Contacts of the helix formed by residues 170 - 181 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLU* 4.6 18.9 + - + +
97B LYS* 5.1 7.7 - - - +
169B TRP* 1.3 71.9 - - - +
171B SER* 1.3 60.2 + - - +
172B GLU* 3.8 22.9 - - - +
173B ASP* 2.9 66.0 + - - +
174B ILE* 3.3 6.4 + - - +
272B ARG* 6.6 0.2 - - - -
273B ASN* 3.3 28.4 - - + +
778B NAD 4.8 1.0 + - - +
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Residues in contact with SER 171 (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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169B TRP 3.4 5.1 + - - -
170B LYS* 1.3 71.4 - - - +
172B GLU* 1.3 72.9 + - - +
174B ILE* 3.6 14.2 + - - +
175B THR* 3.0 26.0 + - - -
202B VAL* 5.8 1.0 - - - +
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Residues in contact with GLU 172 (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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170B LYS* 3.8 25.6 - - - +
171B SER* 1.3 92.5 + - - +
173B ASP* 1.3 59.5 + - - +
175B THR* 3.4 6.6 + - - -
176B GLN* 2.9 46.8 + - - +
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Residues in contact with ASP 173 (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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94B GLU* 3.5 25.1 - - - +
96B LEU* 3.8 28.9 - - + +
169B TRP* 5.1 7.2 - - + -
170B LYS* 2.9 50.6 + - + +
172B GLU* 1.3 80.6 - - - +
174B ILE* 1.3 52.0 + - - +
176B GLN* 3.1 4.3 + - - +
177B ILE* 2.7 46.4 + - + +
778B NAD 4.4 6.6 + - - +
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Residues in contact with ILE 174 (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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163B PHE* 3.9 58.1 - - + +
169B TRP* 3.6 35.0 - - + +
170B LYS 3.3 7.2 + - - +
171B SER* 3.7 13.5 - - - +
172B GLU 3.3 0.2 - - - -
173B ASP* 1.3 78.9 - - - +
175B THR* 1.3 64.1 + - - +
177B ILE* 3.2 7.8 + - - +
178B VAL* 3.0 27.6 + - + +
202B VAL* 4.8 14.6 - - + -
203B LEU* 4.3 13.2 - - + -
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Residues in contact with THR 175 (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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171B SER 3.0 14.6 + - - -
172B GLU* 3.8 9.6 - - - -
173B ASP 3.3 0.6 - - - -
174B ILE* 1.3 78.6 - - - +
176B GLN* 1.3 60.5 + - + +
178B VAL* 3.5 1.4 - - - +
179B ALA* 2.9 38.1 + - + +
202B VAL* 3.3 33.3 - - + +
205B LYS* 6.3 0.2 - - - +
206B HIS* 4.3 12.1 - - - +
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Residues in contact with GLN 176 (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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96B LEU* 4.0 23.3 - - + +
100B ARG* 3.5 20.3 + - - +
172B GLU* 2.9 39.0 + - - +
173B ASP* 3.7 4.7 + - - +
175B THR* 1.3 78.5 - - + +
177B ILE* 1.3 59.0 + - - +
179B ALA* 4.7 0.4 - - - -
180B ASN* 2.7 57.9 + - - +
181B TYR* 3.7 2.9 - - - -
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Residues in contact with ILE 177 (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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95B THR* 4.6 3.8 - - + -
96B LEU* 3.9 31.2 - - + +
99B LEU* 3.8 23.8 - - + -
153B LEU* 4.3 14.6 - - + -
163B PHE* 4.9 5.8 - - + -
169B TRP* 3.8 33.0 - - + -
173B ASP* 2.7 27.1 + - + +
174B ILE* 3.2 7.4 + - - +
176B GLN* 1.3 72.3 - - - +
178B VAL* 1.3 60.6 + - + +
181B TYR* 3.0 15.8 + - - +
182B GLY 2.9 32.1 + - - +
183B LEU* 4.6 8.5 - - + -
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Residues in contact with VAL 178 (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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163B PHE* 4.7 3.4 - - + -
174B ILE 3.0 22.1 + - - +
175B THR* 3.5 9.2 - - - +
177B ILE* 1.3 77.9 - - + +
179B ALA* 1.3 60.6 + - - +
182B GLY* 4.0 6.3 + - - +
183B LEU* 3.7 25.1 - - + -
202B VAL* 4.7 4.3 - - + +
203B LEU* 3.5 31.6 - - + -
206B HIS* 3.9 30.5 - - + +
209B ASN* 2.9 32.7 - - - +
210B ILE* 3.9 10.8 - - + -
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Residues in contact with ALA 179 (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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175B THR* 2.9 23.8 + - + +
176B GLN* 4.7 0.4 - - - -
178B VAL* 1.3 81.7 - - - +
180B ASN* 1.3 70.7 + - - +
206B HIS* 3.5 34.1 - - + +
209B ASN* 3.7 7.7 - - - +
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Residues in contact with ASN 180 (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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103B GLN* 5.6 0.7 - - - +
150B LYS* 6.0 1.9 - - - +
176B GLN* 2.7 48.5 + - - +
179B ALA* 1.3 84.0 - - - +
181B TYR* 1.3 80.0 + - + +
209B ASN* 4.7 0.2 - - - -
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Residues in contact with TYR 181 (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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96B LEU* 3.6 24.5 - - + -
99B LEU* 3.7 46.2 - - + -
100B ARG* 3.4 36.2 + - + +
103B GLN* 3.7 24.8 - - + +
150B LYS* 5.6 1.7 - - - +
151B VAL* 3.5 22.9 - - + +
152B LYS* 2.9 32.0 + - - +
176B GLN 3.7 7.6 - - - -
177B ILE* 3.0 8.5 + - - +
180B ASN* 1.3 102.9 - - + +
182B GLY* 1.3 62.8 + - - +
209B ASN* 3.4 4.1 - - - +
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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