Contacts of the helix formed by residues 85 - 98 (chain B) in PDB entry 3KXK
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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ILE* 5.5 1.1 - - - -
62B ILE 3.2 9.6 - - - +
63B PHE* 5.2 0.2 - - - -
64B GLU 3.0 13.1 - - - +
65B GLN* 3.9 2.3 - - - -
66B LEU* 3.4 23.0 + - + -
71B PHE* 3.3 19.1 - - + -
84B LEU* 1.3 75.7 - - - +
86B LYS* 1.3 67.1 + - - +
87B ILE* 3.7 5.6 + - - +
88B LEU* 2.9 28.1 + - - +
89B LEU* 2.9 25.0 + - - +
114B TYR* 2.6 27.6 + - - -
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Residues in contact with LYS 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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12B PHE* 5.8 6.1 - - - -
62B ILE 3.4 4.1 + - - -
63B PHE* 3.5 54.2 + - + +
64B GLU* 2.9 28.2 + - - +
65B GLN* 5.2 2.5 - - + +
85B ASP* 1.3 76.9 - - - +
87B ILE* 1.3 59.6 + - + +
89B LEU* 3.3 5.0 + - - +
90B LEU* 2.9 53.6 + - + +
238B ARG 5.4 2.8 + - - -
239B GLY* 4.3 12.7 + - - +
241B PRO* 4.0 21.5 - - + -
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Residues in contact with ILE 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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65B GLN* 3.8 18.8 - - + +
85B ASP* 3.3 8.3 + - - +
86B LYS* 1.3 78.2 - - + +
88B LEU* 1.3 63.5 + - - +
90B LEU* 3.4 1.9 + - - +
91B LEU* 3.1 29.4 + - + +
114B TYR* 3.3 52.9 - - + +
241B PRO* 3.9 18.6 - - + -
243B GLN* 3.6 29.2 - - + +
244B ILE* 3.8 27.1 - - + +
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Residues in contact with LEU 88 (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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71B PHE* 3.5 31.0 - - + -
75B ARG* 4.0 17.5 - - - +
83B VAL 4.0 0.2 - - - +
84B LEU* 3.6 27.1 - - + -
85B ASP* 2.9 17.0 + - - +
87B ILE* 1.3 76.9 - - - +
89B LEU* 1.3 62.4 + - - +
91B LEU* 3.5 14.7 + - + +
92B GLU* 3.1 30.2 + - - +
111B ARG* 4.7 13.2 - - + +
114B TYR* 3.9 22.9 - - + -
115B GLU* 4.0 15.0 - - - +
118B ILE* 5.3 0.9 - - + -
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Residues in contact with LEU 89 (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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19B LEU* 4.4 15.3 - - + +
20B VAL* 4.0 17.3 - - + -
23B ALA* 4.0 23.8 - - + -
25B TYR* 4.8 1.1 - - + -
61B ILE* 4.0 35.2 - - + -
63B PHE* 4.6 18.2 - - + -
84B LEU* 4.6 8.4 - - + +
85B ASP 2.9 19.7 + - - +
86B LYS* 3.5 5.2 - - - +
88B LEU* 1.3 74.3 - - - +
90B LEU* 1.3 66.8 + - + +
92B GLU* 3.2 15.1 + - - +
93B ILE* 3.1 34.1 + - + +
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Residues in contact with LEU 90 (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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19B LEU* 4.1 28.3 - - + -
63B PHE* 5.5 0.7 - - + -
86B LYS* 2.9 41.4 + - + +
87B ILE 3.8 0.2 - - - +
89B LEU* 1.3 77.4 - - + +
91B LEU* 1.3 57.9 + - - +
93B ILE* 3.1 10.6 + - + +
94B PHE* 2.8 40.4 + - + -
237B ILE* 3.7 36.6 - - + -
239B GLY 5.5 0.2 - - - +
240B ILE* 5.3 0.7 - - + -
241B PRO* 3.8 13.0 - - + -
244B ILE* 3.6 31.6 - - + -
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Residues in contact with LEU 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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87B ILE* 3.1 28.3 + - + +
88B LEU* 3.7 13.0 - - + +
89B LEU 3.3 0.2 - - - -
90B LEU* 1.3 77.4 - - - +
92B GLU* 1.3 62.0 + - + +
94B PHE* 3.1 14.1 + - + +
95B ALA* 3.0 20.6 + - - +
107B ILE* 3.5 26.1 - - + +
110B ALA* 4.0 15.5 - - + +
111B ARG* 3.7 39.3 - - + +
114B TYR* 5.2 0.7 - - + -
244B ILE* 3.5 32.3 - - + -
