Contacts of the helix formed by residues 203 - 216 (chain B) in PDB entry 2QCT
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 ASP 203 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER* 3.7 25.7 + - - +
202B ILE* 1.3 76.5 - - - +
204B PRO* 1.3 76.2 - - + +
205B ILE 3.1 1.3 - - - -
206B LEU* 2.8 19.6 + - - +
207B GLU* 3.1 18.9 + - - +
288B GLU* 3.6 14.6 - - - +
292B ARG* 3.5 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 4.5 2.5 - - - +
168B ASP* 3.5 31.6 - - + +
169B TYR* 4.0 4.6 - - + -
190B TYR* 3.8 17.0 - - + +
200B SER 4.8 0.2 - - - +
201B SER* 3.3 20.9 - - - +
203B ASP* 1.3 95.4 - - + +
205B ILE* 1.3 55.9 + - - +
206B LEU 3.1 0.2 - - - -
207B GLU* 2.9 25.3 + - - +
208B LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 3.9 19.9 + - + +
193B TRP* 3.8 34.5 - - + -
194B PRO* 4.4 12.6 - - + -
202B ILE* 3.1 35.9 - - + +
203B ASP 3.0 1.6 + - - -
204B PRO* 1.3 80.0 - - - +
206B LEU* 1.3 69.5 + - + +
208B LEU* 3.8 16.8 - - + +
209B ILE* 3.1 27.5 + - + +
236B VAL* 4.6 10.5 - - + -
237B ILE* 4.6 6.5 - - + -
240B ILE* 4.7 7.2 - - + -
281B LEU* 4.8 3.4 - - + -
285B ALA* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE 3.6 10.3 - - - +
203B ASP* 2.8 7.7 + - - +
205B ILE* 1.3 95.3 - - + +
207B GLU* 1.3 61.5 + - - +
208B LEU 3.1 1.3 - - - -
209B ILE* 3.0 7.6 + - + +
210B TRP* 2.8 29.9 + - - +
240B ILE* 4.4 13.0 - - + -
244B TRP* 5.6 1.0 + - - -
285B ALA* 3.8 20.6 - - + +
288B GLU* 4.1 18.4 - - + -
289B LEU* 3.8 27.1 - - + -
292B ARG* 3.4 38.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 5.7 2.6 - - - +
167B SER* 3.8 17.5 + - - -
169B TYR* 3.4 18.4 + - + +
203B ASP* 3.1 12.6 + - - +
204B PRO* 2.9 35.8 - - - +
206B LEU* 1.3 77.0 - - - +
208B LEU* 1.3 56.7 + - - +
210B TRP* 3.1 9.7 + - - +
211B ASP* 2.9 27.9 + - - +
292B ARG* 4.9 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 4.8 5.8 - - + -
169B TYR* 3.4 45.7 + - + -
188B PHE* 4.0 24.0 - - + -
190B TYR* 4.0 28.5 - - + -
204B PRO 2.9 14.6 + - - +
205B ILE* 3.8 16.6 - - + +
207B GLU* 1.3 75.5 - - - +
209B ILE* 1.3 71.6 + - + +
211B ASP* 3.2 2.8 + - - +
212B VAL* 3.1 32.3 + - + +
237B ILE* 4.3 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 6.2 0.4 - - + -
205B ILE* 3.1 19.5 + - + +
206B LEU* 3.0 10.8 + - + +
208B LEU* 1.3 82.8 - - + +
210B TRP* 1.3 58.6 + - - +
212B VAL* 2.9 26.7 - - + +
213B ARG* 3.2 10.0 + - - +
237B ILE* 3.4 46.2 - - + +
240B ILE* 4.4 14.8 - - + +
241B ASP* 3.5 29.6 - - + +
244B TRP* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU 2.8 12.6 + - - +
207B GLU* 3.3 12.6 - - - +
208B LEU 3.0 0.2 - - - -
209B ILE* 1.3 77.7 - - - +
211B ASP* 1.3 74.7 + - - +
213B ARG* 3.2 8.4 + - + +
214B CYS* 3.0 58.6 + - - -
244B TRP* 4.1 32.3 - + - +
248B LYS* 6.2 1.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 2.9 27.5 + - - -
169B TYR* 2.6 30.5 + - - +
171B ILE* 3.7 4.1 - - + +
188B PHE* 3.6 17.3 - - + -
207B GLU 2.9 9.9 + - - +
208B LEU 3.2 5.4 + - - +
210B TRP* 1.3 84.6 - - - +
212B VAL* 1.3 65.0 + - - +
214B CYS* 2.8 13.3 + - - +
215B TYR* 2.8 29.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 4.4 8.3 - - + +
126B VAL* 4.0 22.0 - - + -
188B PHE* 3.7 39.0 - - + -
208B LEU* 3.1 16.2 + - + +
209B ILE* 2.9 30.5 - - + +
211B ASP* 1.3 74.3 - - - +
213B ARG* 1.3 77.4 + - + +
215B TYR* 2.7 22.0 + - - +
216B GLN* 3.0 12.8 + - - +
223B ILE* 5.7 8.5 - - + +
241B ASP* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA 5.7 0.2 + - - -
99B TYR* 4.0 8.3 + - - -
209B ILE 3.4 16.6 - - - +
210B TRP* 3.2 10.4 + - + +
211B ASP 3.2 0.6 - - - -
212B VAL* 1.3 82.3 - - + +
214B CYS* 1.3 59.5 + - - +
215B TYR 3.2 0.6 - - - -
216B GLN 2.7 22.8 + - - -
217B GLU* 2.6 61.8 + - + +
223B ILE* 3.7 22.6 - - - +
241B ASP* 2.6 38.0 + - - +
244B TRP* 4.6 3.6 - - + +
245B MET* 3.9 14.5 - - - +
248B LYS* 3.1 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B TRP* 3.0 60.9 + - - -
211B ASP* 2.8 15.9 + - - +
213B ARG* 1.3 78.9 - - - +
215B TYR* 1.3 68.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.5 15.7 - - + +
124B ILE* 3.8 16.4 - - + -
164B LYS* 5.4 5.5 + - - +
171B ILE* 3.7 22.2 - - + +
186B TYR* 3.4 58.1 - + + -
188B PHE* 3.8 18.8 - + - -
211B ASP* 2.8 33.4 - - + -
212B VAL 2.7 7.6 + - - +
214B CYS* 1.3 90.7 - - + +
216B GLN* 1.3 60.4 + - - +
219B ASP* 5.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.9 14.8 - - + +
124B ILE* 3.5 23.1 - - + +
212B VAL 3.0 8.2 + - - +
213B ARG* 2.7 33.0 + - - -
214B CYS 3.7 0.6 - - - -
215B TYR* 1.3 81.0 - - - +
217B GLU* 1.3 54.0 + - - +
219B ASP* 3.6 29.4 + - + +
221B VAL* 2.3 52.8 - - - +
222B PRO 3.9 0.8 + - - -
223B ILE* 2.9 28.7 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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