Contacts of the helix formed by residues 209 - 219 (chain C) in PDB entry 2O2C
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 209 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASN* 4.3 6.8 + - - -
202C ASN* 4.4 5.2 + - - +
204C GLY 3.3 18.7 - - - +
205C ILE* 3.8 7.4 - - - -
206C GLY 3.0 7.1 + - - +
207C GLY 3.3 1.8 + - - -
208C SER* 1.3 76.9 - - - +
210C LEU* 1.3 79.9 + - - +
211C GLY 3.3 2.0 - - - -
212C PRO* 3.3 7.9 - - - +
213C VAL* 3.0 44.8 + - - +
231C PHE* 3.8 15.6 - - - +
232C VAL 4.7 0.5 - - - +
233C SER* 3.6 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASN* 6.3 0.2 - - - +
443B ALA* 4.5 12.3 - - + -
206C GLY* 2.9 21.7 + - - +
207C GLY* 5.5 0.2 - - - -
209C ASP* 1.3 83.7 - - - +
211C GLY* 1.3 56.6 + - - +
213C VAL* 3.8 6.8 - - + +
214C MET* 2.9 33.6 + - - +
400C ARG* 4.5 13.4 - - + +
403C ALA* 3.7 40.2 - - + +
404C TYR* 3.7 14.5 - - + +
407C GLN* 3.2 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLY 4.7 1.0 + - - -
207C GLY* 4.8 4.1 + - - -
209C ASP 4.7 0.4 - - - +
210C LEU* 1.3 76.2 - - - +
212C PRO* 1.3 65.7 - - - +
214C MET* 3.8 1.4 - - - +
215C ALA* 2.9 35.0 + - - +
329C MET* 4.1 11.7 - - - -
337C ILE* 4.4 4.7 - - - -
404C TYR* 3.4 26.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ASN* 4.5 4.0 - - - +
207C GLY 4.6 1.3 - - - +
208C SER 4.7 3.6 - - - +
209C ASP* 3.3 19.1 - - - +
211C GLY* 1.3 86.3 - - - +
213C VAL* 1.3 53.7 + - - +
216C THR* 2.7 39.4 + - - +
231C PHE* 3.7 20.9 - - + -
329C MET* 4.9 3.4 - - + -
333C ILE* 3.6 40.8 - - + +
336C PRO* 3.9 15.0 - - + -
337C ILE* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ASP* 3.0 36.1 + - - +
210C LEU* 3.8 9.0 - - + +
212C PRO* 1.3 75.1 - - - +
214C MET* 1.3 64.6 + - - +
216C THR* 3.2 5.1 + - - -
217C GLU* 3.1 34.6 + - + +
231C PHE* 3.6 35.0 - - + -
399C TRP* 5.8 1.1 - - + -
400C ARG* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C LEU 2.9 22.4 + - - +
211C GLY 4.2 1.6 - - - +
213C VAL* 1.3 75.2 - - - +
215C ALA* 1.3 63.8 + - - +
217C GLU* 3.5 2.1 + - - +
218C ALA* 2.9 31.6 + - + +
329C MET* 3.9 28.3 - - + -
397C TYR 4.5 1.2 - - - +
398C LEU* 4.9 2.8 - - + -
400C ARG* 3.8 34.0 - - + +
401C LEU* 3.9 21.3 - - + +
404C TYR* 3.9 19.5 - - + -
539C LEU* 3.9 23.8 - - + -
543C ILE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLY 2.9 17.9 + - - +
214C MET* 1.3 80.6 - - + +
216C THR* 1.3 60.8 + - - +
219C LEU* 2.9 36.1 + - + +
329C MET* 4.1 11.2 - - + -
337C ILE* 3.6 30.7 - - + +
349C LEU* 5.0 0.2 - - + -
539C LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C PRO 2.7 26.4 + - - +
213C VAL 3.2 6.8 + - - -
215C ALA* 1.3 75.3 - - - +
217C GLU* 1.3 66.0 + - - +
219C LEU* 3.8 2.3 - - - -
220C LYS* 3.3 23.9 + - - +
223C SER* 5.6 0.2 - - - -
229C LEU* 3.8 29.0 - - + +
231C PHE* 3.4 20.6 - - + -
336C PRO 4.0 4.9 - - - +
337C ILE* 3.9 29.6 - - + +
340C SER* 4.1 9.8 + - - -
341C ILE* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C VAL* 3.1 28.1 + - + +
214C MET* 3.7 5.2 - - - +
216C THR* 1.3 82.2 + - - +
218C ALA* 1.3 60.7 + - - +
219C LEU 3.5 0.3 + - - -
220C LYS* 3.6 30.5 + - - +
231C PHE* 5.6 4.6 - - + -
397C TYR* 3.3 36.0 - - - +
399C TRP* 2.8 40.8 + - + +
400C ARG* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C MET 2.9 19.1 + - - +
215C ALA 3.7 4.5 - - - +
217C GLU* 1.3 77.4 - - - +
219C LEU* 1.3 63.7 + - + +
220C LYS 3.5 1.7 + - - -
221C PRO* 4.2 3.6 - - - +
222C PHE* 5.4 0.2 - - - -
397C TYR* 3.3 27.7 + - - +
398C LEU* 3.8 26.2 - - + -
534C LEU* 3.9 12.3 - - + +
539C LEU* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C ALA* 2.9 18.9 + - + +
216C THR 3.8 3.1 - - - -
218C ALA* 1.3 83.5 - - + +
220C LYS* 1.3 63.3 + - - +
221C PRO* 3.3 5.6 - - - -
222C PHE* 3.0 24.4 + - + +
223C SER 3.6 6.1 + - - -
337C ILE* 5.0 0.9 - - + -
341C ILE* 3.6 39.2 - - + +
349C LEU* 4.6 10.3 - - + -
534C LEU* 4.3 6.7 - - + +
535C THR 3.9 8.1 - - - +
536C PRO* 3.7 38.8 - - + -
539C LEU* 3.9 27.8 - - + -
----------------------------------------------------------
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