Contacts of the helix formed by residues 174 - 189 (chain F) in PDB entry 6QXT
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 SER 174 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E VAL* 4.9 11.8 - - - +
172F TYR 3.8 2.2 + - - -
173F PHE* 1.3 75.2 - - - +
175F LYS* 1.3 62.4 + - - +
176F ASP* 3.2 7.2 - - - -
177F GLU* 3.0 12.7 + - - +
178F ILE* 2.8 27.1 + - - +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE 4.0 0.2 + - - -
174F SER* 1.3 72.7 - - - +
176F ASP* 1.3 57.6 + - - +
178F ILE* 3.2 9.0 + - - +
179F TYR* 2.9 27.0 + - - +
201F GLU 4.7 13.7 - - - +
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Residues in contact with ASP 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F SER* 3.2 5.0 - - - -
175F LYS* 1.3 78.0 - - - +
177F GLU* 1.3 57.7 + - - +
179F TYR* 3.1 9.7 + - - +
180F GLN* 2.9 27.0 + - - +
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Residues in contact with GLU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F PHE* 5.1 13.5 - - + -
173F PHE* 3.9 12.1 - - + -
174F SER* 3.0 24.7 + - - +
176F ASP* 1.3 78.9 - - - +
178F ILE* 1.3 57.2 + - - +
180F GLN* 3.2 9.3 + - - +
181F ILE* 2.9 28.1 + - - +
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Residues in contact with ILE 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F LEU* 6.1 6.1 - - + +
173F PHE* 4.5 9.8 - - + +
174F SER 2.8 12.4 + - - +
175F LYS* 3.5 12.1 - - - +
177F GLU* 1.3 73.6 - - - +
179F TYR* 1.3 61.0 + - - +
181F ILE* 3.2 7.1 + - - +
182F LEU* 2.9 30.2 + - - +
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Residues in contact with TYR 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LYS 2.9 13.7 + - - +
176F ASP* 3.1 13.0 + - - +
178F ILE* 1.3 77.4 - - - +
180F GLN* 1.3 56.1 + - - +
182F LEU* 3.5 4.6 + - - +
183F GLU* 2.9 31.6 + - - +
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Residues in contact with GLN 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ASP 2.9 13.3 + - - +
177F GLU* 3.2 11.4 + - - +
179F TYR* 1.3 75.7 - - - +
181F ILE* 1.3 57.9 + - - +
183F GLU* 3.9 4.2 - - - +
184F TYR* 2.9 31.7 + - - +
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Residues in contact with ILE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F GLU 2.9 17.0 + - - +
178F ILE* 3.2 8.7 + - - +
180F GLN* 1.3 77.0 - - - +
182F LEU* 1.3 57.6 + - - +
184F TYR* 3.8 4.8 - - - +
185F THR* 2.9 28.1 + - - -
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Residues in contact with LEU 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLY* 5.6 6.8 + - - -
178F ILE 2.9 15.9 + - - +
179F TYR* 4.0 4.9 - - - +
181F ILE* 1.3 75.1 - - - +
183F GLU* 1.3 59.5 + - - +
185F THR* 3.0 8.5 + - - -
186F LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F TYR 2.9 19.7 + - - +
180F GLN* 4.1 4.9 - - - +
182F LEU* 1.3 77.2 - - - +
184F TYR* 1.3 61.1 + - - +
186F LYS* 3.6 8.9 + - - +
187F LEU* 3.5 17.3 + - - +
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Residues in contact with TYR 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F LEU* 6.3 3.1 - - + -
180F GLN 2.9 20.4 + - - +
181F ILE* 3.9 5.6 - - - +
183F GLU* 1.3 73.5 - - - +
185F THR* 1.3 61.2 + - - +
187F LEU* 3.2 7.7 + - - +
188F SER* 2.9 29.3 + - - -
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Residues in contact with THR 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.3 5.3 - - - +
17F GLY* 4.2 22.4 - - - -
152F LEU* 6.3 2.7 - - - -
181F ILE 2.9 19.8 + - - -
182F LEU* 3.0 8.5 + - - -
184F TYR* 1.3 73.8 - - - +
186F LYS* 1.3 65.2 + - - +
188F SER* 3.8 6.1 - - - +
189F GLN* 3.0 22.3 + - - -
190F ALA* 4.0 10.9 + - - +
192F VAL* 5.4 6.5 - - - -
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Residues in contact with LYS 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.4 14.5 - - + +
182F LEU 2.9 11.4 + - - +
183F GLU* 3.8 11.9 - - - +
184F TYR 3.2 0.2 - - - -
185F THR* 1.3 77.5 - - - +
187F LEU* 1.3 59.1 + - - +
189F GLN* 3.8 8.3 + - - +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU 3.5 9.0 + - - +
184F TYR* 3.2 10.8 + - - +
186F LYS* 1.3 78.0 - - - +
188F SER* 1.3 61.4 + - - +
189F GLN* 3.2 3.8 + - - +
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Residues in contact with SER 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 4.6 9.4 - - - +
152F LEU* 4.9 15.5 - - - -
156F LYS* 5.9 2.9 - - - +
184F TYR 2.9 17.6 + - - -
185F THR* 3.3 6.9 + - - -
187F LEU* 1.3 74.8 - - - +
189F GLN* 1.3 62.8 + - - +
190F ALA* 2.9 20.7 + - - +
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Residues in contact with GLN 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 5.7 5.8 - - - +
49B SER* 4.5 18.6 - - - -
16F LEU* 4.9 8.1 + - - +
185F THR 3.0 10.1 + - - -
186F LYS 3.8 6.5 + - - +
187F LEU 3.2 5.5 - - - +
188F SER* 1.3 76.7 - - - +
190F ALA* 1.3 64.2 + - - +
191F ASP* 4.7 0.9 - - - +
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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