Contacts of the helix formed by residues 31 - 40 (chain s) 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 PRO 31 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27s GLN 5.3 0.7 - - - +
29s THR 3.8 6.7 - - - +
30s HIS* 1.3 82.9 - - - +
32s ASP* 1.3 68.8 + - + +
33s LEU 3.5 0.2 - - - -
34s LYS* 3.1 26.8 - - + +
35s THR* 4.4 3.6 + - - +
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Residues in contact with ASP 32 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30s HIS* 3.5 10.1 - - - +
31s PRO* 1.3 88.1 - - + +
33s LEU* 1.3 79.4 + - + +
34s LYS 3.1 4.7 - - - -
35s THR* 3.3 19.5 + - - +
36s SER* 4.5 2.9 + - - -
79s LYS* 4.4 18.5 + - - +
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Residues in contact with LEU 33 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26s LEU* 4.1 24.7 - - + +
27s GLN* 4.6 0.9 - - - -
30s HIS* 3.8 11.7 + - + +
32s ASP* 1.3 90.9 - - - +
34s LYS* 1.3 59.7 + - - +
35s THR 3.4 0.2 - - - -
36s SER* 4.0 5.6 - - - +
37s LEU* 2.8 58.1 + - + +
76s ALA* 4.4 19.7 - - + -
79s LYS* 4.2 23.6 - - + +
80s LEU* 4.7 13.2 - - + +
83s GLU* 4.4 20.9 - - + -
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Residues in contact with LYS 34 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27s GLN* 3.8 26.7 - - - +
30s HIS 3.7 3.2 + - - -
31s PRO* 3.1 21.9 + - + +
32s ASP 3.1 0.4 - - - -
33s LEU* 1.3 78.0 - - - +
35s THR* 1.3 58.4 + - + +
37s LEU* 3.7 0.3 - - - +
38s GLU* 2.7 67.2 + - + +
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Residues in contact with THR 35 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31s PRO 5.2 3.1 - - - +
32s ASP 3.3 14.1 + - - +
34s LYS* 1.3 86.0 - - + +
36s SER* 1.3 72.1 + - - +
38s GLU* 3.3 18.9 - - - +
39s SER* 3.7 6.1 + - - -
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Residues in contact with SER 36 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32s ASP 4.5 3.3 + - - -
33s LEU* 3.6 9.1 + - - -
34s LYS 3.3 0.4 - - - -
35s THR* 1.3 80.2 + - - +
37s LEU* 1.3 65.8 + - - +
39s SER* 3.1 15.8 + - - -
40s ILE* 3.1 17.0 + - - +
72s VAL* 3.3 25.2 - - - +
75s SER* 4.0 9.8 + - - -
76s ALA* 4.0 22.8 - - - +
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Residues in contact with LEU 37 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5s LYS* 2.7 45.1 + - - +
23s LEU* 3.6 33.0 - - + +
26s LEU* 3.9 25.1 - - + -
27s GLN* 3.8 11.4 - - + +
33s LEU* 2.8 45.8 + - + +
36s SER* 1.3 70.2 - - - +
38s GLU* 1.3 67.4 + - - +
39s SER 3.0 1.8 - - - -
40s ILE* 3.4 32.6 + - + -
80s LEU* 4.6 7.9 - - + -
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Residues in contact with GLU 38 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5s LYS* 4.8 2.6 - - - +
27s GLN* 3.9 19.9 + - - +
34s LYS* 2.7 61.3 + - + +
35s THR* 3.3 12.1 - - - +
37s LEU* 1.3 79.6 - - - +
39s SER* 1.3 62.1 + - - +
40s ILE 4.2 2.8 - - - +
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Residues in contact with SER 39 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35s THR 3.7 4.7 + - - -
36s SER 3.1 10.7 + - - -
38s GLU* 1.3 82.1 - - - +
40s ILE* 1.3 66.5 + - - +
41s ILE* 3.4 10.9 - - - +
69s SER* 3.3 14.4 + - - -
72s VAL* 3.1 31.6 - - - +
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Residues in contact with ILE 40 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5s LYS* 3.8 16.8 - - - +
23s LEU* 5.0 2.7 - - + -
36s SER* 3.1 18.3 + - - +
37s LEU* 3.4 43.3 + - + +
38s GLU 4.2 2.1 - - - +
39s SER* 1.3 77.1 - - - +
41s ILE* 1.3 71.6 + - - +
42s LEU* 3.7 17.0 - - + -
63s ILE* 5.9 0.7 - - + -
65s VAL* 4.7 11.4 - - + -
69s SER* 3.7 11.2 - - - +
72s VAL* 4.4 11.2 - - + -
73s LEU* 4.5 17.5 - - + +
76s ALA* 6.4 0.9 - - + -
80s LEU* 3.8 22.9 - - + -
94s PHE* 6.0 0.7 - - + -
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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