Contacts of the helix formed by residues 200 - 217 (chain C) in PDB entry 2JC6
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 LYS 200 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C HIS* 2.6 76.2 + - + +
139C GLY* 4.4 17.6 - - - -
140C ILE 4.8 0.2 - - - +
141C VAL* 3.7 25.1 - - + +
199C SER* 1.3 70.1 - - - +
201C ALA* 1.3 64.6 + - - +
202C VAL 3.0 4.4 + - - -
203C ASP* 3.0 12.4 + - - -
204C CYS* 3.9 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU* 4.4 0.9 - - - +
199C SER* 3.1 15.9 + - - +
200C LYS* 1.3 77.3 - - - +
202C VAL* 1.3 62.0 + - - +
204C CYS* 3.0 23.4 + - - +
205C TRP 3.2 4.2 + - - -
264C PRO* 3.7 36.3 - - + +
267C ARG* 2.9 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 4.7 4.0 - - + -
143C ARG* 4.4 20.9 - - + +
188C VAL* 6.0 1.8 - - + -
189C ALA* 4.2 7.6 + - + +
191C GLU* 3.2 22.4 - - - +
192C VAL* 3.8 28.7 - - + -
198C TYR* 3.8 17.0 - - + -
199C SER 3.4 17.0 + - - +
201C ALA* 1.3 78.4 - - - +
203C ASP* 1.3 69.8 + - - +
205C TRP* 3.5 5.5 + - - +
206C SER* 3.2 23.1 + - - +
267C ARG* 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.8 14.0 - - + +
135C LEU* 5.5 0.3 - - - +
136C HIS* 2.9 32.8 + - - +
141C VAL* 3.5 8.8 - - - +
142C HIS* 3.0 31.8 + - - +
143C ARG* 2.9 29.1 + - - -
145C LEU* 3.7 11.0 + - + +
200C LYS 3.0 3.6 + - - +
202C VAL* 1.3 76.9 - - - +
204C CYS* 1.3 58.1 + - - +
206C SER* 3.2 8.0 + - - -
207C ILE* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C HIS* 4.1 12.3 - - - -
200C LYS 4.1 4.7 - - - -
201C ALA* 3.0 13.6 + - - +
203C ASP* 1.3 74.7 - - - +
205C TRP* 1.3 64.9 + - - +
207C ILE* 3.3 7.0 + - - +
208C GLY 3.1 17.3 + - - -
259C LEU* 3.1 23.8 - - + +
267C ARG* 4.1 4.5 - - - -
268C TYR 3.3 26.9 - - - +
269C THR* 4.0 3.8 - - - -
270C CYS* 3.8 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C GLY 5.3 0.6 + - - -
187C TYR 3.6 21.6 + - - -
188C VAL 3.7 10.3 + - - -
189C ALA* 3.7 14.8 - - + -
190C PRO* 3.7 36.8 - - + -
201C ALA 3.2 2.8 + - - -
202C VAL 3.5 6.3 - - - +
204C CYS* 1.3 78.7 - - - +
206C SER* 1.3 65.9 + - - +
208C GLY* 3.1 4.7 + - - -
209C VAL* 3.0 33.7 + - + +
221C PHE* 3.7 36.8 - + - -
233C ILE* 4.6 3.8 - - + -
236C ALA* 4.1 10.3 - - + -
238C TYR* 5.4 0.2 - + - -
259C LEU 3.5 12.6 - - - -
260C MET* 3.6 43.1 - - + +
261C GLU 3.8 16.6 - - - -
262C LYS 4.2 1.3 - - - -
267C ARG* 3.5 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ARG 5.6 2.8 + - - -
145C LEU* 3.8 37.1 + - - +
187C TYR* 3.6 15.7 + - - -
188C VAL* 5.6 0.3 - - - -
189C ALA 5.7 0.2 + - - -
202C VAL* 3.2 13.3 + - - +
203C ASP* 3.2 13.4 + - - -
205C TRP* 1.3 81.0 - - - +
207C ILE* 1.3 57.1 + - - +
209C VAL* 3.2 8.3 + - - +
210C ILE* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 3.9 30.7 - - + +
128C VAL* 4.0 19.5 - - + -
129C LEU* 3.6 31.9 - - + -
132C VAL* 4.0 17.9 - - + -
145C LEU* 4.2 6.5 - - + -
203C ASP 3.0 21.2 + - - +
204C CYS* 3.6 10.1 - - - +
205C TRP 3.2 0.4 - - - -
206C SER* 1.3 71.7 - - - +
208C GLY* 1.3 60.1 + - - +
210C ILE* 3.3 6.9 + - + +
211C ALA* 2.8 28.2 + - - +
259C LEU* 4.1 8.7 - - + -
270C CYS* 3.9 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C CYS 3.1 7.7 + - - -
205C TRP 3.1 8.2 + - - -
207C ILE* 1.3 76.3 - - - +
209C VAL* 1.3 55.9 + - - +
211C ALA* 3.2 6.1 + - - +
212C TYR* 2.9 29.3 + - - +
256C ILE* 4.1 6.6 - - - +
259C LEU* 3.6 25.9 - - - +
260C MET* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PRO* 6.0 0.2 - - + -
