Contacts of the strand formed by residues 33 - 40 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14N VAL* 3.7 32.5 - - + -
17N ASP* 3.2 35.9 + - - +
18N MET* 4.0 23.7 - - + +
21N ARG 5.5 0.2 + - - -
31N LYS 4.3 3.6 - - - +
32N ARG* 1.3 83.7 - - - +
34N LYS* 1.3 64.9 + - - +
35N ALA* 3.2 1.8 + - - +
36N VAL* 3.4 28.3 - - + +
54N GLU* 3.7 13.7 - - - +
55N ILE 3.5 7.9 - - - +
56N LEU* 3.8 14.6 - - + -
57N VAL* 4.5 0.9 - - - -
86N ASP* 3.4 12.2 - - - +
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Residues in contact with LYS 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N MET* 5.5 0.9 - - - +
32N ARG 3.3 6.1 + - - -
33N LYS* 1.3 72.7 - - - +
35N ALA* 1.3 56.7 + - - +
55N ILE* 2.8 9.1 + - + +
56N LEU 4.0 2.2 - - - -
57N VAL* 3.3 39.8 - - + +
60N VAL* 3.7 10.1 - - - +
67N PRO* 3.3 43.1 - - + +
84N LEU 4.0 0.5 - - - +
85N TYR* 3.4 23.8 + - + +
86N ASP* 2.7 49.4 + - + +
88N THR* 4.2 18.6 - - - +
162N GLU* 3.4 24.5 + - - -
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Residues in contact with ALA 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N LYS 4.4 0.2 - - - -
34N LYS* 1.3 79.1 - - - +
36N VAL* 1.3 69.9 + - - +
37N LEU* 6.4 0.4 - - + -
54N GLU* 3.7 0.7 - - - +
55N ILE* 2.7 58.7 + - + +
71N PHE* 4.4 7.2 - - + -
84N LEU 3.0 9.2 - - - +
85N TYR* 3.3 28.0 - - + -
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Residues in contact with VAL 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N VAL* 4.3 9.4 - - + -
18N MET* 5.4 7.4 - - + -
33N LYS* 3.4 43.5 - - + +
35N ALA* 1.3 81.2 - - - +
37N LEU* 1.3 66.1 + - - +
38N PHE* 3.2 30.4 - - + -
49N LEU* 6.2 1.8 - - + -
54N GLU* 4.3 10.8 - - + +
83N ALA* 3.3 5.2 - - - +
84N LEU* 2.8 50.5 + - + +
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Residues in contact with LEU 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N ALA* 6.0 0.7 - - + -
36N VAL* 1.3 74.4 - - - +
38N PHE* 1.3 61.5 + - - +
49N LEU* 3.8 4.7 - - - +
50N GLU* 2.9 31.6 + - + +
53N LYS* 3.3 54.0 + - + +
54N GLU* 4.9 1.8 - - - +
55N ILE* 6.4 1.6 - - + -
71N PHE* 4.1 6.7 - - + -
74N MET* 3.9 17.5 - - + +
75N LEU* 3.4 35.4 - - + -
81N ARG* 4.4 16.8 - - + -
82N TYR 4.0 4.0 - - - +
83N ALA* 3.4 23.3 - - + -
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Residues in contact with PHE 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N VAL* 3.5 39.9 - - + -
14N VAL* 3.2 35.0 - - + -
15N PHE* 5.3 0.2 - - - -
36N VAL* 3.2 37.0 - - + -
37N LEU* 1.3 74.9 - - - +
39N CYS* 1.3 60.9 + - - +
47N ILE* 5.2 3.1 - - + -
48N ILE 3.5 9.9 - - - +
49N LEU* 4.2 7.2 - - + -
81N ARG* 3.7 2.8 - - - +
82N TYR* 2.5 60.1 + - + +
83N ALA* 4.1 1.6 - - - -
84N LEU* 3.3 36.1 - - + -
101N PHE* 4.7 7.0 - + + -
124N ILE* 6.0 1.3 - - + -
127N LYS* 6.0 0.2 - - - -
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Residues in contact with CYS 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N PHE* 1.3 77.0 - - - +
40N LEU* 1.3 73.4 + - + +
41N SER* 5.6 0.9 - - - -
47N ILE* 4.0 5.2 - - - +
48N ILE* 3.0 45.5 + - - +
50N GLU* 3.4 35.9 - - - -
80N CYS 5.2 2.2 - - - +
81N ARG* 4.6 18.6 - - + +
82N TYR* 4.3 3.1 - - - -
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Residues in contact with LEU 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N VAL* 4.1 16.2 - - + -
39N CYS* 1.3 84.3 - - + +
41N SER* 1.3 65.9 + - - +
42N GLU* 5.1 0.5 - - - +
44N LYS* 3.5 46.0 + - + +
46N ASN 3.5 15.5 - - - +
47N ILE* 4.3 9.2 - - + +
80N CYS 5.6 2.7 - - - +
82N TYR* 3.4 33.0 - - + +
113N SER* 5.7 1.6 - - - +
116N ILE* 3.6 24.5 - - + -
117N TYR* 4.6 9.6 - - + -
120N 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