Contacts of the helix formed by residues 35 - 42 (chain S) in PDB entry 3J0O
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 35 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24S LEU 2.9 25.3 + - - -
25S ALA* 3.5 20.9 + - - -
27S GLY* 5.7 0.7 - - - -
29S ASN* 4.5 20.9 - - - -
31S GLU* 5.8 0.2 - - - -
32S LYS* 3.2 14.8 + - - +
33S LEU 3.8 2.2 + - - -
34S ILE* 1.3 77.9 - - - +
36S ASP* 1.3 56.1 + - - +
37S GLU* 2.7 25.0 + - - +
38S LEU* 3.0 16.3 + - - +
39S ALA* 3.4 5.7 + - - +
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Residues in contact with ASP 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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29S ASN* 5.3 4.9 + - - +
31S GLU* 4.9 2.8 - - - +
32S LYS* 2.6 36.9 + - - -
34S ILE 4.3 0.8 - - - +
35S SER* 1.3 71.9 - - - +
37S GLU* 1.3 60.6 + - - +
39S ALA* 2.9 28.8 - - + +
40S ALA* 3.6 4.5 + - - +
51S LYS* 3.9 17.5 + - - -
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Residues in contact with GLU 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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24S LEU* 3.1 54.5 - - + +
27S GLY* 6.3 0.4 - - - -
29S ASN* 5.9 1.6 - - - +
35S SER* 2.7 13.3 + - - +
36S ASP* 1.3 74.9 - - - +
38S LEU* 1.3 55.8 + - - +
39S ALA 2.7 13.8 + - - -
40S ALA* 2.8 22.5 + - - +
41S LEU* 3.9 3.5 + - - +
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Residues in contact with LEU 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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21S LEU* 4.5 9.2 - - + -
24S LEU* 4.6 4.5 - - + -
25S ALA* 3.7 30.1 - - + +
33S LEU 4.1 3.8 - - - +
34S ILE* 3.6 31.4 - - + -
35S SER* 3.0 8.6 + - - +
37S GLU* 1.3 79.4 - - - +
39S ALA* 1.3 57.9 + - - +
41S LEU* 3.0 30.4 + - + +
42S PHE* 2.6 40.8 - - + -
91S ILE* 4.4 2.5 - - + -
92S PRO* 3.5 37.9 - - + -
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Residues in contact with ALA 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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34S ILE* 4.4 5.6 - - + +
35S SER 3.4 3.9 + - - +
36S ASP* 2.9 30.3 + - + +
37S GLU 2.7 0.8 + - - -
38S LEU* 1.3 81.1 - - - +
40S ALA* 1.3 59.7 + - - +
41S LEU 2.9 1.9 + - - -
42S PHE* 3.2 12.9 + - - -
47S ARG* 3.4 27.8 - - + +
50S VAL* 6.6 0.4 - - + -
51S LYS* 6.0 7.6 - - + -
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Residues in contact with ALA 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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36S ASP 3.6 3.3 + - - +
37S GLU* 2.8 16.2 + - - +
39S ALA* 1.3 73.9 - - - +
41S LEU* 1.3 62.1 - - + +
42S PHE 4.5 2.8 - - - +
47S ARG* 5.5 2.7 + - - +
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Residues in contact with LEU 41 (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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16S LYS* 4.7 24.2 - - + -
21S LEU* 3.7 29.4 - - + -
24S LEU* 3.9 14.6 - - + -
37S GLU 4.5 2.7 - - - +
38S LEU* 3.0 26.4 + - + +
39S ALA 2.9 2.0 + - - -
40S ALA* 1.3 81.5 - - + +
42S PHE* 1.3 67.8 + - + +
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Residues in contact with PHE 42 (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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34S ILE* 4.2 16.2 - - + -
38S LEU* 2.6 54.1 - - + -
39S ALA* 3.2 4.9 + - - +
40S ALA 4.5 1.7 - - - +
41S LEU* 1.3 84.6 - - + +
43S ASP* 1.3 62.4 + - - +
46S THR* 3.4 33.2 - - + -
47S ARG* 2.9 30.5 + - + -
50S VAL* 6.2 0.4 - - + -
89S ILE* 4.0 10.3 - - + -
90S VAL 4.2 8.3 - - - -
91S ILE* 5.4 1.1 - - - -
92S PRO* 4.8 8.7 - - + -
117S ILE* 4.4 8.5 - - + -
118S GLY* 3.2 40.6 - - - -
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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