186C GLY 4.9 0.7 - - - +
187C TYR* 3.5 40.2 - - + +
205C TRP* 3.0 44.8 + - + +
206C SER* 3.2 9.6 + - - +
208C GLY* 1.3 75.4 - - - +
210C ILE* 1.3 64.1 + - + +
212C TYR* 3.4 4.0 + - - +
213C ILE* 3.1 32.1 + - + +
220C PRO* 4.0 14.6 - - + -
221C PHE* 5.0 2.2 - - + -
260C MET* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 3.8 16.8 - - + -
128C VAL* 4.8 12.1 - - + -
145C LEU* 4.2 13.7 - - + +
146C LYS* 4.0 26.9 - - - +
147C PRO* 3.8 25.1 - - + -
150C LEU* 4.3 24.2 - - + -
206C SER 2.9 21.1 + - - +
207C ILE* 3.3 8.0 + - + +
209C VAL* 1.3 75.2 - - + +
211C ALA* 1.3 65.8 + - - +
213C ILE* 3.3 9.6 + - - +
214C LEU* 2.9 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE* 3.8 19.9 - - + +
207C ILE 2.8 20.1 + - - +
208C GLY* 3.5 5.6 - - - +
210C ILE* 1.3 74.9 - - - +
212C TYR* 1.3 60.7 + - - +
214C LEU* 3.4 4.4 + - - +
215C LEU* 3.3 27.5 + - - +
255C PHE* 3.9 27.1 - - + -
256C ILE* 4.0 12.8 - - + -
278C TRP* 4.9 5.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C GLY 2.9 13.3 + - - +
209C VAL* 3.4 12.3 - - - +
211C ALA* 1.3 72.4 - - - +
213C ILE* 1.3 65.3 + - - +
215C LEU 3.2 9.9 + - - -
216C CYS* 3.3 25.3 + - - -
218C TYR* 3.3 41.1 - + - -
220C PRO* 3.4 41.4 + - + +
238C TYR* 4.2 8.3 - + - -
239C GLU 2.5 29.5 + - - -
240C PHE* 4.0 17.3 - + - -
241C ASP* 3.6 1.6 + - - -
245C TRP* 3.4 33.7 + + - -
256C ILE* 3.8 18.0 - - + +
260C MET* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 3.8 29.8 - - + -
147C PRO* 4.0 19.7 - - + -
187C TYR* 3.8 30.3 - - + +
209C VAL* 3.1 25.6 + - + +
210C ILE* 3.8 5.4 - - - +
212C TYR* 1.3 75.3 - - - +
214C LEU* 1.3 62.7 + - + +
215C LEU 3.1 0.2 + - - -
217C GLY* 2.6 33.4 + - - -
218C TYR 3.8 19.5 - - - +
219C PRO* 3.9 11.0 - - + -
220C PRO* 4.3 0.9 - - + -
293C VAL* 4.6 0.7 - - - +
297C ILE* 5.7 0.2 - - + -
301C PHE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.9 21.3 - - + -
107C PHE* 5.3 7.9 - - + -
110C ILE* 3.7 29.4 - - + -
116C TYR* 2.8 37.2 + - - +
121C ALA* 4.1 19.1 - - + +
124C LEU* 4.1 15.7 - - + -
125C ILE* 3.9 33.7 - - + -
147C PRO* 5.6 1.1 - - + -
150C LEU* 5.9 0.9 - - + -
210C ILE* 2.9 25.3 + - + +
211C ALA 3.7 5.6 - - - +
212C TYR 3.3 0.4 - - - -
213C ILE* 1.3 76.0 - - + +
215C LEU* 1.3 60.7 + - - +
216C CYS 3.5 0.2 - - - -
293C VAL* 4.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLU* 3.8 26.2 - - + -
121C ALA* 3.7 25.6 - - + -
211C ALA 3.3 12.5 + - - +
212C TYR 3.2 1.2 + - - -
213C ILE 3.1 1.0 - - - -
214C LEU* 1.3 78.1 - - - +
216C CYS* 1.3 61.6 + - - +
244C TYR 4.6 3.8 - - - +
245C TRP* 3.6 31.8 - - + -
248C ILE* 3.8 23.2 - - + +
252C ALA* 3.5 31.2 - - + -
256C ILE* 4.2 6.1 - - + -
278C TRP* 4.0 11.9 - - + -
289C ILE* 4.2 10.5 - - + +
293C VAL* 3.7 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 3.4 26.7 - - - -
213C ILE 3.1 1.2 + - - -
214C LEU 3.5 0.6 - - - -
215C LEU* 1.3 82.3 - - - +
217C GLY* 1.3 59.0 + - - +
218C TYR* 3.3 50.4 + - + +
244C TYR* 4.5 9.2 - - + +
245C TRP* 3.6 20.9 - - + +
292C SER* 4.0 2.1 + - - +
293C VAL* 3.7 15.2 + - - -
296C GLN* 3.2 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 2.6 24.3 + - - -
216C CYS* 1.3 72.0 - - - +
218C TYR* 1.3 56.4 + - - +
293C VAL* 3.8 14.7 - - - +
296C GLN* 3.1 31.0 - - - +
297C ILE* 3.4 11.3 + - - -
301C PHE* 3.4 18.1 - - - -
----------------------------------------------------------
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