Contacts of the helix formed by residues 242 - 253 (chain C) in PDB entry 2OB1
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 ARG 242 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASN 3.2 17.5 + - - +
241C ASP* 1.3 71.8 + - - +
243C PHE* 1.3 54.5 + - - +
244C GLY 3.3 2.5 - - - -
245C ALA* 3.2 15.4 + - + -
246C ILE* 2.8 64.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE 3.6 12.1 - - - -
241C ASP* 3.1 18.5 + - - +
242C ARG* 1.3 76.3 - - - +
244C GLY* 1.3 62.9 + - - +
246C ILE* 3.2 10.2 + - - +
247C MET* 2.9 63.4 + - + +
316C VAL* 4.6 6.3 - - + -
317C MET* 3.9 30.5 - - + -
320C HIS* 3.2 57.0 - + + +
321C TYR* 4.0 15.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLY* 3.2 12.8 + - - -
241C ASP 4.7 1.2 + - - -
242C ARG* 3.3 0.8 - - - +
243C PHE* 1.3 79.4 - - - +
245C ALA* 1.3 60.5 + - - +
248C GLN* 3.2 32.3 + - - +
262C LEU* 3.7 14.7 - - - +
263C MET* 3.5 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ASP 5.6 0.2 - - - +
242C ARG* 3.2 24.7 + - + +
244C GLY* 1.3 76.1 - - - +
246C ILE* 1.3 58.4 + - + +
248C GLN* 4.0 7.5 - - - +
249C SER* 3.0 29.3 + - - -
263C MET* 4.4 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ARG* 2.8 67.5 + - + +
243C PHE* 3.7 7.4 - - - +
245C ALA* 1.3 73.1 - - + +
247C MET* 1.3 58.8 + - - +
249C SER* 3.2 7.9 - - - -
250C ASN* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PRO* 3.4 16.6 - - + -
243C PHE* 2.9 40.9 + - + +
244C GLY 4.1 2.2 - - - +
246C ILE* 1.3 75.8 - - - +
248C GLN* 1.3 59.9 + - - +
250C ASN* 3.3 6.6 + - + +
251C LEU* 2.9 32.3 + - + +
259C MET* 3.4 23.1 - - + +
262C LEU* 3.0 45.1 - - + -
321C TYR* 4.0 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 3.2 19.5 + - - +
245C ALA* 4.1 6.0 - - - +
247C MET* 1.3 72.9 - - - +
249C SER* 1.3 67.2 + - - +
251C LEU* 3.5 9.9 + - + +
252C LYS* 3.2 20.4 + - - +
257C LEU 4.8 1.4 - - - +
258C GLU* 6.4 0.2 - - - +
259C MET* 2.9 35.9 + - + +
260C PRO* 4.8 4.8 + - - +
262C LEU* 3.9 17.7 - - + +
263C MET* 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ALA 3.0 20.8 + - - -
246C ILE* 3.2 10.3 - - - -
248C GLN* 1.3 80.7 - - - +
250C ASN* 1.3 63.5 + - - +
252C LYS* 3.2 8.1 + - - +
253C GLU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE* 2.8 38.6 + - - +
247C MET* 3.3 6.7 + - + +
249C SER* 1.3 74.4 + - - +
251C LEU* 1.3 62.7 + - - +
253C GLU* 3.3 20.9 + - - +
255C ARG* 3.2 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TYR* 4.4 4.0 - - + +
247C MET* 2.9 21.7 + - + +
248C GLN* 3.7 8.3 - - - +
249C SER 3.3 0.2 - - - -
250C ASN* 1.3 76.0 - - - +
252C LYS* 1.3 61.3 + - - +
255C ARG* 3.1 16.8 - - + +
256C ASN 3.1 7.6 + - - -
257C LEU* 3.0 55.9 + - + +
258C GLU* 4.1 4.3 - - - -
259C MET* 3.4 64.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLN 3.2 9.6 + - - +
249C SER* 3.2 12.7 + - - +
250C ASN 3.2 0.4 - - - -
251C LEU* 1.3 77.1 - - - +
253C GLU* 1.3 71.0 + - - +
254C SER 3.0 4.2 + - - -
256C ASN* 3.1 47.5 + - - +
257C LEU 3.4 25.0 + - - +
258C GLU* 3.2 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER* 3.0 40.0 + - - +
250C ASN* 3.3 19.4 + - - +
252C LYS* 1.3 79.7 - - - +
254C SER* 1.3 60.4 + - - +
255C ARG* 2.5 38.9 + - - -
----------------------------------------------------------
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