Contacts of the helix formed by residues 108 - 120 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105X ILE* 2.9 13.9 + - + +
106X ASP 3.0 0.6 - - - -
107X GLN* 1.3 82.1 - - - +
109X PRO* 1.3 58.9 - - - +
110X VAL 3.5 0.2 + - - -
111X LEU* 4.1 12.1 - - + -
112X LYS* 2.9 30.0 + - - +
201X TRP* 3.4 29.8 - - + +
205X GLU* 3.4 21.3 - - + +
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Residues in contact with PRO 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X ASP* 3.8 13.9 - - - +
107X GLN 3.3 9.0 - - - +
108X ALA* 1.3 88.4 - - - +
110X VAL* 1.3 60.7 + - + +
112X LYS* 3.8 5.1 - - + +
113X ALA* 2.9 30.5 + - - +
205X GLU* 3.1 11.4 - - + +
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Residues in contact with VAL 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X PRO* 1.3 71.5 - - + +
111X LEU* 1.3 65.0 + - - +
113X ALA* 3.3 7.5 + - - +
114X ALA* 3.1 21.0 + - - +
150X LYS* 4.3 22.7 - - + -
205X GLU* 2.9 23.6 + - - +
208X TYR* 3.7 21.8 - - + -
209X ILE* 4.3 14.1 - - + -
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Residues in contact with LEU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ILE* 5.6 0.2 - - + -
108X ALA* 4.0 4.5 - - + +
110X VAL* 1.3 72.8 - - - +
112X LYS* 1.3 57.7 + - - +
114X ALA* 3.1 4.7 + - - +
115X ILE* 2.8 38.3 + - + +
144X LEU* 4.3 4.9 - - + -
153X LEU* 3.9 24.0 - - + -
170X VAL* 3.6 15.3 - - + -
201X TRP* 3.8 19.3 - - + -
204X ALA* 3.5 36.1 - - + -
205X GLU* 2.8 23.5 + - - +
208X TYR* 3.6 34.5 - - + -
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Residues in contact with LYS 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ILE* 3.7 37.3 - - + +
106X ASP* 2.7 36.3 + - - +
108X ALA* 2.9 21.2 + - - +
109X PRO* 3.8 4.3 - - + +
111X LEU* 1.3 76.1 - - - +
113X ALA* 1.3 65.8 + - - +
115X ILE* 3.1 9.6 + - + +
116X GLU* 2.9 56.4 + - + +
122X PHE* 4.0 20.1 - - + -
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Residues in contact with ALA 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X PRO 2.9 18.8 + - - +
110X VAL* 3.3 6.7 + - - +
112X LYS* 1.3 75.0 - - - +
114X ALA* 1.3 62.9 + - - +
116X GLU* 3.4 14.0 + - - +
117X GLN* 3.0 25.6 + - - +
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Residues in contact with ALA 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X VAL 3.1 12.3 + - - +
111X LEU 3.4 9.2 - - - +
113X ALA* 1.3 78.5 - - - +
115X ILE* 1.3 60.4 + - - +
117X GLN* 3.5 10.2 + - - +
118X ARG* 3.1 23.7 + - - +
151X GLY 5.1 0.2 - - - +
153X LEU* 3.6 14.3 - - + +
208X TYR* 3.3 29.2 - - + +
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Residues in contact with ILE 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ILE* 4.9 0.9 - - + -
111X LEU* 2.8 35.3 + - + +
112X LYS* 3.1 10.1 + - - +
114X ALA* 1.3 73.4 - - - +
116X GLU* 1.3 61.9 + - + +
118X ARG 3.0 1.2 + - - -
119X TRP* 2.8 39.1 + - + +
121X SER 4.4 0.2 - - - +
122X PHE* 4.3 19.1 - - + -
125X PHE* 3.3 44.6 - - + -
144X LEU* 4.1 16.4 - - + -
153X LEU* 3.5 19.1 - - + -
201X TRP* 4.3 12.8 - - + -
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Residues in contact with GLU 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X LYS* 2.9 52.3 + - + +
113X ALA* 3.8 12.1 + - - +
115X ILE* 1.3 75.4 - - + +
117X GLN* 1.3 58.9 + - - +
120X GLY* 2.7 47.0 + - - +
121X SER* 4.1 4.4 - - - +
122X PHE* 4.2 16.4 + - - +
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Residues in contact with GLN 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X ALA 3.0 18.2 + - - +
114X ALA* 3.7 9.6 - - - +
116X GLU* 1.3 78.5 - - - +
118X ARG* 1.3 67.4 + - - +
120X GLY* 4.6 1.0 + - - -
152X LYS* 5.0 10.0 + - - +
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Residues in contact with ARG 118 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASP* 3.4 20.4 + - - +
152B LYS* 3.1 37.7 - - - +
114X ALA 3.1 14.0 + - - +
115X ILE 3.0 1.4 + - - -
117X GLN* 1.3 87.4 - - - +
119X TRP* 1.3 102.8 + - + +
120X GLY 3.5 0.4 - - - -
152X LYS* 6.3 2.7 - - - -
153X LEU* 3.3 17.8 + - + +
154X ASP* 3.1 20.2 + - - +
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Residues in contact with TRP 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X ILE* 2.8 29.9 + - + +
118X ARG* 1.3 114.0 - - + +
120X GLY* 1.3 56.6 + - - +
121X SER 3.1 18.7 + - - +
124X LYS* 3.4 23.0 - - + +
125X PHE* 3.6 41.5 - + - +
128X ALA* 4.1 26.3 - - + +
144X LEU* 4.1 7.0 - - + -
153X LEU* 4.0 35.7 - - + -
154X ASP* 4.3 0.9 - - - -
155X ILE* 3.7 26.0 - - + +
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Residues in contact with GLY 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116X GLU* 2.7 30.8 + - - +
117X GLN 4.5 1.0 + - - -
118X ARG 3.5 2.0 - - - -
119X TRP* 1.3 72.0 - - - +
121X SER* 1.3 58.8 + - - -
124X LYS* 4.9 6.5 - - - -
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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