Contacts of the helix formed by residues 166 - 175 (chain A) in PDB entry 1K86
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 PHE 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.6 47.1 - - + -
126A ALA* 4.2 3.4 - - + -
127A SER* 3.7 21.5 - - - -
137A PHE* 3.5 45.3 - + - -
162A LEU 3.8 6.5 - - - -
163A THR 3.7 8.7 - - - +
164A ALA 3.0 0.6 - - - -
165A HIS* 1.3 81.2 - - + +
167A ARG* 1.3 68.1 + - - +
168A GLY 3.1 12.9 + - - +
171A CYS* 3.9 11.4 - - + +
174A LEU* 3.9 22.6 - - + +
179A LYS* 3.7 16.7 + - + +
181A PHE* 4.3 7.9 - + - -
219A PHE* 3.6 23.4 - - + -
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Residues in contact with ARG 167 (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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160A LYS* 3.5 16.2 + - - +
163A THR 3.4 3.8 + - - -
164A ALA* 2.8 29.1 + - + +
166A PHE* 1.3 74.3 - - - +
168A GLY* 1.3 64.3 + - - +
169A ALA 3.5 0.2 + - - -
170A ARG* 3.1 22.5 + - + +
213A ILE* 2.9 30.8 - - - +
214A PRO* 3.3 28.5 - - - +
215A VAL* 3.3 40.8 - - - +
216A GLU* 3.2 16.2 - - + +
219A PHE* 3.7 3.5 - - - -
229B TYR* 4.8 1.6 + - - +
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Residues in contact with GLY 168 (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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166A PHE 3.1 12.5 + - - +
167A ARG* 1.3 69.8 - - - +
169A ALA* 1.3 57.6 + - - -
170A ARG 3.1 5.4 + - - -
171A CYS 3.6 8.3 + - - +
175A LEU* 3.6 17.8 - - - +
179A LYS* 5.3 4.0 + - - +
216A GLU* 3.1 38.4 + - - +
219A PHE* 4.6 1.6 - - - -
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Residues in contact with ALA 169 (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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167A ARG 3.5 0.4 + - - -
168A GLY* 1.3 68.9 - - - -
170A ARG* 1.3 56.1 + - - +
171A CYS 2.9 8.9 + - - +
172A LYS* 3.5 40.6 + - + +
175A LEU* 3.7 15.5 - - + +
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Residues in contact with ARG 170 (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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124A LYS* 4.8 6.5 - - - +
127A SER* 4.6 4.2 + - - +
164A ALA* 3.6 33.9 + - - +
165A HIS* 3.1 49.0 + - - +
167A ARG* 3.1 17.0 + - - +
168A GLY 3.0 2.0 - - - -
169A ALA* 1.3 78.0 - - - +
171A CYS* 1.3 59.1 + - - +
172A LYS 4.0 0.2 - - - -
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Residues in contact with CYS 171 (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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127A SER* 3.1 31.4 - - - +
131A HIS* 4.1 9.0 - - - -
165A HIS 3.7 12.3 - - - +
166A PHE* 3.9 16.8 - - + +
168A GLY 3.6 6.5 + - - +
170A ARG* 1.3 82.8 - - - +
172A LYS* 1.3 65.7 + - - +
173A THR* 3.2 8.1 - - - -
174A LEU* 2.9 48.7 + - + +
175A LEU 3.6 2.9 + - - -
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Residues in contact with LYS 172 (chain A).
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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169A ALA* 3.5 36.5 + - + +
170A ARG 4.0 0.2 - - - -
171A CYS* 1.3 74.6 - - - +
173A THR* 1.3 60.3 + - + +
175A LEU* 3.0 35.1 + - + +
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Residues in contact with THR 173 (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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127A SER 5.2 1.3 - - - +
128A GLU 5.6 1.6 - - - +
129A GLU 3.9 17.0 - - - +
130A ASP* 3.8 13.2 - - - +
131A HIS* 2.5 39.6 + - + +
132A THR* 4.1 6.4 + - - +
171A CYS* 4.4 10.3 - - - -
172A LYS* 1.3 74.3 - - + +
174A LEU* 1.3 56.3 + - - +
175A LEU 3.5 0.6 - - - +
177A LYS* 3.2 24.4 + - - -
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Residues in contact with LEU 174 (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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131A HIS* 3.5 43.1 - - + +
134A ALA* 5.0 0.4 - - + -
136A CYS 4.1 23.1 - - - +
137A PHE* 3.6 24.0 - - + -
166A PHE* 3.9 23.1 - - + -
171A CYS* 2.9 15.8 + - + +
173A THR* 1.3 76.6 - - - +
175A LEU* 1.3 65.3 + - - +
176A GLU 3.5 0.2 + - - -
177A LYS* 3.1 46.0 + - + +
178A PRO 5.2 1.1 - - - +
179A LYS* 3.5 18.4 + - + +
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Residues in contact with LEU 175 (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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168A GLY* 3.6 28.5 - - - +
169A ALA* 3.7 22.4 - - + +
171A CYS 3.6 2.4 + - - -
172A LYS* 3.0 22.4 + - + +
173A THR 3.5 0.5 - - - +
174A LEU* 1.3 78.2 - - - +
176A GLU* 1.3 90.0 + - + +
177A LYS* 3.0 10.8 + - - +
179A LYS* 4.7 4.7 - - - +
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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