Contacts of the helix formed by residues 90 - 103 (chain B) in PDB entry 1K8R
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 ASP 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ARG* 3.6 6.3 + - + +
89B GLY* 1.3 71.0 - - - +
91B TYR* 1.3 61.6 + - - +
92B GLN* 3.0 11.0 + - - +
93B LYS* 2.8 55.0 + - + +
94B THR* 3.0 24.3 + - - +
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Residues in contact with TYR 91 (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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89B GLY 2.9 11.4 + - - +
90B ASP* 1.3 70.6 + - - +
92B GLN* 1.3 69.3 + - + +
94B THR* 3.9 5.0 - - - -
95B LEU* 2.9 45.6 + - + +
110B PHE 5.8 0.2 - - - -
111B ILE* 3.7 20.5 - - + +
112B VAL* 3.6 45.0 + - + +
123B ILE* 4.7 15.0 + - + -
124B THR 4.8 6.5 - - - -
125B GLU* 3.8 29.8 - - - +
126B GLU* 5.9 4.5 - - + +
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Residues in contact with GLN 92 (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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90B ASP* 3.0 6.5 + - - +
91B TYR* 1.3 91.6 - - + +
93B LYS* 1.3 62.4 + - + +
95B LEU* 3.4 6.6 + - + +
96B ALA* 3.1 22.5 + - - +
107B ALA* 4.3 19.8 - - + +
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Residues in contact with LYS 93 (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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90B ASP* 2.8 42.5 + - + +
92B GLN* 1.3 73.7 - - + +
94B THR* 1.3 64.1 + - - +
96B ALA* 3.1 9.5 + - - +
97B ILE* 3.0 30.8 + - + +
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Residues in contact with THR 94 (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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73B LEU* 4.1 6.7 - - + -
75B PHE* 4.0 27.1 - - + -
85B VAL* 4.3 9.1 - - + +
86B GLN 5.0 0.8 + - - +
87B SER* 2.8 39.8 - - - -
88B ARG 4.4 1.7 + - - -
90B ASP* 3.0 19.9 + - - +
91B TYR* 3.9 4.5 - - - -
93B LYS* 1.3 74.3 - - - +
95B LEU* 1.3 66.2 + - - +
97B ILE* 3.2 13.8 + - + +
98B ALA* 2.9 22.0 + - - +
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Residues in contact with LEU 95 (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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75B PHE* 4.6 5.8 - - + -
91B TYR* 2.9 35.0 + - + +
92B GLN* 3.8 6.3 - - + +
94B THR* 1.3 77.4 - - - +
96B ALA* 1.3 57.4 + - - +
98B ALA* 3.4 5.0 + - - +
99B LEU* 2.9 38.6 + - + +
107B ALA* 3.9 27.8 - - + +
110B PHE* 3.9 23.3 - - + +
111B ILE 5.2 1.1 - - - -
112B VAL* 3.7 28.9 - - + -
145B ILE* 4.2 25.1 - - + -
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Residues in contact with ALA 96 (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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92B GLN 3.1 13.3 + - - +
93B LYS* 3.1 13.2 + - - +
95B LEU* 1.3 74.8 - - - +
97B ILE* 1.3 66.2 + - + +
99B LEU* 3.2 6.9 + - - +
100B LYS* 3.1 21.1 + - - +
107B ALA* 4.6 13.5 - - + +
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Residues in contact with ILE 97 (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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85B VAL* 4.1 20.9 - - + -
86B GLN 4.9 12.8 - - - +
93B LYS* 3.0 19.6 + - + +
94B THR* 3.2 14.6 + - + +
96B ALA* 1.3 76.5 - - + +
98B ALA* 1.3 62.9 + - - +
100B LYS* 3.0 18.4 + - + +
101B LYS* 3.1 18.2 + - + +
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Residues in contact with ALA 98 (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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75B PHE* 4.0 26.7 - - + -
83B ARG* 6.0 1.6 - - + -
85B VAL* 4.4 12.5 - - + +
94B THR 2.9 16.3 + - - +
95B LEU* 3.5 8.7 - - - +
97B ILE* 1.3 78.1 - - - +
99B LEU* 1.3 62.7 + - - +
100B LYS 3.2 0.9 + - - -
101B LYS* 3.2 12.3 + - - +
102B PHE* 3.3 19.9 + - - -
145B ILE* 3.9 18.6 - - + -
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Residues in contact with LEU 99 (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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95B LEU* 2.9 36.7 + - + +
96B ALA* 3.2 6.2 + - - +
98B ALA* 1.3 75.5 - - - +
100B LYS* 1.3 56.3 + - - +
102B PHE* 3.4 2.8 + - + +
103B SER 2.9 7.3 + - - -
104B LEU* 2.8 76.5 + - + +
106B ASP 4.0 13.9 - - - +
107B ALA* 4.0 9.9 - - + -
110B PHE* 3.8 23.8 - - + -
145B ILE* 3.5 28.7 - - + -
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Residues in contact with LYS 100 (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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96B ALA 3.1 10.6 + - - +
97B ILE* 3.0 15.3 + - + +
99B LEU* 1.3 75.1 - - - +
101B LYS* 1.3 61.7 + - + +
102B PHE 3.0 5.9 + - - -
103B SER* 3.1 18.8 + - - +
104B LEU 5.0 1.5 + - - +
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Residues in contact with LYS 101 (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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25A GLN* 5.4 3.3 - - - +
33A ASP* 3.7 23.9 + - - +
35A THR* 5.8 3.6 + - - +
36A ILE 6.2 0.9 - - - +
38A ASP* 3.1 40.3 + - - -
40A TYR* 5.0 4.5 + - - -
83B ARG* 2.8 39.5 + - + +
84B ALA 3.6 7.2 - - - +
85B VAL* 3.6 26.2 - - + -
97B ILE* 3.1 20.0 + - + +
98B ALA* 3.6 8.7 - - - +
100B LYS* 1.3 76.8 - - + +
102B PHE* 1.3 56.6 + - - +
103B SER* 5.1 0.9 + - - -
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Residues in contact with PHE 102 (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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25A GLN* 6.0 0.2 - - - -
75B PHE* 3.4 35.2 - - + -
77B ALA* 3.6 27.1 - - + -
78B CYS* 3.8 26.4 - - - -
81B GLN* 3.5 38.1 - - + -
82B THR* 3.7 1.6 - - - -
83B ARG* 3.4 38.9 + - + +
98B ALA 3.3 20.0 + - - +
99B LEU* 4.0 4.7 - - + +
100B LYS 3.0 0.8 - - - -
101B LYS* 1.3 78.2 - - - +
103B SER* 1.3 70.4 + - - +
104B LEU* 4.1 19.9 - - + +
145B ILE* 4.2 7.9 - - + -
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Residues in contact with SER 103 (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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25A GLN* 4.1 22.0 + - - -
99B LEU 2.9 4.5 + - - -
100B LYS* 3.1 16.7 + - - +
101B LYS 5.1 0.7 + - - -
102B PHE* 1.3 84.2 + - - +
104B LEU* 1.3 68.4 + - - +
105B GLU* 5.4 2.5 - - - +
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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