Contacts of the helix formed by residues 109 - 120 (chain B) in PDB entry 1K0N
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR 5.5 0.2 - - - +
107B GLY* 3.9 13.3 + - - -
108B LEU* 1.3 74.6 + - - +
110B ILE* 1.3 65.7 + - - +
111B PHE 3.4 0.8 + - - -
112B ALA* 3.4 9.5 + - + +
113B LYS* 3.2 46.6 + - - +
136B ALA* 3.7 23.5 - - - +
139B VAL* 6.0 2.4 - - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLY* 3.3 24.9 - - - +
108B LEU 3.2 1.6 - - - -
109B ASP* 1.3 78.8 - - - +
111B PHE* 1.3 66.4 + - - +
113B LYS* 3.3 3.3 + - - +
114B PHE* 3.0 20.6 + - - +
133B LEU* 3.9 16.1 - - + +
136B ALA* 3.9 24.0 - - + -
137B LEU* 3.9 20.6 - - + -
140B LEU* 3.5 37.7 - - + -
180B LEU* 5.6 0.4 - - + -
184B LEU* 3.9 21.3 - - + -
187B VAL* 4.2 12.3 - - + -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO* 4.6 11.7 - - + -
107B GLY 4.8 0.2 + - - -
108B LEU 4.2 6.3 + - - +
109B ASP 3.4 0.6 - - - -
110B ILE* 1.3 79.4 - - - +
112B ALA* 1.3 65.0 + - - +
114B PHE* 3.1 15.7 + + - +
115B SER* 2.9 34.3 + - - -
183B LYS* 3.6 62.6 - - + -
186B ILE* 3.9 26.0 - - + -
187B VAL* 4.0 6.5 - - + -
233B TYR* 3.7 21.3 - - - -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU 5.0 1.7 + - - +
109B ASP* 3.4 11.9 + - - +
110B ILE 3.3 0.6 - - - -
111B PHE* 1.3 80.0 - - - +
113B LYS* 1.3 66.7 + - + +
115B SER* 3.1 9.7 + - - -
116B ALA* 3.1 21.7 + - - +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 3.2 42.9 + - - +
110B ILE 3.8 5.8 - - - +
112B ALA* 1.3 80.3 - - + +
114B PHE* 1.3 62.7 - - - +
116B ALA* 3.3 7.2 + - + +
117B TYR* 3.0 24.7 + - - +
129B LEU* 4.6 3.1 - - - +
132B GLY* 4.0 25.6 - - - +
133B LEU* 3.9 23.3 - - + +
136B ALA* 4.3 4.5 - - + -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE 3.0 13.7 + - - +
111B PHE* 3.1 31.2 + + - +
113B LYS* 1.3 76.4 - - - +
115B SER* 1.3 69.4 + - - +
117B TYR* 3.3 1.5 + + - +
118B ILE* 2.9 37.8 + - + +
133B LEU* 3.9 20.4 - - + +
186B ILE* 4.3 4.9 - - + -
187B VAL* 3.9 20.4 - - + -
190B VAL* 3.7 37.9 - - + -
191B CYS* 3.6 28.3 - - - -
233B TYR* 3.6 33.0 - + - -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 2.9 26.6 + - - -
112B ALA* 3.4 12.2 - - - -
114B PHE* 1.3 89.0 - - - +
116B ALA* 1.3 60.4 + - - +
118B ILE* 3.5 5.2 - - - +
119B LYS* 3.1 50.4 + - - +
233B TYR* 5.3 2.0 + - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.1 11.4 + - - +
113B LYS* 3.7 10.1 - - + +
114B PHE 3.3 0.2 - - - -
115B SER* 1.3 77.8 - - - +
117B TYR* 1.3 62.4 + - - +
119B LYS* 3.6 4.1 + - - +
120B ASN* 3.5 16.1 + - - +
129B LEU* 3.7 29.9 - - + +
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS 3.0 17.2 + - - +
114B PHE* 3.6 6.5 - - - +
116B ALA* 1.3 80.3 - - - +
118B ILE* 1.3 64.4 + - + +
120B ASN* 3.8 6.9 + - - +
126B ASN* 3.1 30.8 + - - -
129B LEU* 3.9 20.4 - - + +
130B GLU* 3.7 38.2 + - + -
133B LEU* 3.6 20.0 - - + -
191B CYS* 4.0 23.6 - - - -
195B ARG* 3.0 59.0 + - + +
197B PHE* 3.7 17.7 - + - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE* 2.9 36.2 + - + +
115B SER* 3.5 12.8 - - - +
117B TYR* 1.3 88.7 - - + +
119B LYS* 1.3 68.5 + - + +
120B ASN 3.4 0.2 - - - -
190B VAL* 3.9 20.9 - - + +
191B CYS* 4.3 9.0 - - - -
194B TYR* 4.4 4.9 - - + -
195B ARG* 3.7 34.2 + - + +
233B TYR* 4.6 9.6 - - + -
236B VAL* 4.6 0.2 - - + -
237B ALA* 3.4 24.7 - - + -
238B LYS 2.9 26.9 + - - +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B SER* 3.1 36.4 + - - +
116B ALA* 4.5 3.8 - - - +
117B TYR 3.5 0.2 - - - -
118B ILE* 1.3 77.7 - - + +
120B ASN* 1.3 63.0 + - - +
121B SER* 3.7 1.6 + - - -
233B TYR* 6.0 0.9 - - - -
236B VAL* 3.8 38.1 - - + +
238B LYS* 3.9 16.4 - - + +
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Residues in contact with ASN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 3.5 6.1 + - - +
117B TYR 3.8 4.5 + - - +
118B ILE 3.4 0.8 - - - -
119B LYS* 1.3 79.7 - - - +
121B SER* 1.3 58.8 + - - +
122B ASN* 3.0 46.6 + - - +
125B LEU* 3.7 13.8 - - - +
126B ASN* 3.8 15.4 - - - +
129B LEU* 3.5 27.5 - - + +
195B ARG* 2.9 25.1 + - - -
238B LYS* 3.7 4.3 - - - +
240B LEU* 3.7 8.8 - - - +
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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