Contacts of the strand formed by residues 79 - 87 (chain B) in PDB entry 3K8G
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 THR 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 3.3 22.2 - - + +
75B ILE 2.5 24.9 + - - -
76B VAL* 3.0 16.6 + - - +
77B ASP 3.5 1.5 - - - +
78B ARG* 1.3 76.1 - - - +
80B THR* 1.3 63.3 + - - +
81B ALA 3.5 23.3 - - - +
82B VAL* 3.8 20.6 - - + -
97B GLY* 4.2 0.9 - - - -
98B SER 3.6 7.2 - - - +
101B TYR* 2.6 19.4 + - - +
302B MPD 3.6 11.6 + - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PRO* 3.7 3.1 - - - +
52B VAL* 2.8 29.9 + - - +
53B ALA* 4.2 3.0 + - - +
78B ARG 5.1 2.0 - - - +
79B THR* 1.3 76.0 - - - +
81B ALA* 1.3 55.8 + - - +
98B SER* 2.8 30.8 + - - +
99B GLY* 4.1 8.0 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 3.9 32.1 - - + +
50B PHE 3.4 7.4 - - - +
51B PRO* 4.3 1.8 - - + -
52B VAL* 4.4 0.7 - - - -
79B THR* 3.5 2.9 - - - +
80B THR* 1.3 85.2 + - - +
82B VAL* 1.3 64.6 + - - +
83B TYR* 4.2 11.8 - - + +
96B PHE 3.9 0.7 - - - +
97B GLY* 3.4 3.5 - - - -
98B SER* 2.9 32.7 + - - -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.9 7.1 - - + +
49B TYR* 3.5 5.7 - - - -
50B PHE* 2.9 50.3 + - + +
52B VAL* 4.5 8.5 - - + -
59B ILE* 5.8 6.3 - - + -
79B THR* 3.8 8.7 - - + -
81B ALA* 1.3 75.8 - - - +
83B TYR* 1.3 74.2 + - - +
84B GLY* 4.8 0.4 - - - +
95B LEU* 4.3 19.5 - - + -
96B PHE 3.5 5.2 - - - +
302B MPD 3.8 41.1 - - + +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASP* 5.7 0.2 - - - -
36B PRO* 3.5 44.9 - - + +
37B LEU* 4.3 17.3 - - + -
40B VAL* 3.7 7.9 - - + +
48B LEU 3.4 6.3 - - - +
49B TYR* 3.5 30.0 + + + -
81B ALA* 4.2 20.7 - - + +
82B VAL* 1.3 76.0 - - - +
84B GLY* 1.3 58.9 + - - +
95B LEU* 3.2 4.9 - - - +
96B PHE* 2.8 50.4 + + + +
98B SER* 4.5 10.3 - - - -
178B CYS* 3.1 40.2 + - + -
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 5.3 0.9 - - - +
40B VAL* 4.4 4.7 - - - +
46B VAL 4.5 0.2 - - - -
47B TYR* 3.4 8.7 - - - +
48B LEU* 2.8 43.7 + - - +
82B VAL* 4.8 0.6 - - - +
83B TYR* 1.3 76.4 - - - +
85B ALA* 1.3 62.0 + - - +
93B PHE* 5.8 1.3 - - - -
94B ARG 3.3 7.4 - - - -
95B LEU* 3.8 13.0 - - - -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.8 24.2 - - + +
44B ALA* 3.6 12.8 - - + -
46B VAL 3.3 5.6 - - - -
47B TYR* 3.8 6.5 - - + -
84B GLY* 1.3 75.3 - - - +
86B PHE* 1.3 60.4 + - - +
87B PHE* 3.6 25.6 - - + -
93B PHE* 3.4 6.3 - - - -
94B ARG 2.9 31.8 + - - +
95B LEU* 4.8 0.8 - - - +
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 3.5 1.2 - - - +
45B ASP* 2.8 30.3 + - + -
46B VAL* 2.8 33.0 + - + -
85B ALA* 1.3 73.0 - - - +
87B PHE* 1.3 65.0 + - - +
88B ALA* 3.7 33.7 - - + -
91B LYS* 4.5 6.3 - - + -
92B GLU 3.2 25.8 - - - -
93B PHE* 3.7 34.9 - + + -
280B LEU* 3.2 54.5 - - + -
281B TYR* 4.4 5.8 - - + -
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL 3.7 7.0 - - - -
41B GLY 4.1 2.2 - - - -
42B SER 3.4 24.7 - - - -
43B GLY 3.8 7.2 - - - -
44B ALA* 3.6 25.6 - - + -
45B ASP* 3.5 3.6 - - - -
85B ALA* 3.6 26.9 - - + -
86B PHE* 1.3 75.8 - - - +
88B ALA* 1.3 67.4 + - - +
89B ARG 3.4 1.3 - - - +
90B SER* 3.4 18.2 - - - +
91B LYS* 3.0 16.3 + - - -
92B GLU* 2.9 25.3 + - + -
94B ARG* 3.2 53.4 - - + -
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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