Contacts of the helix formed by residues 175 - 185 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173G GLU 4.3 6.5 - - - +
174G MET* 1.3 77.3 - - - +
176G GLU* 1.3 58.4 + - - +
177G ALA* 3.4 9.8 + - - +
178G GLU* 3.0 41.2 + - - +
179G GLN* 2.9 27.9 + - - +
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Residues in contact with GLU 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G THR* 1.3 74.9 - - - +
177G ALA* 1.3 61.8 + - - +
179G GLN* 3.6 17.3 - - - +
180G GLN* 3.1 24.6 + - - +
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Residues in contact with ALA 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G THR* 3.1 9.5 + - - +
176G GLU* 1.3 80.0 - - - +
178G GLU* 1.3 64.3 + - + +
180G GLN* 3.4 5.4 + - - +
181G GLN* 3.1 22.6 + - - +
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Residues in contact with GLU 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ARG* 2.7 32.9 + - - -
169G TYR* 4.1 20.0 - - + -
173G GLU 4.2 2.3 - - - +
174G MET* 3.6 17.8 - - + +
175G THR* 3.0 42.0 + - - +
177G ALA* 1.3 77.3 - - + +
179G GLN* 1.3 63.8 + - - +
181G GLN* 3.3 8.1 + - - +
182G LEU* 3.0 26.8 + - - +
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Residues in contact with GLN 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G MET* 3.8 34.4 + - + +
175G THR 2.9 14.4 + - - +
176G GLU* 3.6 24.2 - - - +
177G ALA 3.3 0.2 - - - -
178G GLU* 1.3 76.0 - - - +
180G GLN* 1.3 58.2 + - - +
182G LEU* 3.1 6.9 + - - +
183G ILE* 2.9 42.6 + - + +
188G LEU* 4.0 13.9 - - + +
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Residues in contact with GLN 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G GLU 3.1 14.9 + - - +
177G ALA* 3.6 6.1 - - - +
179G GLN* 1.3 76.3 - - - +
181G GLN* 1.3 67.7 + - - +
183G ILE* 3.1 24.4 + - - +
184G ASP* 2.9 45.1 + - - +
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Residues in contact with GLN 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G TYR* 6.0 2.0 - - - +
177G ALA 3.1 13.4 + - - +
178G GLU* 3.3 11.4 + - - +
180G GLN* 1.3 75.1 - - - +
182G LEU* 1.3 59.7 + - + +
184G ASP* 3.2 15.1 + - - +
185G ASP* 3.0 60.4 + - - +
218G LYS* 3.4 17.1 - - - +
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Residues in contact with LEU 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169G TYR* 4.2 31.4 - - + +
174G MET* 3.5 30.5 - - - -
178G GLU 3.0 15.9 + - - +
179G GLN 3.1 6.3 + - - +
181G GLN* 1.3 75.8 - - + +
183G ILE* 1.3 62.9 + - - +
185G ASP* 3.5 5.6 + - - +
186G HIS 3.1 3.1 + - - -
187G PHE* 2.9 47.9 + - + -
188G LEU* 3.4 15.4 + - + +
212G ILE* 4.2 19.3 - - + -
214G HIS* 4.1 24.7 - - + +
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Residues in contact with ILE 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G GLN* 2.9 34.0 + - + +
180G GLN* 3.5 27.1 - - - +
182G LEU* 1.3 77.8 - - - +
184G ASP* 1.3 64.7 + - - +
186G HIS* 3.1 24.4 + - - +
188G LEU* 3.4 29.4 - - + -
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Residues in contact with ASP 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G GLN* 2.9 39.6 + - - +
181G GLN* 3.5 19.5 - - - +
183G ILE* 1.3 80.5 - - - +
185G ASP* 1.3 60.1 + - - +
186G HIS* 3.4 15.7 + - - -
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Residues in contact with ASP 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G GLN* 3.0 33.3 + - - +
182G LEU* 3.5 5.8 + - - +
183G ILE 3.3 0.2 - - - -
184G ASP* 1.3 76.2 - - - +
186G HIS* 1.3 72.3 + - - +
187G PHE* 3.3 39.1 - - + -
214G HIS* 5.2 1.2 + - - -
218G LYS* 2.9 44.5 + - - +
235G 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