Contacts of the helix formed by residues 108 - 120 (chain Y) in PDB entry 1KKC
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 ALA 108 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105Y ILE* 2.9 17.5 + - + +
107Y GLN* 1.3 78.2 - - - +
109Y PRO* 1.3 56.6 - - - +
110Y VAL 3.4 0.2 - - - -
111Y LEU* 3.3 12.7 + - + -
112Y LYS* 2.8 31.4 + - - +
201Y TRP* 3.4 31.9 - - + +
205Y GLU* 3.3 20.4 - - + +
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Residues in contact with PRO 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Y ASP* 3.5 14.1 - - - +
107Y GLN* 3.3 7.9 - - - +
108Y ALA* 1.3 89.0 - - - +
110Y VAL* 1.3 64.0 - - + +
112Y LYS* 3.9 5.3 - - + +
113Y ALA* 3.1 25.5 + - - +
205Y GLU* 3.0 11.4 - - + +
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Residues in contact with VAL 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y PRO* 1.3 77.1 - - + +
111Y LEU* 1.3 62.5 + - - +
113Y ALA* 3.4 5.7 + - - +
114Y ALA* 3.1 21.5 + - - +
150Y LYS* 3.9 29.2 - - + -
205Y GLU* 2.9 22.4 + - - +
208Y TYR* 3.9 16.4 - - + -
209Y ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y ALA* 3.8 4.9 - - + +
110Y VAL* 1.3 71.3 - - - +
112Y LYS* 1.3 55.0 + - - +
114Y ALA* 3.1 2.8 + - - +
115Y ILE* 2.8 59.8 + - + +
144Y LEU* 4.4 1.8 - - + -
153Y LEU* 3.9 19.3 - - + -
170Y VAL* 3.6 14.4 - - + -
201Y TRP* 3.8 19.3 - - + -
204Y ALA* 3.5 37.5 - - + +
205Y GLU* 2.8 22.5 + - - +
208Y TYR* 3.7 25.4 - - + -
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Residues in contact with LYS 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Y ILE* 3.7 42.5 - - + +
106Y ASP* 2.8 30.8 + - - +
108Y ALA* 2.8 23.1 + - - +
109Y PRO* 3.9 5.6 - - + +
111Y LEU* 1.3 73.3 - - - +
113Y ALA* 1.3 58.3 + - - +
115Y ILE* 3.1 8.0 + - + +
116Y GLU* 2.8 61.1 + - + +
122Y PHE* 5.0 11.2 - - + -
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Residues in contact with ALA 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y PRO 3.1 19.0 + - - +
110Y VAL* 3.6 6.5 - - - +
111Y LEU 3.2 0.2 - - - -
112Y LYS* 1.3 76.1 - - - +
114Y ALA* 1.3 56.4 + - - +
116Y GLU* 3.1 16.8 + - - +
117Y GLN* 3.0 28.4 + - - +
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Residues in contact with ALA 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y VAL 3.1 9.9 + - - +
111Y LEU 3.1 8.0 + - - +
113Y ALA* 1.3 79.2 - - - +
115Y ILE* 1.3 62.8 + - - +
117Y GLN* 3.4 9.0 + - - +
118Y ARG* 3.1 24.8 + - - +
151Y GLY 5.2 0.2 - - - +
153Y LEU* 3.7 13.5 - - + +
208Y TYR* 3.3 29.4 - - + +
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Residues in contact with ILE 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105Y ILE* 4.9 0.2 - - + -
111Y LEU* 2.8 39.6 + - + +
112Y LYS* 3.1 10.5 + - - +
114Y ALA* 1.3 78.8 - - - +
116Y GLU* 1.3 57.2 + - - +
118Y ARG 3.4 0.2 + - - -
119Y TRP* 2.9 39.3 + - + +
121Y SER 4.6 0.2 - - - +
122Y PHE* 4.3 19.7 - - + -
125Y PHE* 3.5 39.7 - - + -
144Y LEU* 4.0 14.4 - - + -
153Y LEU* 3.5 19.3 - - + -
201Y TRP* 4.1 15.5 - - + -
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Residues in contact with GLU 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y LYS* 2.8 47.4 + - + +
113Y ALA* 3.1 17.6 + - - +
115Y ILE* 1.3 77.7 - - - +
117Y GLN* 1.3 55.7 + - - +
120Y GLY* 2.6 46.8 + - - +
121Y SER* 4.0 4.8 - - - +
122Y PHE* 4.2 18.3 + - - +
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Residues in contact with GLN 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Y ALA 3.0 15.4 + - - +
114Y ALA* 3.7 8.3 - - - +
116Y GLU* 1.3 77.0 - - - +
118Y ARG* 1.3 61.9 + - - +
120Y GLY* 4.4 1.6 + - - -
152Y LYS* 4.4 17.6 - - - +
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Residues in contact with ARG 118 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 4.0 14.8 + - - +
152A LYS* 3.0 50.2 - - - +
114Y ALA 3.1 17.1 + - - +
117Y GLN* 1.3 79.8 - - - +
119Y TRP* 1.3 103.9 + - + +
120Y GLY 3.6 0.2 - - - -
152Y LYS* 6.0 4.7 - - - +
153Y LEU* 3.4 19.8 + - + +
154Y ASP* 3.1 11.7 + - - +
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Residues in contact with TRP 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Y ILE* 2.9 30.1 + - + +
118Y ARG* 1.3 114.3 - - + +
120Y GLY* 1.3 56.8 + - - +
121Y SER 3.2 4.3 + - - +
124Y LYS* 3.2 26.7 - - - +
125Y PHE* 3.5 45.1 - + + +
128Y ALA* 4.3 16.7 - - + +
144Y LEU* 3.5 24.0 - - + -
153Y LEU* 3.8 31.4 - - + -
154Y ASP* 4.6 2.5 - - - -
155Y ILE* 3.6 31.8 - - + +
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Residues in contact with GLY 120 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Y GLU* 2.6 33.9 + - - +
117Y GLN 4.3 1.6 + - - -
118Y ARG 3.6 1.2 - - - -
119Y TRP* 1.3 72.0 - - - +
121Y SER* 1.3 59.5 + - - +
124Y LYS* 4.3 7.6 - - - -
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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