Contacts of the strand formed by residues 33 - 40 (chain S) in PDB entry 3J0S
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 LYS 33 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S VAL* 3.7 33.2 - - + -
17S ASP* 3.2 36.6 + - - +
18S MET* 4.0 23.7 - - + +
21S ARG 5.5 0.2 + - - -
31S LYS 4.3 4.0 - - - +
32S ARG* 1.3 82.5 - - - +
34S LYS* 1.3 64.5 + - - +
35S ALA* 3.2 1.2 + - - +
36S VAL* 3.4 29.6 - - + +
54S GLU* 3.7 14.1 - - - +
55S ILE 3.5 8.1 - - - +
56S LEU* 3.8 14.8 - - + -
57S VAL* 4.5 0.7 - - - -
86S ASP* 3.4 11.9 - - - +
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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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18S MET* 5.5 1.1 - - - +
32S ARG 3.3 6.1 + - - -
33S LYS* 1.3 72.7 - - - +
35S ALA* 1.3 57.0 + - - +
55S ILE* 2.8 9.7 + - + +
56S LEU 4.0 1.3 - - - -
57S VAL* 3.3 41.2 - - + +
60S VAL* 3.7 10.8 - - - +
67S PRO* 3.3 43.8 - - + +
84S LEU 4.0 0.3 - - - +
85S TYR* 3.4 23.4 + - + +
86S ASP* 2.7 49.9 + - + +
88S THR* 4.2 17.7 - - - +
162S GLU* 3.4 24.4 + - - -
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Residues in contact with ALA 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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33S LYS 4.4 0.4 - - - -
34S LYS* 1.3 78.8 - - - +
36S VAL* 1.3 69.2 + - - +
37S LEU* 6.0 0.9 - - + -
54S GLU* 3.7 1.3 - - - +
55S ILE* 2.7 59.4 + - + +
71S PHE* 4.4 7.4 - - + -
84S LEU 3.0 8.5 - - - +
85S TYR* 3.3 27.4 - - + -
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Residues in contact with VAL 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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14S VAL* 4.3 9.4 - - + -
18S MET* 5.4 7.4 - - + -
33S LYS* 3.4 42.6 - - + +
35S ALA* 1.3 80.8 - - - +
37S LEU* 1.3 64.0 + - - +
38S PHE* 3.2 32.5 - - + -
49S LEU* 6.2 1.6 - - + -
54S GLU* 4.3 11.9 - - + +
83S ALA* 3.3 5.8 - - - +
84S LEU* 2.8 50.2 + - + +
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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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35S ALA* 6.0 0.4 - - + -
36S VAL* 1.3 74.9 - - - +
38S PHE* 1.3 61.6 + - - +
49S LEU* 3.8 4.5 - - - +
50S GLU* 2.9 32.7 + - + +
53S LYS* 3.3 52.7 + - + +
54S GLU* 4.9 1.8 - - - +
55S ILE* 6.4 0.9 - - + -
71S PHE* 4.1 7.6 - - + -
74S MET* 3.9 17.9 - - + +
75S LEU* 3.4 34.5 - - + -
81S ARG* 4.4 16.4 - - + -
82S TYR 4.0 3.8 - - - +
83S ALA* 3.4 23.8 - - + -
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Residues in contact with PHE 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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11S VAL* 3.5 38.8 - - + -
14S VAL* 3.2 36.1 - - + -
15S PHE 5.0 0.2 - - - -
36S VAL* 3.2 37.2 - - + -
37S LEU* 1.3 75.5 - - - +
39S CYS* 1.3 62.6 + - - +
47S ILE* 5.2 2.9 - - + -
48S ILE 3.5 10.1 - - - +
49S LEU* 4.2 6.3 - - + -
81S ARG* 3.7 3.0 - - - +
82S TYR* 2.5 58.1 + - + +
83S ALA* 4.1 2.0 - - - -
84S LEU* 3.3 36.1 - - + -
101S PHE* 4.7 6.1 - + + -
124S ILE* 6.0 1.1 - - + -
127S LYS* 5.6 0.2 - - - -
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Residues in contact with CYS 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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38S PHE* 1.3 77.5 - - - +
40S LEU* 1.3 73.7 + - + +
41S SER* 5.6 0.7 - - - -
47S ILE* 4.0 5.1 - - - +
48S ILE* 3.0 44.2 + - - +
50S GLU* 3.4 36.6 - - - -
80S CYS 5.2 2.7 - - - +
81S ARG* 4.6 18.2 - - + -
82S TYR* 4.3 3.1 - - - -
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Residues in contact with LEU 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 VAL* 4.1 15.7 - - + -
39S CYS* 1.3 83.2 - - + +
41S SER* 1.3 64.9 + - - +
42S GLU* 5.1 0.5 - - - +
44S LYS* 3.5 44.4 + - + +
46S ASN 3.5 14.8 - - - +
47S ILE* 4.3 9.2 - - + -
80S CYS 5.6 3.1 - - - +
82S TYR* 3.4 33.0 - - + +
113S SER* 5.7 2.0 - - - +
116S ILE* 3.6 24.9 - - + -
117S TYR* 4.6 9.9 - - + -
120S SER* 5.0 1.6 - - - +
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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