Contacts of the helix formed by residues 106 - 114 (chain B) in PDB entry 3KHE
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 TYR 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.8 19.5 - - + +
39B THR* 3.4 16.8 + - - -
42B LEU 4.9 0.7 - - - -
43B THR* 2.6 45.2 + - + -
46B PHE* 3.6 37.1 - + + -
55B GLY* 3.0 19.0 + - - +
105B GLU* 1.3 75.2 - - - +
107B SER* 1.3 69.7 + - - +
109B PHE* 3.1 4.0 + + - +
110B VAL* 2.8 51.7 + - + +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.5 0.7 - - - -
30B GLY 4.8 1.6 + - - -
31B SER* 3.3 38.8 + - - -
105B GLU* 3.2 4.1 - - - +
106B TYR* 1.3 93.7 - - - +
108B GLU* 1.3 56.4 + - - +
110B VAL* 3.7 8.6 - - - +
111B THR* 2.9 34.6 + - - -
196B GOL 3.5 12.6 - - - -
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Residues in contact with GLU 108 (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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27B LEU* 4.4 8.1 - - + -
96B VAL* 3.5 16.2 - - - +
97B ASP* 3.8 0.5 - - - +
98B PHE* 3.1 43.4 + - + +
99B ASP* 3.1 14.6 + - - +
103B TYR 3.1 4.2 - - - +
104B ILE* 3.4 6.7 - - + -
105B GLU* 2.9 30.1 + - + +
107B SER* 1.3 74.9 - - - +
109B PHE* 1.4 60.4 + - - +
111B THR* 3.5 3.5 + - - -
112B VAL* 3.1 32.2 + - - +
193B CA 2.5 29.8 - - - -
196B GOL 5.1 0.2 - - - +
197B MG 3.7 10.4 - - - -
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Residues in contact with PHE 109 (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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8B ALA* 4.1 7.2 - - + -
12B MET* 4.0 22.7 - - + -
42B LEU* 3.5 35.2 - - + -
45B ILE* 3.8 24.2 - - + -
46B PHE* 3.7 30.1 - + + -
49B LEU* 3.9 20.2 - - + -
57B LEU* 4.2 8.3 - - + -
96B VAL* 4.7 3.4 - - - -
104B ILE* 3.8 12.2 - - + +
105B GLU 3.0 10.4 + - - +
106B TYR* 3.4 7.9 - + - +
108B GLU* 1.4 72.3 - - - +
110B VAL* 1.3 72.2 + - + +
112B VAL* 3.3 1.6 + - - -
113B CYS* 2.9 48.9 + - - +
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Residues in contact with VAL 110 (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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30B GLY 3.8 19.7 - - - +
39B THR* 3.9 26.2 - - + -
42B LEU* 4.0 16.6 - - + +
106B TYR* 2.8 61.0 + - + +
107B SER* 3.7 9.9 - - - +
109B PHE* 1.3 75.2 - - + +
111B THR* 1.3 66.5 + - - +
113B CYS 3.1 0.3 + - - -
114B MET* 2.8 33.9 + - + +
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Residues in contact with THR 111 (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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26B MET* 3.7 42.8 - - + +
27B LEU* 3.6 21.6 + - - +
30B GLY* 3.6 17.7 - - - -
98B PHE* 4.0 15.3 - - + -
107B SER 2.9 22.3 + - - -
108B GLU 3.5 5.2 - - - -
109B PHE 3.4 0.2 - - - -
110B VAL* 1.3 79.2 - - - +
112B VAL* 1.3 58.6 + - - +
114B MET* 3.9 0.7 + - - -
116B LYS* 2.9 25.1 + - - -
119B LEU* 4.3 6.6 - - + +
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Residues in contact with VAL 112 (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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11B ASN* 4.0 9.1 - - - +
12B MET* 3.8 40.2 - - + +
15B PHE* 3.8 49.5 - - + -
96B VAL* 3.8 17.5 - - + -
98B PHE* 3.9 8.5 - - + -
108B GLU 3.1 16.6 + - - +
109B PHE 4.0 1.6 - - - +
111B THR* 1.3 83.5 - - + +
113B CYS* 1.3 60.3 + - - +
114B MET 4.1 0.2 - - - +
116B LYS* 2.8 18.0 + - - +
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Residues in contact with CYS 113 (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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8B ALA* 3.7 24.0 - - + -
11B ASN* 3.9 20.0 + - + -
12B MET* 3.7 30.3 - - - -
42B LEU* 3.9 25.0 - - + +
109B PHE* 2.9 40.3 + - + +
112B VAL* 1.3 77.2 - - - +
114B MET* 1.3 64.2 + - - +
115B ASP 3.5 1.7 + - - -
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Residues in contact with MET 114 (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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34B THR* 3.8 26.0 - - + -
38B GLU* 4.4 21.3 - - + +
39B THR* 4.6 9.6 - - - -
42B LEU* 3.7 16.8 - - + +
110B VAL* 2.8 20.2 + - - +
111B THR 4.6 3.1 - - - +
112B VAL 3.4 1.4 - - - +
113B CYS* 1.3 77.4 - - - +
115B ASP* 1.4 71.4 + - - +
116B LYS* 2.8 25.1 + - - +
118B LEU* 4.0 16.4 - - + -
119B LEU* 3.9 26.7 - - + +
124B ARG* 3.9 25.1 - - - +
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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