Contacts of the helix formed by residues 174 - 189 (chain b) 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 b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25a VAL* 4.9 12.0 - - - +
172b TYR 3.8 2.4 + - - -
173b PHE* 1.3 75.3 - - - +
175b LYS* 1.3 62.7 + - - +
176b ASP* 3.2 7.0 - - - -
177b GLU* 3.0 12.6 + - - +
178b ILE* 2.8 27.5 + - - +
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Residues in contact with LYS 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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173b PHE 4.0 0.4 + - - -
174b SER* 1.3 73.3 - - - +
176b ASP* 1.3 57.6 + - - +
178b ILE* 3.2 8.8 + - - +
179b TYR* 2.9 27.3 + - - +
201b GLU 4.7 14.6 - - - +
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Residues in contact with ASP 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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174b SER* 3.2 5.4 - - - -
175b LYS* 1.3 78.0 - - - +
177b GLU* 1.3 58.1 + - - +
179b TYR* 3.1 9.2 + - - +
180b GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 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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145b PHE* 5.1 13.7 - - + -
173b PHE* 3.9 12.1 - - + -
174b SER* 3.0 24.3 + - - +
176b ASP* 1.3 78.7 - - - +
178b ILE* 1.3 58.0 + - - +
180b GLN* 3.2 8.5 + - - +
181b ILE* 2.9 27.9 + - - +
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Residues in contact with ILE 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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170b LEU* 6.1 6.3 - - + +
173b PHE* 4.5 9.8 - - + +
174b SER 2.8 12.2 + - - +
175b LYS* 3.2 12.1 + - - +
177b GLU* 1.3 72.5 - - - +
179b TYR* 1.3 61.8 + - - +
181b ILE* 3.2 8.5 + - - +
182b LEU* 2.9 30.2 + - - +
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Residues in contact with TYR 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 LYS 2.9 13.3 + - - +
176b ASP* 3.1 13.4 + - - +
178b ILE* 1.3 78.1 - - - +
180b GLN* 1.3 57.3 + - - +
182b LEU* 3.9 4.6 - - - +
183b GLU* 2.9 32.1 + - - +
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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 ASP 2.9 12.9 + - - +
177b GLU* 3.2 11.4 + - - +
179b TYR* 1.3 77.1 - - - +
181b ILE* 1.3 57.7 + - - +
183b GLU* 3.9 4.4 - - - +
184b TYR* 2.9 31.5 + - - +
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Residues in contact with ILE 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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177b GLU 2.9 16.9 + - - +
178b ILE* 3.2 8.0 + - - +
180b GLN* 1.3 78.1 - - - +
182b LEU* 1.3 58.2 + - - +
184b TYR* 3.5 4.1 + - - +
185b THR* 2.9 28.6 + - - -
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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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17b GLY* 5.6 6.8 + - - -
178b ILE 2.9 15.8 + - - +
179b TYR* 4.0 4.9 - - - +
181b ILE* 1.3 75.4 - - - +
183b GLU* 1.3 60.5 + - - +
185b THR* 3.0 8.2 + - - -
186b LYS* 2.9 28.8 + - - +
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Residues in contact with GLU 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 TYR 2.9 20.1 + - - +
180b GLN* 4.1 5.2 - - - +
182b LEU* 1.3 76.7 - - - +
184b TYR* 1.3 61.3 - - - +
186b LYS* 3.6 8.6 + - - +
187b LEU* 3.5 16.8 + - - +
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Residues in contact with TYR 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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152b LEU* 6.3 3.1 - - + -
180b GLN 2.9 20.1 + - - +
181b ILE* 3.9 5.2 - - - +
183b GLU* 1.3 75.0 - - - +
185b THR* 1.3 60.5 + - - +
187b LEU* 3.2 8.4 + - - +
188b SER* 2.9 29.6 + - - -
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Residues in contact with THR 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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16b LEU* 4.3 4.7 - - - +
17b GLY* 4.2 22.7 - - - -
152b LEU* 6.3 2.2 - - - -
181b ILE 2.9 19.8 + - - -
182b LEU* 3.0 8.0 + - - -
184b TYR* 1.3 73.3 - - - +
186b LYS* 1.3 65.4 + - - +
188b SER* 3.8 5.8 - - - +
189b GLN* 3.0 22.7 + - - -
190b ALA* 4.0 9.8 + - - +
192b VAL* 5.4 7.0 - - - -
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Residues in contact with LYS 186 (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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16b LEU* 4.4 15.1 - - + +
182b LEU 2.9 11.8 + - - +
183b GLU* 3.8 12.1 - - - +
184b TYR 3.2 0.2 - - - -
185b THR* 1.3 78.7 - - - +
187b LEU* 1.3 58.4 + - - +
189b GLN* 3.8 8.0 + - - +
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Residues in contact with LEU 187 (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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183b GLU 3.5 9.6 + - - +
184b TYR* 3.2 11.2 + - - +
186b LYS* 1.3 77.4 - - - +
188b SER* 1.3 63.4 + - - +
189b GLN* 3.2 3.8 + - - +
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Residues in contact with SER 188 (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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152b LEU* 4.8 15.3 - - - -
156b LYS* 5.9 3.8 - - - +
184b TYR 2.9 16.4 + - - -
185b THR* 3.3 7.2 + - - -
187b LEU* 1.3 75.6 - - - +
189b GLN* 1.3 62.7 + - - +
190b ALA* 2.9 21.6 + - - +
49f SER* 4.4 10.0 - - - +
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Residues in contact with GLN 189 (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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16b LEU* 4.9 7.7 + - - +
185b THR 3.0 9.7 + - - -
186b LYS 3.8 6.5 + - - +
187b LEU 3.2 6.1 - - - +
188b SER* 1.3 76.7 - - - +
190b ALA* 1.3 64.8 + - - +
191b ASP* 3.8 0.7 + - - +
49f SER* 4.2 20.5 - - - -
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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