Contacts of the helix formed by residues 106 - 114 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.7 10.7 - - + +
39A THR* 3.3 17.3 + - - +
42A LEU 4.8 0.2 - - - -
43A THR* 2.6 39.9 + - + -
46A PHE* 3.5 29.1 - + + -
55A GLY 3.0 18.3 + - - +
105A GLU* 1.3 71.8 - - - +
107A SER* 1.3 71.3 + - - +
109A PHE* 3.1 4.2 + - - +
110A VAL* 2.8 49.2 + - + +
122B ARG* 4.0 32.3 + - + -
123B GLU* 3.8 9.4 + - + +
126B LEU* 3.4 31.4 - - + -
176B PHE* 5.3 2.9 - + - -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.4 0.4 - - - -
30A GLY 4.7 1.8 + - - -
31A SER* 3.5 34.3 + - - -
106A TYR* 1.3 85.1 - - - +
108A GLU* 1.3 64.2 + - - +
110A VAL* 3.9 7.0 - - - +
111A THR* 2.9 30.5 + - - -
122B ARG* 3.8 19.8 + - - +
123B GLU* 3.0 23.9 + - - -
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.2 14.8 - - + +
96A VAL* 3.6 16.1 - - - +
97A ASP* 3.8 0.5 - - - +
98A PHE* 3.2 37.0 + - + +
99A ASP* 3.0 15.3 + - - +
103A TYR 3.1 4.3 - - - +
104A ILE* 3.2 5.9 - - + -
105A GLU* 2.8 35.0 + - + +
107A SER* 1.3 77.4 - - - +
109A PHE* 1.3 59.4 + - - +
111A THR* 3.4 3.3 + - - -
112A VAL* 3.2 23.2 + - - +
192A CA 2.5 29.9 - - - -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.0 13.9 - - + -
12A MET* 4.2 16.6 - - + -
42A LEU* 3.4 37.0 - - + -
45A ILE* 3.7 24.5 - - + -
46A PHE* 3.6 30.5 - + + -
49A LEU* 3.9 20.0 - - + -
57A LEU* 4.2 8.1 - - + -
96A VAL* 4.8 3.6 - - - -
104A ILE* 3.7 12.4 - - + +
105A GLU 2.9 11.2 + - - +
106A TYR 3.1 9.4 - - - +
108A GLU* 1.3 72.9 - - - +
110A VAL* 1.3 73.7 + - + +
112A VAL* 3.4 1.5 + - - +
113A CYS* 2.9 45.6 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY* 3.6 23.6 - - - +
34A THR* 4.7 0.2 - - - +
39A THR* 4.0 22.0 - - + -
42A LEU* 4.3 20.0 - - + -
106A TYR* 2.8 59.1 + - + +
107A SER* 3.9 7.0 - - - +
108A GLU 3.5 0.2 - - - -
109A PHE* 1.3 81.6 - - + +
111A THR* 1.3 64.9 + - - +
114A MET* 2.9 36.8 + - + +
122B ARG* 5.9 0.7 - - - +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.4 46.4 - - + +
27A LEU* 3.6 19.6 + - - +
30A GLY* 3.6 21.2 - - - -
98A PHE* 4.4 10.8 - - + -
107A SER 2.9 21.6 + - - -
108A GLU 3.6 5.4 - - - -
109A PHE 3.3 0.2 - - - -
110A VAL* 1.3 79.4 - - - +
112A VAL* 1.3 59.0 + - - +
114A MET* 4.0 1.8 + - - +
116A LYS* 2.8 24.4 + - - -
119A LEU* 4.4 6.5 - - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN* 4.0 10.3 - - - +
12A MET* 3.9 28.7 - - + +
15A PHE* 3.5 63.6 - - + -
96A VAL* 4.0 15.3 - - + -
98A PHE* 3.7 15.0 - - + -
108A GLU 3.2 9.1 + - - +
109A PHE 4.2 2.0 - - - +
110A VAL 3.3 0.2 - - - -
111A THR* 1.3 80.4 - - - +
113A CYS* 1.3 60.9 + - - +
116A LYS* 2.9 16.6 + - - +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 3.6 38.3 - - + -
11A ASN* 3.8 21.3 + - - -
12A MET* 3.7 20.0 - - - -
42A LEU* 3.6 26.6 - - + +
109A PHE* 2.9 33.2 + - + +
110A VAL 4.4 0.2 - - - +
112A VAL* 1.3 76.8 - - - +
114A MET* 1.3 64.7 + - - +
115A ASP 3.5 1.7 + - - -
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 3.8 25.6 - - + -
38A GLU* 4.3 18.8 - - + +
39A THR* 4.7 10.5 - - - -
42A LEU* 3.7 17.0 - - + +
110A VAL* 2.9 21.4 + - - +
111A THR* 4.5 4.0 - - - +
112A VAL 3.4 1.0 - - - +
113A CYS* 1.3 77.2 - - - +
115A ASP* 1.3 71.5 + - - +
116A LYS* 2.8 28.8 + - - +
118A LEU* 3.8 14.8 - - + -
119A LEU* 3.7 33.7 - - + +
124A ARG* 3.8 19.3 - - - +
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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