Contacts of the helix formed by residues 234 - 244 (chain B) in PDB entry 3C9G
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 LEU 234 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 4.7 20.0 - - + -
191B ILE* 3.4 28.5 - - + -
214B PHE* 5.0 2.5 - - + -
232B TYR 3.4 12.6 - - - +
233B SER* 1.3 72.3 - - - +
235B ASP* 1.3 56.5 + - - +
236B ARG 3.4 1.8 - - - -
237B PHE* 3.2 12.3 + - + +
238B ARG* 2.8 49.1 + - + +
293B PHE* 3.6 24.7 - - + -
303B PHE* 5.0 1.8 - - + -
306B TYR* 4.6 16.6 - - + +
307B ILE* 4.3 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B SER* 3.2 17.6 + - - +
234B LEU* 1.3 80.1 + - - +
236B ARG* 1.3 52.4 + - - +
238B ARG* 3.2 11.2 + - - +
239B GLU* 2.8 53.2 + - - +
306B TYR* 4.6 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN* 3.0 27.0 + - - +
213B ILE 3.6 14.8 - - - +
215B PRO* 3.9 22.8 - - + +
233B SER* 4.5 2.3 + - - +
234B LEU 3.4 0.4 - - - -
235B ASP* 1.3 76.4 - - - +
237B PHE* 1.3 60.6 + - - +
239B GLU* 3.1 8.6 + - - +
240B LEU* 2.8 54.8 + - + +
243B LYS* 5.3 9.3 - - - +
275B SER* 3.0 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE* 3.7 21.4 + - + +
214B PHE* 4.2 19.5 - + + -
233B SER 5.5 0.2 + - - -
234B LEU* 3.2 15.5 + - + +
236B ARG* 1.3 77.3 - - - +
238B ARG* 1.3 62.9 + - - +
240B LEU* 4.0 1.2 - - - +
241B LEU* 3.1 54.4 + - + +
254B ILE* 5.4 3.1 - - + -
265B ILE* 5.3 3.8 - - + -
267B LEU* 4.2 18.2 - - + -
277B ILE* 3.5 31.9 - - + -
279B PHE* 4.4 14.4 - + - -
293B PHE* 4.0 31.2 - + - -
307B ILE* 4.1 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 2.8 27.9 + - + +
235B ASP* 3.6 13.2 + - - +
237B PHE* 1.3 73.0 - - + +
239B GLU* 1.3 79.8 + - - +
241B LEU* 3.4 3.9 + - - -
242B ARG* 2.9 53.7 + - - +
306B TYR* 3.1 79.0 + - - +
307B ILE* 4.2 13.5 - - + +
315B ARG* 4.2 12.1 - - - +
316B PRO 4.3 1.8 + - - -
317B VAL* 4.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASP* 2.8 45.5 + - - +
236B ARG* 3.1 14.3 + - - +
238B ARG* 1.3 86.5 + - - +
240B LEU* 1.3 62.1 + - + +
242B ARG* 3.4 7.5 + - - +
243B LYS* 3.0 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASN 4.0 4.5 - - - +
213B ILE* 3.9 29.6 - - + -
236B ARG* 2.8 59.6 + - + +
239B GLU* 1.3 71.3 - - + +
241B LEU* 1.3 65.2 + - - +
242B ARG 3.1 0.2 + - - -
243B LYS* 3.2 11.8 + - + -
244B GLN* 3.0 42.8 + - + +
275B SER* 3.2 27.1 - - - +
277B ILE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PHE* 3.1 46.5 + - + +
238B ARG* 3.4 5.1 + - - +
240B LEU* 1.3 78.2 - - - +
242B ARG* 1.3 57.3 + - - +
245B ARG 3.3 2.9 + - - -
246B ILE* 3.0 57.6 + - + +
247B LEU* 3.8 17.1 - - + +
250B ALA* 4.2 11.2 - - + -
277B ILE* 3.7 16.4 - - + -
279B PHE* 4.1 14.1 - - + -
307B ILE* 3.7 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ARG* 2.9 44.9 + - - +
239B GLU* 3.7 7.2 - - - +
240B LEU 3.1 0.6 - - - -
241B LEU* 1.3 75.9 - - - +
243B LYS* 1.3 61.8 + - + +
244B GLN 3.1 1.6 - - - -
245B ARG* 3.0 25.1 + - - +
247B LEU* 3.8 25.5 - - + +
306B TYR 3.0 26.3 + - - -
307B ILE 3.0 22.8 + - - -
309B PRO* 3.5 13.8 - - - +
315B ARG* 2.8 50.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ARG* 5.3 8.5 - - - +
239B GLU* 3.0 46.8 + - - +
240B LEU* 3.8 16.2 - - + +
242B ARG* 1.3 76.7 - - + +
244B GLN* 1.3 61.6 + - + +
245B ARG* 3.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.0 36.1 + - - +
243B LYS* 1.3 81.0 - - + +
245B ARG* 1.3 73.8 + - - +
246B ILE* 3.2 22.3 - - + +
275B SER 3.2 25.1 + - - -
276B ARG* 3.3 33.9 + - - +
277B ILE* 3.3 30.8 + - - +
----------------------------------------------------------
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