Contacts of the helix formed by residues 43 - 54 (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 ASP 43 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41S LEU 4.0 0.6 + - - -
42S PHE* 1.3 75.9 - - - +
44S ALA* 1.3 67.0 + - - +
45S LYS* 3.3 15.3 - - - +
46S THR* 2.9 37.0 + - - -
47S ARG* 3.0 19.3 + - - +
118S GLY 3.5 14.0 - - - +
120S TYR* 5.2 3.2 - - - -
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Residues in contact with ALA 44 (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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42S PHE 3.9 0.2 + - - -
43S ASP* 1.3 72.1 - - - +
45S LYS* 1.3 53.6 + - + +
47S ARG* 3.2 22.6 + - - +
48S ARG* 2.7 37.2 + - - +
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Residues in contact with LYS 45 (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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43S ASP* 3.3 12.2 + - - +
44S ALA* 1.3 78.6 - - + +
46S THR* 1.3 64.2 + - - +
48S ARG* 3.0 22.6 - - + +
49S ARG* 3.2 8.7 + - - +
120S TYR* 4.2 16.3 + - + +
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Residues in contact with THR 46 (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* 5.6 1.1 - - + -
42S PHE* 3.4 33.0 - - + -
43S ASP* 2.9 29.2 + - - -
45S LYS* 1.3 74.7 - - - +
47S ARG* 1.3 66.0 + - - +
49S ARG* 3.1 13.8 + - - +
50S VAL* 3.1 27.9 + - + +
89S ILE* 3.1 37.5 - - + +
118S GLY 3.7 7.3 + - - -
120S TYR* 4.1 6.2 + - - -
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Residues in contact with ARG 47 (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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39S ALA* 3.4 28.6 + - + +
40S ALA* 5.5 2.6 - - - +
42S PHE* 2.9 34.1 + - + +
43S ASP 3.0 11.5 + - - +
44S ALA* 3.6 18.8 - - - +
46S THR* 1.3 76.8 - - - +
48S ARG* 1.3 64.0 + - - +
50S VAL* 4.8 4.7 - - - +
51S LYS* 2.9 33.9 + - + +
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Residues in contact with ARG 48 (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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44S ALA 2.7 17.5 + - - +
45S LYS* 3.0 18.8 - - + +
47S ARG* 1.3 74.8 - - - +
49S ARG* 1.3 59.4 + - - +
51S LYS* 3.5 3.5 - - - +
52S ARG* 2.8 68.2 + - - +
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Residues in contact with ARG 49 (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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45S LYS 3.2 6.5 + - - +
46S THR* 3.1 10.2 + - - +
48S ARG* 1.3 82.8 - - - +
50S VAL* 1.3 67.9 + - + +
52S ARG* 2.9 6.0 + - - +
53S GLY 2.9 33.0 + - - +
54S ILE* 5.2 12.1 - - + +
58S TYR* 3.2 21.4 + - - -
87S SER* 2.5 55.8 + - - -
88S MET* 5.1 0.4 - - - -
89S ILE* 4.5 13.3 - - + +
120S TYR* 3.6 21.0 - - - +
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Residues in contact with VAL 50 (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 LYS* 5.9 5.8 - - + -
34S ILE* 3.5 58.1 - - + +
39S ALA* 6.6 0.4 - - + -
42S PHE* 6.2 0.7 - - + -
46S THR* 3.1 27.3 + - + +
47S ARG* 4.2 4.0 - - - +
49S ARG* 1.3 79.2 - - + +
51S LYS* 1.3 62.7 + - + +
52S ARG 3.1 2.1 + - - -
53S GLY 4.0 2.3 + - - -
54S ILE* 3.9 30.0 - - + +
89S ILE* 5.4 1.6 - - + -
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Residues in contact with LYS 51 (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 LYS* 4.2 9.4 - - - +
36S ASP* 3.9 23.4 + - - -
39S ALA* 6.0 8.5 - - + -
47S ARG* 2.9 22.5 + - + +
48S ARG* 3.5 3.1 - - - +
50S VAL* 1.3 76.5 - - - +
52S ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 52 (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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48S ARG* 2.8 59.5 + - - +
49S ARG* 2.9 8.1 + - - +
50S VAL 4.1 1.3 - - - -
51S LYS* 1.3 82.4 - - - +
53S GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 53 (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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49S ARG* 2.9 16.4 + - - +
50S VAL 4.7 0.4 - - - -
52S ARG* 1.3 79.4 - - - +
54S ILE* 1.3 63.5 + - - +
55S SER* 4.0 2.3 + - - -
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Residues in contact with ILE 54 (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 LYS* 6.1 5.4 - - + -
33S LEU* 4.5 17.7 - - + -
34S ILE* 4.5 21.8 - - + +
49S ARG* 3.9 13.8 + - + +
50S VAL* 3.9 34.5 - - + +
53S GLY* 1.3 76.9 - - - +
55S SER* 1.3 76.6 + - - +
56S GLU* 3.4 9.9 - - - +
58S TYR* 4.5 17.5 - - + -
88S MET* 4.6 7.2 - - + -
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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