247B ALA* 4.4 3.1 - - + -
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Residues in contact with GLU 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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2B LYS* 6.1 0.2 - - - -
23B ALA* 5.2 3.8 - - + -
25B TYR* 3.1 35.5 + - - -
82B GLU* 5.5 1.7 - - - +
84B LEU* 3.2 35.8 - - + +
88B LEU* 3.1 18.7 + - + +
89B LEU* 3.2 9.9 + - - +
91B LEU* 1.3 75.4 - - + +
93B ILE* 1.3 62.0 + - + +
95B ALA* 3.3 8.1 + - - +
96B LEU* 3.2 29.5 + - + +
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Residues in contact with ILE 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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19B LEU* 3.4 51.8 - - + +
22B GLY* 5.4 3.1 - - - +
23B ALA* 3.7 19.7 - - + +
89B LEU* 3.1 21.4 + - + +
90B LEU* 3.1 13.7 + - + +
92B GLU* 1.3 74.5 - - - +
94B PHE* 1.3 71.0 + - + +
96B LEU* 3.1 16.5 + - + +
97B HIS* 3.0 45.9 + - + +
234B VAL* 5.0 0.4 - - + -
235B PRO* 4.7 11.0 - - + -
237B ILE* 6.0 2.0 - - + -
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Residues in contact with PHE 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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90B LEU* 2.8 27.3 + - + -
91B LEU* 3.1 22.6 + - + +
93B ILE* 1.3 78.9 - - + +
95B ALA* 1.3 57.4 + - - +
97B HIS* 3.2 3.5 + - - +
98B ALA* 2.8 28.8 + - - +
107B ILE* 3.4 16.6 - - + +
234B VAL* 3.9 16.4 - - + -
237B ILE* 3.6 27.6 - - + -
240B ILE* 5.4 1.8 - - + -
244B ILE* 3.9 29.8 - - + -
247B ALA* 4.2 5.6 - - + -
248B PHE* 3.5 55.4 - + + -
251B THR* 3.8 11.9 - - - +
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Residues in contact with ALA 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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91B LEU 3.0 12.3 + - - +
92B GLU* 3.7 11.2 - - - +
93B ILE 3.2 0.2 - - - -
94B PHE* 1.3 76.6 - - - +
96B LEU* 1.3 63.3 + - + +
98B ALA* 3.5 16.5 + - - +
104B LYS* 4.4 13.2 - - + -
107B ILE* 3.5 19.7 - - + +
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Residues in contact with LEU 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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22B GLY 4.0 8.3 - - - +
23B ALA* 3.7 37.5 - - + +
24B ASN* 4.5 16.8 - - - +
92B GLU* 3.2 17.6 + - + +
93B ILE* 3.1 13.3 + - + +
95B ALA* 1.3 81.4 - - + +
97B HIS* 1.3 65.4 + - + +
98B ALA 3.6 3.5 + - - +
216B PRO 5.2 0.3 - - - +
217B LYS* 3.9 25.9 - - + +
218B ARG* 5.9 0.9 + - - -
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Residues in contact with HIS 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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22B GLY* 5.0 4.0 - - - -
93B ILE* 3.0 43.3 + - + +
94B PHE 3.2 4.2 + - - +
96B LEU* 1.3 77.2 - - + +
98B ALA* 1.3 64.5 + - - +
99B GLY 3.4 2.4 + - - -
193B THR* 5.4 1.8 + - - -
217B LYS* 3.7 38.6 + - + +
218B ARG* 4.0 10.4 + - - -
231B VAL* 5.9 0.3 - - - +
232B ASP* 2.8 35.0 + - - +
233B THR* 3.3 15.0 + - - -
234B VAL* 3.7 26.8 + - + +
235B PRO* 4.1 12.5 - - + +
251B THR* 4.4 4.2 - - + +
254B GLU* 3.5 8.7 - - - +
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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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94B PHE 2.8 15.9 + - - +
95B ALA 3.6 12.8 - - - +
96B LEU 3.3 4.7 - - - +
97B HIS* 1.3 78.2 - - - +
99B GLY* 1.3 58.6 + - - +
103B ALA* 4.2 10.5 - - + -
104B LYS* 3.0 34.3 + - + -
107B ILE* 3.8 16.4 - - + -
218B ARG* 4.6 5.1 + - - -
251B THR* 4.3 3.4 - - - -
254B GLU* 3.8 5.8 - - - -
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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