Contacts of the helix formed by residues 48 - 58 (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 PHE 48 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8S GLU* 5.5 9.4 - - + -
12S GLY 6.1 2.0 - - - +
13S ALA* 5.3 3.4 - - + -
38S GLU* 4.9 18.8 + - + +
42S ASN* 5.7 2.0 - - - +
46S ILE 3.8 0.8 + - - -
47S PRO* 1.3 78.5 - - - +
49S SER* 1.3 63.0 + - - +
50S ALA* 3.9 9.0 - - + +
51S THR* 3.2 28.2 + - - +
52S VAL* 3.3 10.9 + - - +
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Residues in contact with SER 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S GLU* 5.6 1.8 - - - +
47S PRO 3.8 1.2 + - - -
48S PHE* 1.3 71.3 - - - +
50S ALA* 1.3 63.4 + - - +
51S THR 3.2 0.9 - - - -
52S VAL* 3.6 9.7 + - - +
53S GLU* 3.3 21.3 + - - +
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Residues in contact with ALA 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S GLY* 4.9 5.2 - - - -
13S ALA* 3.9 12.0 - - + +
26S ILE* 3.8 32.2 - - + +
27S THR 4.9 5.8 - - - +
28S ASN* 5.1 6.7 - - + -
48S PHE* 3.2 6.7 - - + -
49S SER* 1.3 77.4 - - - +
51S THR* 1.3 59.4 + - - +
53S GLU* 3.8 4.3 + - - +
54S LEU* 3.2 26.9 + - - +
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Residues in contact with THR 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S GLU* 6.0 3.8 - - - -
13S ALA* 3.8 18.0 - - - +
47S PRO* 4.5 9.2 - - - -
48S PHE* 3.2 26.3 + - - +
49S SER 3.2 0.2 - - - -
50S ALA* 1.3 78.0 - - - +
52S VAL* 1.3 58.9 + - - +
54S LEU* 3.1 3.3 + - - +
55S LEU* 2.9 33.1 + - - +
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Residues in contact with VAL 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S PRO* 5.4 3.7 - - + +
48S PHE 3.3 8.6 + - - +
49S SER* 3.8 12.8 - - - +
50S ALA 3.4 0.4 - - - -
51S THR* 1.3 80.1 - - - +
53S GLU* 1.3 60.3 + - - +
55S LEU* 3.5 6.6 + - - +
56S LYS* 3.5 18.0 + - - +
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Residues in contact with GLU 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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26S ILE* 5.2 6.7 - - + -
49S SER 3.3 13.8 + - - +
50S ALA* 3.9 6.7 - - - +
51S THR 3.3 0.2 - - - -
52S VAL* 1.3 79.0 - - - +
54S LEU* 1.3 64.4 + - - +
56S LYS* 3.3 7.9 + - - +
57S LYS* 3.2 20.6 + - - +
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Residues in contact with LEU 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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13S ALA* 4.7 12.8 - - + +
14S VAL 6.2 0.4 - - - -
15S ALA* 6.0 6.7 - - + +
24S ASP* 5.8 4.4 - - + +
25S TYR* 5.3 3.4 - - - +
26S ILE* 4.6 13.7 - - + +
50S ALA 3.2 18.8 + - - +
51S THR* 3.1 8.6 + - - +
53S GLU* 1.3 72.7 - - - +
55S LEU* 1.3 57.7 + - - +
56S LYS 3.0 9.3 + - - -
57S LYS* 3.3 6.7 + - - +
58S VAL* 3.2 25.5 + - - +
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Residues in contact with LEU 55 (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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51S THR 2.9 16.6 + - - +
52S VAL* 4.0 6.3 - - - +
53S GLU 3.4 0.2 - - - -
54S LEU* 1.3 75.3 - - - +
56S LYS* 1.3 53.4 + - - +
58S VAL* 2.8 18.6 - - - +
59S ASN* 4.6 3.3 - - - -
60S PRO 5.1 1.7 - - - -
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Residues in contact with LYS 56 (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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52S VAL 3.5 10.1 + - - +
53S GLU* 3.3 11.9 + - - +
54S LEU 3.0 0.6 - - - -
55S LEU* 1.3 77.0 - - - +
57S LYS* 1.3 67.0 + - - +
58S VAL 3.1 7.9 - - - +
59S ASN* 4.7 4.7 - - - +
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Residues in contact with LYS 57 (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 ASP* 5.7 8.1 - - + -
53S GLU 3.2 10.7 + - - +
54S LEU* 3.3 9.4 + - - +
56S LYS* 1.3 79.5 - - - +
58S VAL* 1.3 59.0 + - - +
59S ASN* 4.0 2.1 + - - +
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Residues in contact with VAL 58 (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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15S ALA* 5.6 9.2 - - + -
23S VAL* 6.3 2.7 - - + -
24S ASP* 5.3 13.3 - - + +
54S LEU 3.2 9.7 + - - +
55S LEU* 2.8 27.1 - - - +
56S LYS 3.1 4.7 - - - +
57S LYS* 1.3 77.4 - - - +
59S ASN* 1.3 60.3 + - - +
60S PRO* 3.7 10.2 - - + -
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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