Contacts of the helix formed by residues 29 - 43 (chain Z) in PDB entry 5K0Y
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 THR 29 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z LEU* 1.3 84.5 - - - +
30Z SER* 1.4 65.0 + - - +
31Z ASP* 3.8 20.9 + - - +
32Z ASP* 3.0 32.4 + - - +
33Z VAL* 3.8 13.0 + - - +
60Z VAL* 5.9 0.2 - - - +
66Z VAL* 4.4 8.1 - - - +
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Residues in contact with SER 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z THR* 1.4 74.7 - - - +
31Z ASP* 1.4 66.5 + - - +
32Z ASP 3.3 0.5 + - - -
33Z VAL* 3.4 8.0 - - - +
34Z LYS* 3.2 51.2 + - - +
66Z VAL* 4.3 9.0 - - - +
67Z THR* 3.4 22.7 - - - +
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Residues in contact with ASP 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z THR* 3.8 18.0 + - - +
30Z SER* 1.4 78.5 + - - +
32Z ASP* 1.4 65.4 + - - +
34Z LYS* 3.4 6.8 + - - +
35Z GLU* 3.2 34.4 + - - +
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Residues in contact with ASP 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z LEU* 3.8 18.9 - - + +
29Z THR* 3.0 33.5 + - - +
30Z SER 3.3 1.0 + - - -
31Z ASP* 1.4 81.5 - - - +
33Z VAL* 1.4 68.0 + - + +
35Z GLU* 3.5 14.0 + - - +
36Z GLN* 3.3 21.6 + - - +
58Z HIS* 5.4 5.6 + - + -
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Residues in contact with VAL 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z LEU* 4.2 15.9 - - + -
29Z THR 3.8 9.2 - - - +
30Z SER* 3.4 14.4 - - - +
32Z ASP* 1.4 77.3 - - + +
34Z LYS* 1.4 64.0 + - + +
36Z GLN* 3.6 7.5 - - - +
37Z ILE* 3.0 35.5 + - + +
54Z LEU* 4.5 8.5 - - + +
58Z HIS* 4.4 9.2 - - + -
60Z VAL* 4.0 35.7 - - + -
63Z VAL* 4.6 18.4 - - + -
66Z VAL* 5.2 7.9 - - + -
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Residues in contact with LYS 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z SER* 3.2 40.9 + - - +
31Z ASP* 3.8 6.5 - - - +
32Z ASP 3.3 0.2 - - - -
33Z VAL* 1.4 76.6 - - + +
35Z GLU* 1.4 59.9 + - + +
37Z ILE* 3.4 9.5 + - - +
38Z TYR* 3.0 61.0 + - + +
67Z THR* 5.1 13.8 - - - +
69Z ASN* 5.9 3.4 - - - -
74Z ILE* 4.9 20.0 - - + -
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Residues in contact with GLU 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z ASP* 3.2 26.1 + - - +
32Z ASP* 3.6 14.0 - - - +
34Z LYS* 1.4 74.2 - - + +
36Z GLN* 1.4 57.9 + - - +
38Z TYR* 3.2 14.8 + - + +
39Z LYS* 3.0 30.2 + - - +
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Residues in contact with GLN 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z ASP 3.3 11.3 + - - +
33Z VAL* 3.6 9.2 - - - +
34Z LYS 3.3 0.2 - - - -
35Z GLU* 1.4 78.0 - - - +
37Z ILE* 1.4 54.7 + - - +
39Z LYS* 3.2 36.7 + - - +
40Z LEU* 3.0 54.4 + - + +
53Z ILE* 6.2 0.2 - - + -
54Z LEU* 3.7 25.6 - - + -
58Z HIS* 3.8 25.3 + - + +
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Residues in contact with ILE 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z VAL* 3.0 26.9 + - + +
34Z LYS* 3.5 6.1 - - - +
36Z GLN* 1.4 71.3 - - - +
38Z TYR* 1.4 60.9 + - + +
40Z LEU* 3.4 2.1 + - - +
41Z ALA* 2.9 29.3 + - - +
50Z ILE* 4.0 13.2 - - + +
54Z LEU* 3.8 27.6 - - + -
63Z VAL* 4.3 12.6 - - + -
71Z ILE* 4.3 15.3 - - + -
74Z ILE* 3.7 36.8 - - + -
75Z LEU* 3.4 29.4 - - + -
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Residues in contact with TYR 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Z LYS* 3.0 49.6 + - + +
35Z GLU* 3.6 12.8 - - + +
37Z ILE* 1.4 77.4 - - + +
39Z LYS* 1.4 57.0 + - - +
41Z ALA* 3.8 5.3 - - + +
42Z LYS* 3.1 26.9 + - - +
74Z ILE* 3.6 31.9 - - + +
75Z LEU* 5.5 3.1 - - + -
78Z LYS* 3.6 44.6 + - + +
80Z LEU* 4.2 5.2 - - - +
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Residues in contact with LYS 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z GLU 3.0 16.3 + - - +
36Z GLN* 3.2 35.2 + - - +
37Z ILE 3.3 0.2 - - - -
38Z TYR* 1.4 75.0 - - - +
40Z LEU* 1.4 63.0 + - - +
42Z LYS* 3.3 23.5 - - + +
43Z LYS* 3.5 38.7 - - - +
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Residues in contact with LEU 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Z GLN* 3.0 48.6 + - + +
37Z ILE 3.8 3.4 - - - +
39Z LYS* 1.4 76.9 - - - +
41Z ALA* 1.4 55.3 + - - +
43Z LYS* 3.2 44.3 + - - +
45Z LEU* 3.5 34.3 + - + +
50Z ILE* 3.9 29.8 - - + -
53Z ILE* 3.9 30.3 - - + -
54Z LEU* 4.9 1.8 - - + -
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Residues in contact with ALA 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z ILE 2.9 17.8 + - - +
38Z TYR* 3.8 6.1 - - + +
40Z LEU* 1.4 72.7 - - - +
42Z LYS* 1.4 63.0 + - - +
43Z LYS 3.3 0.2 - - - -
44Z GLY* 3.3 12.1 + - - -
45Z LEU 4.4 5.8 - - - -
50Z ILE* 4.1 8.4 - - + +
75Z LEU* 4.1 32.1 - - + -
80Z LEU* 4.2 25.1 - - + +
81Z ALA* 6.3 0.2 - - - -
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Residues in contact with LYS 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Z TYR 3.1 13.6 + - - +
39Z LYS* 3.3 18.2 - - + +
40Z LEU 3.2 0.2 - - - -
41Z ALA* 1.4 76.1 - - - +
43Z LYS* 1.4 60.0 + - + +
44Z GLY* 3.1 3.5 + - - -
80Z LEU* 4.2 12.0 - - + +
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Residues in contact with LYS 43 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Z LYS* 3.5 46.3 - - - +
40Z LEU* 3.2 24.9 + - - +
42Z LYS* 1.4 75.6 - - + +
44Z GLY* 1.4 58.2 + - - +
45Z LEU* 4.2 21.1 - - + +
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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