.4 - - - +
44F LEU* 5.5 1.6 - - - +
47F PRO* 4.0 10.0 - - - +
48F VAL* 2.9 49.2 + - - +
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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