Contacts of the helix formed by residues 31 - 45 (chain z) in PDB entry 5JPQ
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 SER 31 (chain z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6z VAL* 5.1 14.6 - - - -
28z ARG* 6.2 0.7 - - - -
29z PRO* 5.3 0.4 - - - +
30z SER* 1.3 98.1 - - - +
32z LYS* 1.3 65.2 - - - +
33z VAL* 3.8 5.8 - - - -
34z ILE* 3.3 20.9 - - - -
35z ILE* 2.9 14.6 + - - +
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Residues in contact with LYS 32 (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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104s TRP* 5.5 10.8 - - + -
31z SER* 1.3 72.6 - - - +
33z VAL* 1.3 59.8 + - - +
35z ILE* 3.8 4.3 - - - +
36z LYS* 2.9 30.1 + - - +
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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
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31z SER* 3.0 5.0 - - - -
32z LYS* 1.3 76.2 - - - +
34z ILE* 1.3 72.0 + - - +
36z LYS* 2.7 16.8 + - - +
37z PHE* 2.8 13.1 + - - +
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Residues in contact with ILE 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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6z VAL* 5.2 9.9 - - + +
10z ALA* 5.7 6.7 - - + -
28z ARG* 5.5 7.4 - - + -
30z SER* 2.6 25.4 - - - +
31z SER* 3.2 13.4 + - - -
33z VAL* 1.3 81.0 - - - +
35z ILE* 1.3 59.7 + - - +
37z PHE* 3.0 4.1 + - - +
38z LEU* 2.9 25.0 + - - +
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Residues in contact with ILE 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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30z SER* 3.2 5.9 + - - +
31z SER 2.9 15.0 + - - +
32z LYS* 3.8 4.9 - - - +
34z ILE* 1.3 80.3 - - - +
36z LYS* 1.3 56.2 + - - +
38z LEU* 3.2 10.2 - - - -
39z GLN* 2.9 25.1 + - - +
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Residues in contact with LYS 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 LYS 2.9 19.4 + - - +
33z VAL* 2.7 17.5 + - - +
35z ILE* 1.3 70.2 - - - +
37z PHE* 1.3 60.1 + - - +
39z GLN* 2.9 25.1 - - - +
40z VAL* 2.9 9.7 + - - +
110z ILE* 4.6 22.5 - - + +
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Residues in contact with PHE 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 2.8 9.8 + - - +
34z ILE* 3.8 6.3 - - - +
36z LYS* 1.3 70.9 - - - +
38z LEU* 1.3 55.2 + - - +
39z GLN 2.3 17.0 + - - -
40z VAL* 2.7 19.8 + - - +
41z MET* 2.8 15.8 + - - +
103z ILE* 5.9 7.6 - - + -
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Residues in contact with LEU 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 ILE 2.9 19.4 + - - +
35z ILE* 3.2 10.3 - - - +
37z PHE* 1.3 72.0 - - - +
39z GLN* 1.3 56.5 + - - +
41z MET* 4.5 9.6 - - - -
42z GLN* 4.4 9.2 - - - +
47z ILE* 5.8 3.4 - - - +
50z PHE* 4.0 25.4 + - + +
63z VAL* 5.8 6.3 - - + -
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Residues in contact with GLN 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 ILE 2.9 11.3 + - - +
36z LYS* 2.9 18.1 + - - +
37z PHE 2.3 16.0 + - - -
38z LEU* 1.3 68.1 - - - +
40z VAL* 1.3 53.4 + - - +
41z MET 2.5 17.6 + - - -
42z GLN* 2.7 18.2 + - - -
43z LYS* 2.9 13.3 + - + -
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Residues in contact with VAL 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 LYS 2.9 11.1 + - - +
37z PHE* 2.7 11.1 + - - +
39z GLN* 1.3 70.9 - - - +
41z MET* 1.3 66.7 + - - +
43z LYS* 3.9 9.2 - - - +
44z HIS* 3.1 20.8 + - - +
103z ILE* 5.4 10.3 - - + -
110z ILE 5.1 10.5 - - - +
111z MET* 5.6 2.2 - - - -
112z ASP* 5.1 15.9 - - + -
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Residues in contact with MET 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 PHE 2.8 16.8 + - - +
38z LEU* 4.5 6.3 - - - -
39z GLN 2.5 5.2 + - - +
40z VAL* 1.3 78.2 - - - +
42z GLN* 1.3 66.6 + - - +
44z HIS* 2.8 11.5 + - - +
45z GLY 2.8 16.5 + - - +
46z TYR* 4.5 9.5 - - + +
47z ILE* 4.4 14.8 - - + -
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Residues in contact with GLN 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 LEU 4.4 10.7 + - - +
39z GLN* 2.7 11.0 + - - +
41z MET* 1.3 75.3 - - - +
43z LYS* 1.3 55.8 + - - +
45z GLY* 2.6 34.0 + - - -
47z ILE* 4.4 10.3 - - + +
48z GLY 4.0 19.5 - - - +
50z PHE* 5.7 3.8 - - + +
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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 GLN* 2.9 12.4 + - + +
40z VAL* 3.9 12.8 - - - +
42z GLN* 1.3 75.4 - - - +
44z HIS* 1.3 58.5 + - - +
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Residues in contact with HIS 44 (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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40z VAL 3.1 13.8 + - - +
41z MET* 2.8 7.8 + - - +
43z LYS* 1.3 73.3 - - - +
45z GLY* 1.3 56.9 + - - +
46z TYR* 4.4 0.8 + - + -
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Residues in contact with GLY 45 (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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41z MET 2.8 17.1 + - - +
42z GLN* 2.6 19.4 + - - -
44z HIS* 1.3 80.1 - - - +
46z TYR* 1.3 58.8 + - - +
47z ILE 2.6 23.1 + - - +
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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