Contacts of the helix formed by residues 18 - 26 (chain 3) in PDB entry 6Q8O
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 18 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163 GLY 3.8 2.4 + - - -
173 THR* 1.3 80.6 - - - +
193 VAL* 1.3 64.4 + - - +
203 MET* 3.4 3.6 + - - +
213 ASP* 3.2 9.5 + - - -
223 ALA* 3.1 19.4 + - - +
823 SER 2.8 23.4 + - - -
833 CYS* 3.0 15.4 + - - -
853 THR 3.9 6.8 + - - -
873 VAL* 4.0 0.9 - - - -
4333 ALA* 3.0 28.9 + - - +
4343 ASP* 5.6 0.4 - - - +
4353 LEU* 4.0 12.5 - - - +
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Residues in contact with VAL 19 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183 SER* 1.3 74.1 + - - +
203 MET* 1.3 58.6 + - - +
223 ALA* 3.3 4.8 + - - +
233 VAL* 2.9 33.4 + - + +
503 VAL* 4.1 4.3 - - + -
523 ILE* 4.2 11.0 - - + -
823 SER* 3.7 25.1 - - - +
853 THR* 3.2 22.5 + - - +
863 ALA 3.7 7.9 - - - +
873 VAL* 3.5 20.6 - - + +
913 MET* 3.7 10.8 - - + -
933 VAL* 3.8 34.7 - - + +
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Residues in contact with MET 20 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183 SER* 3.2 2.9 - - - +
193 VAL* 1.3 74.9 - - - +
213 ASP* 1.3 62.7 + - - +
233 VAL* 3.1 9.3 + - - +
243 PHE* 3.0 43.9 + - + -
303 VAL* 3.7 17.7 - - + -
313 PRO 4.0 13.7 - - - +
323 LEU* 3.6 28.7 - - + -
353 SER* 4.1 7.0 - - - -
483 CYS* 4.3 9.9 - - - -
823 SER* 2.8 29.6 + - - +
833 CYS* 3.8 20.2 - - + -
4323 PHE* 4.0 18.4 - - + -
4333 ALA* 4.1 4.7 - - + -
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Residues in contact with ASP 21 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 THR* 3.9 11.7 - - + -
183 SER* 3.2 10.9 + - - +
203 MET* 1.3 76.2 - - - +
223 ALA* 1.3 58.0 + - - +
243 PHE* 5.0 0.4 - - - -
253 HIS* 2.9 25.9 + - - +
4263 TYR* 4.6 5.6 - - + -
4283 HIS* 3.0 22.4 + - + +
4313 PRO* 3.1 17.2 - - + +
4323 PHE* 2.3 36.6 + - - +
4333 ALA* 2.7 39.1 + - - +
4343 ASP* 4.6 0.3 - - - -
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Residues in contact with ALA 22 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43 VAL* 4.6 21.1 - - + -
63 VAL* 4.0 4.5 - - + +
113 VAL* 4.7 6.4 - - + +
133 VAL* 4.6 14.4 - - + -
173 THR* 3.7 12.4 - - + +
183 SER 3.1 13.2 + - - +
193 VAL* 3.6 9.6 - - + +
213 ASP* 1.3 74.6 - - - +
233 VAL* 1.3 67.0 + - - +
253 HIS* 3.2 10.8 + - + +
263 ALA* 2.9 21.8 + - - +
873 VAL* 5.0 3.1 - - + -
933 VAL* 6.6 0.2 - - + -
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Residues in contact with VAL 23 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63 VAL* 3.7 18.1 - - + +
193 VAL* 2.9 24.8 + - + +
203 MET* 3.3 11.7 - - - +
223 ALA* 1.3 75.5 - - - +
243 PHE* 1.3 58.7 + - - +
263 ALA* 2.8 19.4 + - - +
273 GLY 3.0 8.5 + - - -
283 TYR* 3.3 38.0 + - + +
293 ASP 4.0 3.1 - - - +
303 VAL* 4.5 14.1 - - + -
503 VAL* 5.2 3.6 - - + -
823 SER* 5.7 0.2 - - - -
933 VAL* 4.1 25.1 - - + -
953 THR* 4.3 12.6 - - + -
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Residues in contact with PHE 24 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203 MET* 3.0 38.3 + - + +
233 VAL* 1.3 75.5 - - + +
253 HIS* 1.3 58.1 + - - +
273 GLY* 2.9 18.6 + - - -
283 TYR 3.5 19.5 - - - -
293 ASP* 4.2 7.4 - - + -
303 VAL* 3.4 47.6 - - + -
323 LEU* 5.6 2.5 - - + -
1373 TYR* 5.3 0.2 - - - -
4273 ASN* 5.3 1.4 - - - +
4283 HIS* 3.3 36.1 + + + +
4323 PHE* 4.0 29.6 - + - -
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Residues in contact with HIS 25 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113 VAL* 3.3 28.4 - - + +
123 GLU 3.6 15.9 + - - -
133 VAL* 4.5 6.5 - - + -
213 ASP 2.9 18.4 + - - +
223 ALA* 3.3 11.2 - - - +
243 PHE* 1.3 77.7 - - - +
263 ALA* 1.3 57.5 + - - +
273 GLY 3.6 0.2 + - - -
4263 TYR* 4.3 18.0 - + + -
4273 ASN* 3.1 63.1 + - - +
4283 HIS* 3.4 9.8 - - + -
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Residues in contact with ALA 26 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63 VAL* 3.6 33.4 - - + -
93 ARG* 2.2 47.5 + - + +
113 VAL* 3.7 21.0 - - + +
223 ALA 2.9 4.2 + - - -
233 VAL 2.8 11.6 + - - +
253 HIS* 1.3 75.3 - - - +
273 GLY* 1.3 52.3 + - - +
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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