Contacts of the helix formed by residues 36 - 45 (chain a) 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 36 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34a ASN 4.3 0.6 + - - -
35a ILE* 1.3 75.5 - - - +
37a PRO* 1.4 65.2 - - - +
38a GLU* 3.4 6.7 - - - -
39a GLU* 3.2 17.1 + - - +
40a CYS* 3.1 20.0 + - - +
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Residues in contact with PRO 37 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319Z ASP 6.0 0.2 - - - -
320Z GLU* 4.0 35.9 - - + +
323Z ILE* 4.0 16.4 - - + +
324Z ILE* 5.0 5.2 - - + +
35a ILE 4.1 0.4 - - - -
36a SER* 1.4 71.7 - - - +
38a GLU* 1.4 61.1 + - - +
40a CYS* 3.2 21.8 + - + +
41a ILE* 3.4 9.0 + - - +
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Residues in contact with GLU 38 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320Z GLU* 4.8 9.0 - - + +
36a SER* 3.4 5.3 - - - -
37a PRO* 1.4 76.6 - - - +
39a GLU* 1.3 58.9 + - - +
41a ILE* 3.6 7.8 + - - +
42a ARG* 3.3 21.3 + - - +
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Residues in contact with GLU 39 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35a ILE* 4.9 7.6 - - + -
36a SER* 3.2 26.7 + - - +
38a GLU* 1.3 73.8 - - - +
40a CYS* 1.4 60.1 + - - +
42a ARG* 3.8 6.8 - - - +
43a ARG* 3.0 31.9 + - - +
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Residues in contact with CYS 40 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323Z ILE* 5.6 5.6 - - + -
29a LEU* 4.3 33.2 - - + +
30a ILE* 5.1 3.8 - - - +
35a ILE* 5.3 6.0 - - + +
36a SER 3.1 11.4 + - - +
37a PRO* 3.2 14.3 + - + +
39a GLU* 1.4 75.6 - - - +
41a ILE* 1.3 55.9 + - - +
43a ARG* 3.6 4.3 + - - +
44a TRP* 2.9 32.6 + - - +
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Residues in contact with ILE 41 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318Z ILE 5.3 9.0 - - - +
319Z ASP* 5.9 2.0 - - - -
320Z GLU* 5.8 5.8 - - + +
37a PRO 3.4 7.9 + - - +
38a GLU* 3.9 10.3 - - - +
39a GLU 3.3 0.4 - - - -
40a CYS* 1.3 76.4 - - - +
42a ARG* 1.3 59.0 + - - +
44a TRP* 3.9 4.4 - - - +
45a ARG* 2.9 35.4 + - - +
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Residues in contact with ARG 42 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38a GLU 3.3 17.4 + - - +
39a GLU* 3.8 7.6 - - - +
40a CYS 3.4 0.2 - - - -
41a ILE* 1.3 76.3 - - - +
43a ARG* 1.3 61.8 + - - +
45a ARG 4.3 3.8 - - - -
46a GLY 3.2 31.9 + - - -
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Residues in contact with ARG 43 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24a TRP* 4.1 20.3 - - - +
29a LEU* 6.1 3.1 - - + -
39a GLU 3.0 18.5 + - - +
40a CYS* 3.9 4.9 - - - +
42a ARG* 1.3 74.8 - - - +
44a TRP* 1.4 61.3 + - - +
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Residues in contact with TRP 44 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24a TRP* 4.7 18.4 - - - +
25a ASN 5.9 0.2 - - - -
26a ILE* 4.4 24.5 - - + +
29a LEU* 5.9 2.0 - - + -
40a CYS 2.9 21.1 + - - +
41a ILE* 3.9 5.2 - - - +
42a ARG 3.3 0.2 - - - -
43a ARG* 1.4 79.0 - - - +
45a ARG* 1.3 61.5 + - + +
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Residues in contact with ARG 45 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41a ILE 2.9 24.7 + - - +
42a ARG* 4.3 0.7 - - - -
43a ARG 3.6 0.2 - - - -
44a TRP* 1.3 77.2 - - + +
46a GLY* 1.3 61.1 - - - +
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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