Contacts of the helix formed by residues 102 - 112 (chain R) in PDB entry 3K9Q
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 102 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R TYR 2.9 4.8 + - - -
101R THR* 1.3 76.3 - - - +
103R LYS* 1.3 64.8 + - - +
104R ASP* 3.0 28.5 + - - +
105R LYS* 3.2 34.7 + - + +
106R ALA* 3.0 25.2 + - - +
119R ILE* 4.7 3.4 - - - -
123R ALA* 3.9 2.2 - - - +
124R THR* 2.5 37.9 + - - +
125R GLY* 4.1 3.1 + - - -
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Residues in contact with LYS 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R ASP* 1.3 72.7 - - - +
104R ASP* 1.3 69.8 + - - +
106R ALA* 3.4 2.1 + - - +
107R GLN* 3.0 28.8 + - - +
124R THR 2.9 14.0 + - - +
125R GLY* 4.2 10.5 - - - -
126R ASP* 3.2 41.8 + - + +
127R LEU* 3.8 21.7 - - + +
144R THR* 4.6 15.3 + - - -
145R VAL* 4.1 23.3 - - + +
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Residues in contact with ASP 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ASP* 3.0 13.2 + - - +
103R LYS* 1.3 84.0 - - - +
105R LYS* 1.3 63.7 + - + +
107R GLN* 3.0 21.0 - - - +
108R ALA 4.3 0.7 + - - -
111R GLU* 5.5 0.3 - - - +
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Residues in contact with LYS 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R PHE 3.8 23.0 + - - +
100R TYR* 3.4 22.6 - - + -
101R THR* 4.7 10.1 + - - +
102R ASP* 3.2 35.0 + - + +
104R ASP* 1.3 76.3 - - + +
106R ALA* 1.3 61.6 + - - +
107R GLN 3.1 0.4 - - - -
108R ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95R GLU* 5.3 0.2 - - + -
100R TYR* 3.8 22.8 + - + +
102R ASP 3.0 18.2 + - - +
103R LYS 3.9 3.6 - - - +
105R LYS* 1.3 71.5 - - - +
107R GLN* 1.3 66.8 + - - +
108R ALA 3.0 4.0 + - - -
109R HIS* 3.1 24.1 + - + +
117R VAL* 3.9 18.0 - - + +
119R ILE* 4.0 5.8 - - + -
145R VAL* 3.9 22.0 - - + -
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Residues in contact with GLN 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103R LYS* 3.0 18.5 + - - +
104R ASP* 3.0 21.3 - - - +
106R ALA* 1.3 76.3 - - - +
108R ALA* 1.3 52.3 + - - +
110R ILE* 2.8 59.7 + - - +
111R GLU* 3.1 30.1 + - - +
144R THR* 4.6 5.6 + - - -
145R VAL* 4.2 12.3 - - - +
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Residues in contact with ALA 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R ASP* 5.3 1.1 - - - +
80R ALA* 4.2 9.2 - - + -
81R SER* 3.6 32.9 - - - +
100R TYR* 4.4 6.3 - - + -
104R ASP 4.3 0.6 + - - -
105R LYS 3.1 16.5 + - - +
106R ALA 3.0 0.4 + - - -
107R GLN* 1.3 77.6 - - - +
109R HIS* 1.3 55.8 + - - +
111R GLU* 3.4 16.2 + - - +
112R ALA* 3.0 27.7 + - - +
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Residues in contact with HIS 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8R ASN* 3.2 30.8 + - + -
80R ALA* 3.5 19.8 - - + +
83R LEU* 4.4 1.3 - - + -
85R TRP* 3.1 29.2 + - - +
93R VAL* 3.6 26.6 - - + +
95R GLU* 2.8 22.9 + - + -
100R TYR* 4.5 4.0 - + - -
106R ALA* 3.1 24.1 + - - -
108R ALA* 1.3 72.9 - - - +
110R ILE* 1.3 63.8 + - - +
112R ALA* 3.3 2.4 + - - -
113R GLY 3.1 6.6 + - - -
114R ALA* 3.0 23.7 + - + +
117R VAL* 3.4 26.0 - - + -
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Residues in contact with ILE 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R GLN* 2.8 44.4 + - - +
109R HIS* 1.3 73.0 - - - +
111R GLU* 1.3 59.7 + - - +
113R GLY* 2.8 22.7 + - - -
114R ALA 3.4 19.9 - - - +
115R LYS* 3.8 13.7 - - - +
116R LYS* 4.0 6.1 - - - +
117R VAL* 4.0 12.6 - - + -
144R THR* 3.8 35.2 - - + +
145R VAL* 4.6 2.9 - - + -
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Residues in contact with GLU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81R SER* 4.2 14.9 - - - +
104R ASP 5.5 0.2 - - - +
107R GLN* 3.1 33.9 + - + +
108R ALA* 3.6 22.2 + - - +
109R HIS 3.4 0.2 - - - -
110R ILE* 1.3 75.8 - - - +
112R ALA* 1.3 60.6 + - - +
113R GLY* 3.3 2.1 + - - -
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Residues in contact with ALA 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R ALA 3.5 16.2 - - - +
81R SER 3.7 11.4 + - - +
83R LEU 3.3 20.5 - - - +
84R PRO* 4.8 0.3 - - - +
85R TRP* 3.3 15.0 + - + -
86R LYS* 3.0 23.0 + - - +
108R ALA 3.0 17.8 + - - +
109R HIS 3.5 7.0 - - - +
110R ILE 3.2 0.2 - - - -
111R GLU* 1.3 74.0 - - - +
113R GLY* 1.3 55.7 + - - +
114R ALA 3.8 0.7 - - - -
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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