Contacts of the helix formed by residues 20 - 51 (chain F) in PDB entry 5KHU
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 20 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F TYR* 3.8 26.0 - - - +
21F TYR* 3.7 29.8 - - - +
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Residues in contact with TYR 21 (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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20F ALA* 3.7 30.7 - - - +
22F ARG* 3.8 27.6 - - - +
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Residues in contact with ARG 22 (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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21F TYR* 3.8 29.6 - - - +
23F ASP* 3.8 28.3 - - - +
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Residues in contact with ASP 23 (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 ARG* 3.8 25.1 - - - +
24F ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 24 (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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23F ASP* 3.8 30.1 - - - +
25F VAL* 3.8 27.6 - - - +
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Residues in contact with VAL 25 (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 ALA* 3.8 26.2 - - - +
26F PHE* 3.8 28.7 - - - +
28F ALA* 4.6 16.2 - - - +
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Residues in contact with PHE 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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25F VAL* 3.8 30.1 - - - +
27F LEU* 3.8 27.4 - - - +
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Residues in contact with LEU 27 (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 PHE* 3.8 29.4 - - - +
28F ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 28 (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 VAL* 4.6 14.8 - - - +
27F LEU* 3.8 26.5 - - - +
29F GLU* 3.8 29.8 - - - +
31F LEU* 4.6 14.1 - - - +
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Residues in contact with GLU 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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28F ALA* 3.8 25.1 - - - +
30F ARG* 3.8 29.8 - - - +
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Residues in contact with ARG 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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29F GLU* 3.8 29.8 - - - +
31F LEU* 3.8 26.2 - - - +
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Residues in contact with LEU 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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28F ALA* 4.6 15.0 - - - +
30F ARG* 3.8 29.4 - - - +
32F TYR* 3.8 27.4 - - - +
34F GLU* 4.5 18.2 - - - +
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Residues in contact with TYR 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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31F LEU* 3.8 23.6 - - - +
33F ALA* 3.7 29.6 - - - +
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Residues in contact with ALA 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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32F TYR* 3.7 29.4 - - - +
34F GLU* 3.8 26.5 - - - +
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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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31F LEU* 4.5 14.8 - - - +
33F ALA* 3.8 25.4 - - - +
35F VAL* 3.8 29.2 - - - +
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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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34F GLU* 3.8 28.9 - - - +
36F HIS* 3.8 29.6 - - - +
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Residues in contact with HIS 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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35F VAL* 3.8 28.9 - - - +
37F SER* 3.8 29.2 - - - +
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Residues in contact with SER 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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36F HIS* 3.8 29.2 - - - +
38F GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 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 SER* 3.8 30.3 - - - +
39F GLU* 3.8 23.8 - - - +
41F LEU* 4.4 16.4 - - - +
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Residues in contact with GLU 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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38F GLU* 3.8 26.0 - - - +
40F ALA* 3.8 29.8 - - - +
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Residues in contact with ALA 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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39F GLU* 3.8 29.4 - - - +
41F LEU* 3.8 26.0 - - - +
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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
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38F GLU* 4.4 16.8 - - - +
40F ALA* 3.8 27.1 - - - +
42F PHE* 3.8 29.2 - - - +
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Residues in contact with PHE 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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41F LEU* 3.8 29.2 - - - +
43F LEU* 3.8 26.2 - - - +
45F ALA* 4.5 15.3 - - - +
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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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42F PHE* 3.8 26.2 - - - +
44F LEU* 3.7 28.5 - - - +
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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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43F LEU* 3.7 29.4 - - - +
45F ALA* 3.8 26.5 - - - +
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Residues in contact with ALA 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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42F PHE* 4.5 14.1 - - - +
44F LEU* 3.8 29.4 - - - +
46F THR* 3.8 26.0 - - - +
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Residues in contact with THR 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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45F ALA* 3.8 26.0 - - - +
47F CYS* 3.8 28.7 - - - +
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Residues in contact with CYS 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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46F THR* 3.8 28.9 - - - +
48F TYR* 3.8 26.7 - - - +
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Residues in contact with TYR 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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47F CYS* 3.8 25.8 - - - +
49F TYR* 3.7 28.7 - - - +
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Residues in contact with TYR 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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48F TYR* 3.7 29.8 - - - +
50F ARG* 3.8 25.4 - - - +
52F GLY* 4.5 16.6 - - - +
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Residues in contact with ARG 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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49F TYR* 3.8 25.8 - - - +
51F SER* 3.7 29.2 - - - +
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Residues in contact with SER 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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50F ARG* 3.7 30.1 - - - +
52F GLY* 3.7 24.7 - - - +
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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