Contacts of the strand formed by residues 68 - 73 (chain N) in PDB entry 3SN6
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 68 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 4.8 0.4 - - - -
48N VAL* 4.0 16.8 - - + -
60N TYR* 3.0 24.2 - - + -
64N VAL* 2.9 44.3 + - + +
66N GLY* 3.4 6.5 + - - -
67N ARG* 1.3 118.4 - - + +
69N THR* 1.3 66.2 + - - +
81N LEU* 4.1 12.8 - - + -
82N GLN 3.4 2.7 - - - -
83N MET* 3.5 48.2 - - + -
84N ASN 4.2 8.1 - - - -
86N LEU* 4.5 2.9 - - + -
90N ASP* 4.3 15.7 - - + -
94N TYR* 4.0 19.1 - + - -
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Residues in contact with THR 69 (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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60N TYR* 3.1 9.8 + - - +
66N GLY* 5.5 2.9 + - - -
67N ARG 5.4 0.3 - - - -
68N PHE* 1.3 77.6 + - - +
70N ILE* 1.3 67.8 + - - +
71N SER* 3.7 8.7 + - - -
81N LEU* 4.0 1.8 - - - +
82N GLN* 2.9 46.8 + - + +
84N ASN* 5.6 2.9 + - - +
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Residues in contact with ILE 70 (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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34N MET 4.6 1.6 - - - +
35N ASN* 4.6 0.2 - - - -
36N TRP* 3.3 28.3 - - + +
49N SER* 3.0 36.8 - - - +
50N ASP* 4.0 3.6 - - - +
51N ILE* 3.8 30.7 - - + +
58N ILE* 3.5 31.0 - - + +
60N TYR* 2.7 21.2 + - - +
69N THR* 1.3 75.2 - - - +
71N SER* 1.3 60.2 + - - +
79N LEU* 4.3 9.2 - - + -
80N TYR 3.1 17.5 - - - +
81N LEU* 4.1 8.1 - - + -
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Residues in contact with SER 71 (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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19N ARG* 4.1 11.6 + - - -
51N ILE* 4.4 3.6 - - - -
69N THR* 3.7 9.5 + - - -
70N ILE* 1.3 75.9 - - - +
72N ARG* 1.3 60.8 + - - +
80N TYR* 2.7 58.0 + - - +
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Residues in contact with ARG 72 (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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29N PHE* 2.7 46.6 + - + -
30N SER* 4.5 0.2 - - - +
32N TYR 3.0 22.4 + - - -
34N MET* 3.7 9.1 - - - +
51N ILE* 3.5 33.9 + - + +
52N SER 2.9 28.1 + - - -
53N GLN* 3.2 16.0 - - - +
55N GLY* 4.4 6.3 - - - -
71N SER* 1.3 75.8 - - - +
73N ASP* 1.3 57.7 + - - +
74N ASN* 2.9 23.1 + - - +
78N THR 3.8 7.2 - - - +
79N LEU* 3.8 18.8 - - + -
80N TYR* 4.5 0.9 - - - -
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Residues in contact with ASP 73 (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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29N PHE* 4.0 1.4 - - - -
72N ARG* 1.3 71.4 - - - +
74N ASN* 1.3 63.8 + - - +
75N ALA* 3.2 8.7 + - - +
76N LYS* 2.8 46.3 + - - +
77N ASN* 3.2 1.4 + - - -
78N THR* 2.9 49.8 + - + +
80N TYR* 3.7 11.9 - - + -
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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