Contacts of the helix formed by residues 175 - 185 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D GLU 4.4 6.1 - - - +
174D MET* 1.3 75.7 - - - +
176D GLU* 1.3 58.8 + - - +
177D ALA* 3.4 9.8 + - - +
178D GLU* 3.0 41.5 + - - +
179D GLN* 2.8 29.5 + - - +
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D THR* 1.3 74.9 - - - +
177D ALA* 1.3 62.6 + - - +
179D GLN* 3.7 16.2 - - - +
180D GLN* 3.0 25.1 + - - +
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D THR* 3.4 8.7 + - - +
176D GLU* 1.3 78.9 - - - +
178D GLU* 1.3 64.9 + - + +
180D GLN* 3.1 8.1 + - - +
181D GLN* 3.0 22.2 + - - +
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D ARG* 2.7 32.4 + - - -
169D TYR* 4.1 19.9 - - + +
173D GLU 4.2 2.3 - - - +
174D MET* 3.7 17.9 - - + +
175D THR* 3.0 42.6 + - - +
177D ALA* 1.3 73.2 - - + +
179D GLN* 1.3 66.5 + - - +
181D GLN* 3.2 8.4 + - - +
182D LEU* 3.0 27.8 + - - +
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Residues in contact with GLN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D MET* 3.7 35.6 + - + +
175D THR 2.8 16.5 + - - +
176D GLU* 3.7 19.9 - - - +
178D GLU* 1.3 76.6 - - - +
180D GLN* 1.3 63.4 + - - +
182D LEU* 3.4 3.6 + - - +
183D ILE* 3.1 39.5 + - + +
188D LEU* 4.1 12.7 - - + +
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Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLU 3.0 18.5 + - - +
177D ALA* 3.1 7.2 + - - +
179D GLN* 1.3 74.9 - - - +
181D GLN* 1.3 66.9 + - - +
183D ILE* 3.2 21.1 + - - +
184D ASP* 3.1 42.9 + - - +
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Residues in contact with GLN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D TYR* 6.0 2.2 - - - +
177D ALA 3.0 12.7 + - - +
178D GLU* 3.2 11.6 + - - +
180D GLN* 1.3 76.1 - - - +
182D LEU* 1.3 64.2 + - + +
184D ASP* 3.1 15.8 + - - +
185D ASP* 3.0 54.7 + - - +
218D LYS* 3.4 16.1 - - - +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D TYR* 4.2 30.1 - - + +
174D MET* 3.5 31.9 - - - -
178D GLU 3.0 15.7 + - - +
179D GLN 3.7 4.3 - - - +
181D GLN* 1.3 78.1 - - + +
183D ILE* 1.3 62.0 + - - +
185D ASP* 3.5 4.9 + - - +
186D HIS 3.1 3.3 + - - -
187D PHE* 2.9 49.0 + - + +
188D LEU* 3.4 16.2 + - + +
212D ILE* 4.2 18.6 - - + -
214D HIS* 4.1 25.6 - - + +
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Residues in contact with ILE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D GLN* 3.1 30.0 + - + +
180D GLN* 3.2 25.1 + - - +
182D LEU* 1.3 76.1 - - - +
184D ASP* 1.3 64.8 + - - +
186D HIS* 3.2 24.5 + - - +
188D LEU* 3.4 28.9 - - + -
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLN* 3.1 37.4 + - - +
181D GLN* 3.1 19.0 + - - +
183D ILE* 1.3 80.8 - - - +
185D ASP* 1.3 61.3 + - - +
186D HIS* 3.4 16.0 + - - -
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Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLN* 3.0 35.8 + - - +
182D LEU* 4.0 5.3 - - - +
183D ILE 3.3 0.2 - - - -
184D ASP* 1.3 75.2 - - - +
186D HIS* 1.3 73.5 + - - +
187D PHE* 3.4 37.4 - - + -
214D HIS* 5.3 1.6 + - - -
218D LYS* 2.9 44.1 + - - +
235D MET* 6.0 0.5 - - - +
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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