Contacts of the helix formed by residues 175 - 185 (chain B) in PDB entry 1QK1
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 THR 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B GLU 4.3 5.6 - - - +
174B MET* 1.3 74.7 - - - +
176B GLU* 1.3 59.8 + - - +
177B ALA* 3.4 9.7 + - - +
178B GLU* 3.0 43.1 + - - +
179B GLN* 2.8 29.5 + - - +
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Residues in contact with GLU 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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175B THR* 1.3 75.1 - - - +
177B ALA* 1.3 61.8 + - - +
179B GLN* 3.6 17.2 - - - +
180B GLN* 3.0 24.4 + - - +
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Residues in contact with ALA 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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175B THR* 3.1 9.5 + - - +
176B GLU* 1.3 78.7 - - - +
178B GLU* 1.3 63.0 + - + +
180B GLN* 3.1 7.4 + - - +
181B GLN* 3.0 22.5 + - - +
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Residues in contact with GLU 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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167B ARG* 2.7 31.8 + - - -
169B TYR* 4.1 19.7 - - + -
173B GLU 4.1 2.6 - - - +
174B MET* 3.6 18.5 - - + +
175B THR* 3.0 42.7 + - - +
177B ALA* 1.3 76.3 - - + +
179B GLN* 1.3 63.4 + - - +
181B GLN* 3.2 8.0 + - - +
182B LEU* 3.0 28.4 + - - +
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Residues in contact with GLN 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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174B MET* 3.7 36.2 + - + +
175B THR 2.8 16.3 + - - +
176B GLU* 3.6 20.4 - - - +
178B GLU* 1.3 78.6 - - - +
180B GLN* 1.3 61.6 + - - +
182B LEU* 3.7 3.4 + - - +
183B ILE* 3.0 45.3 + - + +
188B LEU* 4.1 8.4 - - + +
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Residues in contact with GLN 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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176B GLU 3.0 17.1 + - - +
177B ALA* 3.5 6.5 - - - +
179B GLN* 1.3 76.2 - - - +
181B GLN* 1.3 67.6 + - - +
183B ILE* 3.1 21.9 + - - +
184B ASP* 3.0 49.8 + - - +
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Residues in contact with GLN 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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169B TYR* 6.0 1.6 - - - +
177B ALA 3.0 12.6 + - - +
178B GLU* 3.5 11.7 - - - +
180B GLN* 1.3 76.9 - - - +
182B LEU* 1.3 59.4 + - + +
184B ASP* 3.1 15.9 + - - +
185B ASP* 2.9 60.7 + - - +
218B LYS* 3.4 15.4 - - - +
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Residues in contact with LEU 182 (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 TYR* 4.2 29.6 - - + -
174B MET* 3.6 31.0 - - - -
178B GLU 3.0 16.0 + - - +
179B GLN 4.0 4.3 - - - +
180B GLN 3.3 0.2 - - - -
181B GLN* 1.3 75.3 - - + +
183B ILE* 1.3 63.0 + - - +
185B ASP* 3.5 5.3 + - - +
186B HIS 3.1 2.9 + - - -
187B PHE* 2.9 48.2 + - + +
188B LEU* 3.4 16.1 + - + +
212B ILE* 4.2 18.6 - - + -
214B HIS* 4.1 25.1 - - + +
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Residues in contact with ILE 183 (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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179B GLN* 3.0 29.6 + - + +
180B GLN* 3.1 27.6 + - - +
182B LEU* 1.3 75.4 - - - +
184B ASP* 1.3 65.4 + - - +
186B HIS* 3.1 24.5 + - - +
188B LEU* 3.4 28.9 - - + -
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Residues in contact with ASP 184 (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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180B GLN* 3.0 41.6 + - - +
181B GLN* 3.1 19.5 + - - +
183B ILE* 1.3 80.1 - - - +
185B ASP* 1.3 61.2 + - - +
186B HIS* 3.2 16.2 + - - -
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Residues in contact with ASP 185 (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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181B GLN* 2.9 41.1 + - - +
182B LEU* 4.0 5.5 - - - +
183B ILE 3.3 0.4 - - - -
184B ASP* 1.3 75.4 - - - +
186B HIS* 1.3 73.2 + - - +
187B PHE* 3.4 37.8 - - + -
214B HIS* 5.3 1.2 + - - -
218B LYS* 2.9 36.2 + - - +
235B MET* 6.0 0.3 - - - +
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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