Contacts of the helix formed by residues 20 - 51 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19H TYR* 3.7 27.8 - - - +
21H TYR* 3.7 29.6 - - - +
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Residues in contact with TYR 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ALA* 3.7 29.8 - - - +
22H ARG* 3.8 28.0 - - - +
24H ALA* 4.4 18.8 - - - +
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Residues in contact with ARG 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H TYR* 3.8 29.2 - - - +
23H ASP* 3.8 26.5 - - - +
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Residues in contact with ASP 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ARG* 3.8 29.4 - - - +
24H ALA* 3.8 26.2 - - - +
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TYR* 4.4 17.5 - - - +
23H ASP* 3.8 25.1 - - - +
25H VAL* 3.8 28.3 - - - +
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Residues in contact with VAL 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ALA* 3.8 28.0 - - - +
26H PHE* 3.8 29.8 - - - +
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Residues in contact with PHE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H VAL* 3.8 29.6 - - - +
27H LEU* 3.8 27.6 - - - +
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 3.8 26.2 - - - +
28H ALA* 3.8 29.6 - - - +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H LEU* 3.8 29.4 - - - +
29H GLU* 3.8 26.7 - - - +
31H LEU* 4.5 15.7 - - - +
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ALA* 3.8 25.6 - - - +
30H ARG* 3.7 29.6 - - - +
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 3.7 29.6 - - - +
31H LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ALA* 4.5 15.7 - - - +
30H ARG* 3.8 26.0 - - - +
32H TYR* 3.8 28.7 - - - +
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Residues in contact with TYR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.8 29.6 - - - +
33H ALA* 3.8 24.7 - - - +
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Residues in contact with ALA 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H TYR* 3.8 25.6 - - - +
34H GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ALA* 3.8 29.2 - - - +
35H VAL* 3.8 26.9 - - - +
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Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H GLU* 3.8 28.9 - - - +
36H HIS* 3.8 29.6 - - - +
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Residues in contact with HIS 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H VAL* 3.8 29.8 - - - +
37H SER* 3.8 26.9 - - - +
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Residues in contact with SER 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H HIS* 3.8 28.7 - - - +
38H GLU* 3.8 29.6 - - - +
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Residues in contact with GLU 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H SER* 3.8 29.2 - - - +
39H GLU* 3.8 24.0 - - - +
41H LEU* 4.2 19.3 - - - +
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Residues in contact with GLU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H GLU* 3.8 25.8 - - - +
40H ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLU* 3.8 28.9 - - - +
41H LEU* 3.8 24.7 - - - +
43H LEU* 4.6 15.5 - - - +
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Residues in contact with LEU 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLU* 4.2 18.4 - - - +
40H ALA* 3.8 26.2 - - - +
42H PHE* 3.8 29.2 - - - +
44H LEU* 4.6 13.5 - - - +
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Residues in contact with PHE 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LEU* 3.8 25.8 - - - +
43H LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ALA* 4.6 13.7 - - - +
42H PHE* 3.8 28.9 - - - +
44H LEU* 3.8 25.8 - - - +
46H THR* 4.7 13.7 - - - +
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H LEU* 4.6 17.5 - - - +
43H LEU* 3.8 27.4 - - - +
45H ALA* 3.7 29.2 - - - +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU* 3.7 29.4 - - - +
46H THR* 3.8 25.6 - - - +
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Residues in contact with THR 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LEU* 4.7 17.7 - - - +
45H ALA* 3.8 24.2 - - - +
47H CYS* 3.8 29.4 - - - +
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Residues in contact with CYS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H THR* 3.8 29.6 - - - +
48H TYR* 3.8 26.2 - - - +
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Residues in contact with TYR 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H CYS* 3.8 25.8 - - - +
49H TYR* 3.7 29.8 - - - +
51H SER* 4.6 15.3 - - - +
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Residues in contact with TYR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H TYR* 3.7 26.2 - - - +
50H ARG* 3.7 29.8 - - - +
54H ALA* 4.2 20.6 - - - +
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Residues in contact with ARG 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H TYR* 3.7 29.8 - - - +
51H SER* 3.7 25.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H TYR* 4.6 16.4 - - - +
50H ARG* 3.7 29.4 - - - +
52H GLY* 3.8 26.5 - - - +
----------------------------------------------------------
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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