Contacts of the helix formed by residues 170 - 181 (chain C) in PDB entry 1KQN
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 LYS 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C GLU* 4.7 18.3 + - + +
97C LYS* 5.5 6.1 - - - +
169C TRP* 1.3 73.4 - - - +
171C SER* 1.3 66.8 + - - +
172C GLU* 3.6 24.2 + - - +
173C ASP* 2.9 55.6 + - - +
174C ILE* 3.2 6.2 + - - +
273C ASN* 3.4 28.8 - - + +
779C NAD 4.7 0.8 + - - -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C TRP 3.4 4.2 + - - -
170C LYS* 1.3 70.5 - - - +
172C GLU* 1.3 77.6 + - - +
174C ILE* 3.2 15.1 + - - +
175C THR* 3.0 25.3 + - - -
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LYS* 3.6 30.5 + - - +
171C SER* 1.3 91.7 + - - +
173C ASP* 1.3 57.4 + - - +
175C THR* 3.3 8.0 + - - -
176C GLN* 2.8 48.9 + - - +
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU* 3.7 24.1 - - - +
96C LEU* 2.9 35.7 - - + +
169C TRP* 5.1 6.3 - - + -
170C LYS* 2.9 51.0 + - + +
172C GLU* 1.3 77.9 - - - +
174C ILE* 1.3 57.1 + - - +
176C GLN* 3.1 4.3 + - - +
177C ILE* 2.7 45.8 + - + +
779C NAD 4.4 3.8 + - - +
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PHE* 3.7 63.9 - - + +
169C TRP* 3.8 24.0 - - + +
170C LYS 3.2 5.4 + - - +
171C SER* 3.2 15.0 + - - +
173C ASP* 1.3 77.3 - - - +
175C THR* 1.3 67.9 + - - +
177C ILE* 3.2 8.7 + - - +
178C VAL* 3.1 22.9 + - + +
202C VAL* 5.0 11.7 - - + -
203C LEU* 4.1 17.3 - - + -
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Residues in contact with THR 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C SER* 3.0 15.8 + - - -
172C GLU* 3.5 10.5 - - - -
173C ASP 3.2 0.2 - - - -
174C ILE* 1.3 77.1 - - - +
176C GLN* 1.3 60.8 + - + +
178C VAL* 3.6 2.0 - - - +
179C ALA* 2.8 37.5 + - + +
202C VAL* 3.7 33.9 - - + +
206C HIS* 4.5 10.3 - - + +
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Residues in contact with GLN 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 3.8 24.6 - - + +
100C ARG* 3.3 21.9 + - - +
172C GLU* 2.8 41.1 + - + +
173C ASP* 3.1 3.9 + - - +
175C THR* 1.3 72.7 - - + +
177C ILE* 1.3 61.0 - - - +
179C ALA* 4.4 0.9 - - - -
180C ASN* 2.7 55.1 + - - +
181C TYR* 3.6 2.9 + - + -
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C THR* 4.9 2.7 - - + -
96C LEU* 4.3 23.1 - - + +
99C LEU* 3.9 24.9 - - + -
153C LEU* 4.7 2.0 - - + -
163C PHE* 4.7 7.2 - - + -
169C TRP* 3.7 33.7 - - + -
173C ASP* 2.7 29.4 + - + +
174C ILE* 3.2 7.2 + - - +
176C GLN* 1.3 72.1 - - - +
178C VAL* 1.3 61.9 + - + +
181C TYR* 3.0 15.6 + - - +
182C GLY 2.8 25.3 + - - +
183C LEU* 3.4 32.8 - - + -
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PHE* 4.6 3.6 - - + -
174C ILE 3.1 12.4 + - - +
175C THR* 3.6 11.2 - - - +
177C ILE* 1.3 78.1 - - + +
179C ALA* 1.3 66.5 + - - +
182C GLY* 4.3 6.5 + - - +
183C LEU* 4.2 18.6 - - + -
202C VAL* 4.4 7.0 - - + +
203C LEU* 4.1 16.8 - - + -
206C HIS* 3.8 27.4 - - + +
209C ASN* 3.2 28.1 - - - +
210C ILE* 3.9 32.3 - - + -
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C THR* 2.8 26.3 + - + +
176C GLN* 4.4 0.4 - - - -
178C VAL* 1.3 81.4 - - - +
180C ASN* 1.3 74.7 + - - +
206C HIS* 3.6 32.0 + - + +
209C ASN* 3.6 11.3 - - - +
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Residues in contact with ASN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C GLN* 2.7 48.2 + - - +
179C ALA* 1.3 86.6 - - - +
181C TYR* 1.3 75.8 + - + +
209C ASN* 6.1 0.2 - - - -
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Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 3.8 21.3 - - + -
99C LEU* 3.9 31.6 - - + -
100C ARG* 3.3 37.0 + - - +
103C GLN* 3.7 34.7 - - + +
150C LYS* 5.7 0.3 - - - +
151C VAL* 3.7 20.5 - - + +
152C LYS* 2.7 40.1 + - - +
176C GLN* 3.7 9.6 - - + -
177C ILE* 3.0 15.2 + - - +
179C ALA 3.6 0.4 - - - -
180C ASN* 1.3 95.7 - - + +
182C GLY* 1.3 60.2 + - - +
209C ASN* 4.4 4.3 - - - -
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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