Contacts of the helix formed by residues 108 - 120 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ILE* 3.0 15.3 + - + +
106A ASP 2.9 0.8 - - - -
107A GLN* 1.3 81.2 - - - +
109A PRO* 1.3 55.3 - - - +
111A LEU* 4.2 11.0 - - + -
112A LYS* 2.8 34.2 + - - +
201A TRP* 3.4 29.4 - - + +
205A GLU* 3.4 23.3 - - + +
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Residues in contact with PRO 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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106A ASP* 3.6 14.8 - - - +
107A GLN* 3.4 8.3 - - - +
108A ALA* 1.3 88.2 - - - +
110A VAL* 1.3 59.9 + - + +
112A LYS* 3.9 5.1 - - + +
113A ALA* 3.0 30.7 + - - +
205A GLU* 3.2 12.6 - - + +
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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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109A PRO* 1.3 76.0 - - + +
111A LEU* 1.3 62.2 + - - +
113A ALA* 3.3 6.1 + - - +
114A ALA* 3.1 21.3 + - - +
150A LYS* 4.0 29.6 - - + +
205A GLU* 2.7 24.2 + - - +
208A TYR* 3.9 19.5 - - + -
209A ILE* 4.3 14.6 - - + -
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Residues in contact with LEU 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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105A ILE* 5.8 0.2 - - + -
108A ALA* 4.0 4.7 - - + +
110A VAL* 1.3 73.9 - - - +
112A LYS* 1.3 60.0 + - - +
114A ALA* 3.1 1.7 + - - +
115A ILE* 2.8 45.5 + - + +
144A LEU* 4.3 2.0 - - + -
153A LEU* 3.8 28.3 - - + -
170A VAL* 3.4 28.7 - - + -
201A TRP* 3.9 18.4 - - + -
204A ALA* 3.5 24.5 - - + +
205A GLU* 2.8 22.0 + - - +
208A TYR* 3.7 28.3 - - + -
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Residues in contact with LYS 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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105A ILE* 3.6 39.9 - - + +
106A ASP* 2.8 34.8 + - - +
108A ALA* 2.8 24.1 + - - +
109A PRO* 3.9 5.4 - - + +
111A LEU* 1.3 74.7 - - - +
113A ALA* 1.3 57.1 + - - +
115A ILE* 3.2 10.0 + - - +
116A GLU* 3.0 59.8 + - + +
122A PHE* 4.2 17.3 - - + -
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Residues in contact with ALA 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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109A PRO 3.0 19.4 + - - +
110A VAL* 3.7 5.8 - - - +
112A LYS* 1.3 76.1 - - - +
114A ALA* 1.3 61.6 + - - +
116A GLU* 3.5 13.4 + - - +
117A GLN* 3.2 23.9 + - - +
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Residues in contact with ALA 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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110A VAL 3.1 11.6 + - - +
111A LEU 3.1 8.4 + - - +
113A ALA* 1.3 75.3 - - - +
115A ILE* 1.3 65.0 + - - +
117A GLN* 3.4 8.8 + - - +
118A ARG* 3.2 23.2 + - - +
151A GLY 5.2 0.2 - - - +
153A LEU* 3.7 15.3 - - + +
208A TYR* 3.2 28.0 - - + +
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Residues in contact with ILE 115 (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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105A ILE* 4.9 0.9 - - + -
111A LEU* 2.8 39.6 + - + +
112A LYS* 3.5 9.6 - - - +
114A ALA* 1.3 78.3 - - - +
116A GLU* 1.3 56.7 + - - +
118A ARG 3.2 0.9 + - - -
119A TRP* 2.9 37.3 + - + +
121A SER 4.3 0.4 - - - +
122A PHE* 4.2 20.0 - - + -
125A PHE* 3.3 41.7 - - + -
144A LEU* 4.1 17.5 - - + -
153A LEU* 3.7 17.9 - - + -
201A TRP* 4.3 13.5 - - + -
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Residues in contact with GLU 116 (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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112A LYS* 3.0 45.9 + - + +
113A ALA* 3.9 12.4 - - - +
115A ILE* 1.3 75.9 - - + +
117A GLN* 1.3 57.6 + - - +
120A GLY* 2.7 47.2 + - - +
121A SER* 3.9 4.0 - - - +
122A PHE* 3.8 21.7 + - - +
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Residues in contact with GLN 117 (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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113A ALA 3.2 17.3 + - - +
114A ALA* 3.7 8.2 - - - +
115A ILE 3.2 0.4 - - - -
116A GLU* 1.3 78.3 - - - +
118A ARG* 1.3 61.2 + - - +
120A GLY* 4.4 1.7 + - - -
152Y LYS* 5.2 10.5 - - - +
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Residues in contact with ARG 118 (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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114A ALA 3.2 14.7 + - - +
117A GLN* 1.3 80.8 - - - +
119A TRP* 1.3 105.0 + - + +
152A LYS* 5.6 6.2 - - - +
153A LEU* 3.2 20.7 + - + +
154A ASP* 2.9 28.9 + - - +
155A ILE 5.7 0.2 - - - +
147Y ASP* 4.1 24.9 + - - +
152Y LYS* 4.9 17.8 - - - +
154Y ASP* 5.5 2.0 + - - -
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Residues in contact with TRP 119 (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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115A ILE* 2.9 24.3 + - + +
118A ARG* 1.3 122.5 - - + +
120A GLY* 1.3 57.2 + - - +
121A SER 3.2 7.6 + - - +
124A LYS* 3.3 23.6 - - + +
125A PHE* 3.8 39.0 - + + +
128A ALA* 4.1 26.4 - - + +
144A LEU* 4.0 13.9 - - + -
153A LEU* 3.9 31.0 - - + -
155A ILE* 3.5 38.2 - - + +
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Residues in contact with GLY 120 (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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116A GLU* 2.7 32.3 + - - +
117A GLN 4.3 1.5 + - - -
118A ARG 3.5 2.2 - - - -
119A TRP* 1.3 71.2 - - - +
121A SER* 1.3 60.1 + - - +
124A LYS* 4.6 7.9 - - - -
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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